2018-03-27 Leonid Mirny (MIT) and Nezar Abdennur, Sameer Abraham, Ed Banigan, Hugo Brandao, Martin Falk, Geoff Fudenberg (UCSF), Anton Goloborodko, Max Imakaev, Carolyn Lu, Johannes Nuebler, Aafke van den Berg; talk at the Keystone Symposium
Dans ce but, l’utilisation des plantes représente un potentiel inestimable pour la recherche de nouvelles substances à pouvoir antioxydant. Ainsi les huiles essentielles et les extraits organiques, suscitent un intérêt croissant comme source potentielle de molécules naturelles bioactives pouvant être employées comme alternatives à certaines substances synthétiques (Bruneton, 1999).
Ce sujet nous a semblé d’autant plus intéressant que la flore Algérienne est extrêmement riche en plantes aromatiques. L’objectif de ce chapitre est de mettre en évidence l’activité antioxydante de l’HE d’O.vulgare.
Três frases ou menos:
1) O documento apresenta as orientações e conteúdos de uma prova parcial de geografia do ensino médio.
2) Inclui questões sobre dinâmicas demográficas, migrações, formação territorial e desigualdades sociais no Brasil.
3) Aborda também a transição demográfica e seus impactos nas políticas públicas.
Les HEs et les extraits d'espèces d'origan sont largement utilisés dans l'industrie pharmaceutique, cosmétique et pour aromatiser et préserver plusieurs produits alimentaires.
Ce travail a pour but, l'étude de cette plante, de divers points de vue.
Guião para exploração do filme "Deus não está morto"António Padrão
O documento apresenta um filme sobre um debate filosófico entre um estudante teísta e um professor ateu sobre a existência de Deus. Inclui propostas de exploração sobre o filme, filósofos como Albert Camus, e argumentos filosóficos sobre teísmo, ateísmo, agnosticismo, o problema do mal e a compatibilidade entre ciência e religião.
Este documento fornece informações sobre os primeiros socorros a serem prestados em acidentes com vítimas, destacando a importância de eliminar riscos secundários, manter as funções vitais e evitar o agravamento das lesões.
O documento lista 19 palavras em português com seus significados e exemplos de uso em frases. As palavras variam em tópicos como medicina, biologia e outros.
O projeto tem como objetivo principal criar atividades que estimulem o aprendizado da língua inglesa de forma lúdica, focando na ortografia correta das palavras. A competição acontecerá em três etapas: entre as salas de aula, entre as turmas e a final entre os melhores de cada turma. Os alunos serão avaliados em sua capacidade de soletrar palavras em inglês.
Dans ce but, l’utilisation des plantes représente un potentiel inestimable pour la recherche de nouvelles substances à pouvoir antioxydant. Ainsi les huiles essentielles et les extraits organiques, suscitent un intérêt croissant comme source potentielle de molécules naturelles bioactives pouvant être employées comme alternatives à certaines substances synthétiques (Bruneton, 1999).
Ce sujet nous a semblé d’autant plus intéressant que la flore Algérienne est extrêmement riche en plantes aromatiques. L’objectif de ce chapitre est de mettre en évidence l’activité antioxydante de l’HE d’O.vulgare.
Três frases ou menos:
1) O documento apresenta as orientações e conteúdos de uma prova parcial de geografia do ensino médio.
2) Inclui questões sobre dinâmicas demográficas, migrações, formação territorial e desigualdades sociais no Brasil.
3) Aborda também a transição demográfica e seus impactos nas políticas públicas.
Les HEs et les extraits d'espèces d'origan sont largement utilisés dans l'industrie pharmaceutique, cosmétique et pour aromatiser et préserver plusieurs produits alimentaires.
Ce travail a pour but, l'étude de cette plante, de divers points de vue.
Guião para exploração do filme "Deus não está morto"António Padrão
O documento apresenta um filme sobre um debate filosófico entre um estudante teísta e um professor ateu sobre a existência de Deus. Inclui propostas de exploração sobre o filme, filósofos como Albert Camus, e argumentos filosóficos sobre teísmo, ateísmo, agnosticismo, o problema do mal e a compatibilidade entre ciência e religião.
Este documento fornece informações sobre os primeiros socorros a serem prestados em acidentes com vítimas, destacando a importância de eliminar riscos secundários, manter as funções vitais e evitar o agravamento das lesões.
O documento lista 19 palavras em português com seus significados e exemplos de uso em frases. As palavras variam em tópicos como medicina, biologia e outros.
O projeto tem como objetivo principal criar atividades que estimulem o aprendizado da língua inglesa de forma lúdica, focando na ortografia correta das palavras. A competição acontecerá em três etapas: entre as salas de aula, entre as turmas e a final entre os melhores de cada turma. Os alunos serão avaliados em sua capacidade de soletrar palavras em inglês.
CTCF binding polarity determines chromatin looping in the following ways:
1) Analysis of 4C-seq data from mouse embryonic stem cells and neural progenitor cells found that chromatin loops preferentially form between CTCF binding sites with convergent orientations of their binding motifs.
2) Editing CTCF binding sites using CRISPR/Cas9 disrupted loops between the edited site and distal convergent CTCF sites, while inversion of the binding motif prevented re-establishment of the loops upon re-insertion.
3) Cohesin association persists at edited CTCF sites that fail to loop, indicating that cohesin recruitment is independent of loop formation and CTCF binding polarity plays a functional role in
This document summarizes recent evidence that the arrangement of chromosomes, gene loci, and nuclear bodies within the cell nucleus is not random but rather exhibits spatial organization that influences gene expression and nuclear processes. Techniques such as fluorescence in situ hybridization and chromosome conformation capture have provided insights into the positioning of chromosomes and genes relative to nuclear landmarks. Chromosomes occupy distinct territories within the nucleus and preferentially localize near the nuclear interior or periphery depending on their gene content. Association with nuclear subcompartments such as the nuclear lamina, nuclear pores, nucleoli, and polycomb bodies can impact the transcriptional state of genes and chromatin domains. Advances in genome-wide and time-lapse imaging approaches are helping to further characterize nuclear organization
This document discusses research into the structure and organization of chromatin at the centromere in Saccharomyces cerevisiae. Key findings include:
- Cohesin is enriched approximately 3-fold in a 50kb region flanking the centromere.
- Deconvolution and model convolution techniques are used to visualize cohesin enrichment and resolve its barrel-shaped organization around the mitotic spindle.
- Heatmap analysis indicates centromere proximal chromatin occupies a similar volumetric space as predicted by cohesin visualization, with decreased localization at the spindle axis.
- Kinetochore components like Cse4 show a more anisotropic localization pattern compared to Ndc80, suggesting regulated anisotropy
ДНК составляет лишь половину объёма хромосомAnatol Alizar
The document describes a study that used a technique called 3D-CLEM (correlative light and electron microscopy) to analyze the structure of mitotic chromosomes at high resolution. Some of the key findings include:
1) 3D-CLEM revealed that prophase chromosomes have a smaller volume than metaphase chromosomes, likely due to the absence of a chromosome periphery structure at that stage of mitosis.
2) The extra volume observed in metaphase chromosomes compared to prophase chromosomes can be almost entirely accounted for by the nucleolar volume.
3) Analysis of wild-type and Ki-67 depleted chromosomes found that the periphery structure comprises 30-47% of the entire chromosome volume and more than 33%
Segmenting Epithelial Cells in High-Throughput RNAi Screens (Miaab 2011)Kevin Keraudren
This document summarizes a proposed method for segmenting epithelial cells in high-throughput RNAi screens using image analysis. The method uses a pipeline that includes pre-processing images using filters to reduce noise and enhance cell structures, segmenting nuclei, generating an edge map of cell-cell contacts, and performing an adaptive watershed segmentation to extract three structures: cell-cell contacts, nuclei, and cell walls. The method is shown to accurately segment these structures and provide reliable quantification of markers in different experimental conditions, distinguishing effects of depleting different actin-binding proteins on cell-cell adhesion receptors and the cytoskeleton.
Pugacheva et al. COMPLETE GB_16.1_p.161_publ.online_08_14_2015 2Victor Lobanenkov
CTCF and BORIS are paralogous proteins that bind to DNA through their nearly identical zinc finger domains. The authors performed ChIP-seq experiments in three cancer cell lines to compare genomic binding patterns of CTCF and BORIS. They found that BORIS selectively occupies a subset (~29-38%) of CTCF binding sites that contain clustered CTCF motifs, termed 2xCTSes. In contrast, the majority of CTCF binding sites contain a single CTCF motif (1xCTSes) and are not occupied by BORIS. 2xCTSes are preferentially located at active promoters and enhancers in cancer cells, and are also enriched in regions retaining histones in sperm. The results suggest there are two
Making effective use of graphics processing units (GPUs) in computationsOregon State University
Graphics processing units (GPUs) are specialized computer processors used in computers and video game systems to accelerate the creation and display of images. Due to their inherent parallel structure, they also have great potential to speed up computations in many scientific and engineering applications. GPUs are attractive for their ability to perform a large number of computations in parallel at an attractive price. Many of the world¹s largest supercomputers use GPUs to achieve their high performance, and personal computers and laptops use them for graphics displays and image processing. This seminar will explore the use of GPUs in general, describe examples of the use of GPUs in computations, and introduce some best practices for GPU computing.
This document summarizes research on mitochondrial DNA (mtDNA) and its mutation rate. It discusses how mtDNA is inherited maternally and generally does not recombine. Two methods for estimating mtDNA mutation rates are pedigree analysis and phylogenetic analysis, which produce rates that differ by around 3 times. Both rates provide accurate estimates of divergence times depending on how closely or distantly sequences are related. The document also explores evidence of mtDNA recombination in one individual who inherited mitochondria from both parents.
Single Molecule Sequence Detection Via Microfluidic Planar Extensional FlowUniv of Cincinnati
1) 164 transcription factors (TFs) are responsible for 277 human diseases or syndromes.
2) The document suggests detecting TF binding sites on DNA using microfluidic planar extensional flow at a stagnation point to stretch DNA for single-molecule detection of TFs.
3) Three additional suggestions for stretching DNA for TF detection include using nanochannels, laminar flow, or stretching DNA in a casting film.
This document summarizes an experiment aiming to knockout the CTNNB1 gene in mouse embryonic stem cells using CRISPR-Cas9 genome editing. It describes designing a guide RNA targeting exon 10 of CTNNB1, cloning it into a vector, transforming E. coli, and testing primers for detecting knockout via PCR and qPCR. Prior studies showed CTNNB1 knockout embryos had defects in ectoderm and mesoderm development. The authors hypothesized knocking out CTNNB1 in stem cells would produce inviable embryos, similar to prior findings.
Advances in Molecular Cytogenetics: Potential for Crop Improvement.pptxKanshouwaModunshim
Title: Exploring Advances in Cytogenetics and Molecular Cytogenetics
Description:
Delve into the intricate world of cytogenetics and its cutting-edge counterpart, molecular cytogenetics, through this insightful presentation. Understand the profound relationship between chromosome structure, behavior, and gene function, with a particular focus on their relevance to crop improvement programs.
Key Points:
Introduction to Cytogenetics: Explore the fundamental principles of cytogenetics, its historical significance, and the recent influence of molecular tools, leading to the emergence of molecular cytogenetics.
Importance in Crop Improvement: Uncover the pivotal role of molecular cytogenetics in crop improvement programs, offering insights into the structural and functional organization of genomes within chromosomes.
Karyotyping: Gain a comprehensive understanding of karyotyping, its significance in identifying chromosomal abnormalities, and its applications in studying evolutionary relationships among different taxa.
Chromosome Identification and Sorting: Learn about the techniques involved in the identification and sorting of individual chromosomes, crucial steps in cytogenetics research for various crops.
Chromosome Banding Techniques: Explore different chromosome banding techniques, such as G-Banding and C-Banding, and understand their applications in detecting structural rearrangements.
CHIAS (Chromosome Image Analyzing System): Get insights into the CHIAS software and its role in mapping and identifying chromosomes automatically.
Flow Cytometry: Discover the applications of flow cytometry in detecting and measuring physical and chemical characteristics of cells, with a focus on its relevance in chromosome research.
In Situ Hybridization: Explore the technique of in situ hybridization, particularly the fluorescent variant, and its applications in precise localization of specific DNA segments.
Genomics and Whole Genome Sequencing: Delve into the realm of genomics and whole-genome sequencing, understanding the approaches like BAC to BAC and Whole Genome Shotgun.
Case Study: Uncover a case study involving the identification of a Wheat-Psathyrostachys huashanica ditelosomic addition line, showcasing the practical applications of the discussed techniques.
Conclusion: Summarize the key takeaways from the presentation, emphasizing the role of these techniques in advancing precision breeding and crop improvement.
Structure and genesis of mitochondrial and chloroplast, DNA replication , tra...Khalid Mukhtar
Presence of precise organelle DNA in mitochondria and chloroplasts became recognized over 3 years ago, proliferation of chloroplast DNA was first validated by the means of Chun et al, illustration of nuclear manipulation of the human mitochondrial genome chloroplast gene transcription managed transcription of cpDNA genes via the means of various factors from the nuclear basis, the number one elements affecting the transcription of cpDNA genes are NEP polymerase and non-intermediate subunits of PEP polymerase, where we explain the mechanism transporting barrel proteins from the outer mitochondrial membrane (OMM) through the TOM complex, and associated with chaperones TIM small cells within the IMS side and inserted into the OMM via sorting means and meeting equipment (SAM), we additionally annotate the chloroplast genome genes for some proteins required for the transcription and translation of encoded genes and, at the extreme, genes for photosynthesis, the locus of these repeats determines the site of unpaired reproduction the short (SSC) and extended unpaired reproductive site (LSC) in the chloroplast genome, leuco = white; plast = living) are colorless plastids that are identified in embryonic and germ cells.
Discussion of latest work on simulating "evolve and resequence" experiments. Covers issues brought up by Burke et al.'s 2010 paper and how the simulations in Baldwin-Brown et al. (2014) address them.
Single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression at the individual cell level, exposing heterogeneity that is hidden in bulk tissue analysis. There are various platforms for scRNA-seq that differ in throughput and customizability. Experimental design considerations include the number of cells to sequence, desired sequencing depth, and controlling for batch effects. The analysis workflow generally involves processing and filtering data, normalization, clustering, differential expression analysis, and trajectory inference to reconstruct cellular responses.
Data Con LA 2022 - Early cancer detection using higher-order genome architectureData Con LA
My (Angela) Chung, Data Enthusiast, San Jose State University
Cancer is a complex disease which requires interactions between cell-intrinsic alterations and tumor microenvironment. The connection between epigenetics and genomic structure plays a key role in chromatin interactions and enhancer-promoter communications for transcriptional activities. Alterations of these components in oncogenic signaling pathway potentially cause cancer cell-intrinsic changes and inappropriate instructions to normal cell cycles, leading to abnormal cell growth.
' Topologically associating domains (TADs) and A/B compartments are the main structures of higher-order chromatin structure. These contact domains, chromatin states, super-enhancers, and histone modifications together regulate transcription and gene expression for normal/abnormal cell cycles.
' Several bioinformatics tools were utilized ' FANC for processing raw FASTQ data to Hi-C contact matrices, JuicerTools for obtaining the locations of contact domains on the entire genome, and CoolBox for visualizing chromatin contacts in different cell lines.
' High-resolution chromatin contacts showed dynamic interactions among chromosomal regions in different cell lines.
' Qualitative and quantitative features were comprehensively engineered from 3D chromatin folding and epigenetic regulators using available packages (scikit learn, pytorch, pandas, numpy, matplotlib, etc.).
' XGBoost multi-class classifier achieved the highest accuracy of 80.90% in classifying normal and cancer cell lines based on chromatin interactions, followed by Random Forest at 73.76% and TabNet classifier at 70.00%.
Multi-molecular views of a stellar nurserySérgio Sacani
New detectors for radio telescopes can map emissions from many different molecules simultaneously across interstellar clouds. One such pioneering study has probed a wide area of a star-forming cloud in the Orion constellation
SYNTHETIC CHROMOSOME PLATFORMs IN PLANTS: CONCEPTS & APPLICATIONskundan Jadhao
This document outlines a seminar on synthetic/artificial chromosomes. It begins by discussing the need for synthetic chromosomes due to limitations of traditional genetic engineering approaches. It then describes various methods that have been used to develop artificial chromosomes, including the bottom-up and top-down methods. Several case studies are presented where telomere-mediated truncation was used to produce engineered minichromosomes in plants with endogenous centromeres. The document concludes by discussing ways that engineered minichromosomes can be amended in planta, such as through site-specific recombination systems and zinc finger nucleases.
Computational Biophysics in the Petascale Computing Erainside-BigData.com
In this deck from the Blue Waters Symposium, Dr. Rommie E. Amaro from UC San Diego presents: Computational Biophysics in the Petascale Computing Era.
"Advances in structural, chemical, and biophysical data acquisition (e.g., protein structures via X-ray crystallography and near atomic cryoEM, isothermal calorimetry, etc.), coupled with the continued exponential growth in computing power and advances in the underlying algorithms are opening a new era for the simulation of biological systems at the molecular level, and at scales never before reached. In this talk I will discuss how the BlueWaters Petascale computing architecture forever altered the landscape and potential of computational biophysics. In particular, new and emerging capabilities for multiscale dynamic simulations that cross spatial scales from the molecular (angstrom) to cellular ultrastructure (near micron), and temporal scales from the picoseconds of macromolecular dynamics to the physiologically important time scales of organelles and cells (milliseconds to seconds) are now possible. These efforts are driven by the outstanding and persistent advances in peta- and exascale computing and availability of multimodal biological datasets, as well as by gaps in current abilities to connect across scales where it is already clear that new approaches will result in novel fundamental understanding of biological phenomena or open new therapeutic avenues."
Watch the video: https://wp.me/p3RLHQ-j1u
Learn more: https://bluewaters.ncsa.illinois.edu/blue-waters-symposium-2018
Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter
This document discusses organizational heterogeneity in the human genome. It finds significant variation in recombination rates of 100 kbp sequences within different GC content ranges. Various methods are used to analyze genome heterogeneity, detect organizational patterns of segments, and estimate heterogeneity between organizational pattern groups. Certain oligonucleotides are found to be important in classifying segments by recombination rate. Functionally related genes tend to reside in organizationally similar genomic regions. The work is supported by the Israeli Ministry of Immigrant Absorption and Israel Council for Higher Education.
This is Best Search Engine Better Than Google (ABSOLUTELY FREE) ATUSIUBATOCHUKWU1
This letter discusses a controversy in the field of membrane mechanics regarding how cholesterol affects the bending modulus of DOPC bilayers. While previous studies using techniques like tube pulling and X-ray scattering found no increase in bending modulus, a recent study using neutron spin echo and NMR relaxation claimed a threefold increase. However, the letter argues this controversy is unnecessary because the different techniques actually measure different properties - relaxation versus mean-square fluctuations. Specifically, the letter contends neutron spin echo is sensitive to viscosity effects rather than directly measuring the Helfrich bending modulus. The letter concludes insisting a single theory applies to all systems prevents a deeper understanding of membrane mechanics.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
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CTCF binding polarity determines chromatin looping in the following ways:
1) Analysis of 4C-seq data from mouse embryonic stem cells and neural progenitor cells found that chromatin loops preferentially form between CTCF binding sites with convergent orientations of their binding motifs.
2) Editing CTCF binding sites using CRISPR/Cas9 disrupted loops between the edited site and distal convergent CTCF sites, while inversion of the binding motif prevented re-establishment of the loops upon re-insertion.
3) Cohesin association persists at edited CTCF sites that fail to loop, indicating that cohesin recruitment is independent of loop formation and CTCF binding polarity plays a functional role in
This document summarizes recent evidence that the arrangement of chromosomes, gene loci, and nuclear bodies within the cell nucleus is not random but rather exhibits spatial organization that influences gene expression and nuclear processes. Techniques such as fluorescence in situ hybridization and chromosome conformation capture have provided insights into the positioning of chromosomes and genes relative to nuclear landmarks. Chromosomes occupy distinct territories within the nucleus and preferentially localize near the nuclear interior or periphery depending on their gene content. Association with nuclear subcompartments such as the nuclear lamina, nuclear pores, nucleoli, and polycomb bodies can impact the transcriptional state of genes and chromatin domains. Advances in genome-wide and time-lapse imaging approaches are helping to further characterize nuclear organization
This document discusses research into the structure and organization of chromatin at the centromere in Saccharomyces cerevisiae. Key findings include:
- Cohesin is enriched approximately 3-fold in a 50kb region flanking the centromere.
- Deconvolution and model convolution techniques are used to visualize cohesin enrichment and resolve its barrel-shaped organization around the mitotic spindle.
- Heatmap analysis indicates centromere proximal chromatin occupies a similar volumetric space as predicted by cohesin visualization, with decreased localization at the spindle axis.
- Kinetochore components like Cse4 show a more anisotropic localization pattern compared to Ndc80, suggesting regulated anisotropy
ДНК составляет лишь половину объёма хромосомAnatol Alizar
The document describes a study that used a technique called 3D-CLEM (correlative light and electron microscopy) to analyze the structure of mitotic chromosomes at high resolution. Some of the key findings include:
1) 3D-CLEM revealed that prophase chromosomes have a smaller volume than metaphase chromosomes, likely due to the absence of a chromosome periphery structure at that stage of mitosis.
2) The extra volume observed in metaphase chromosomes compared to prophase chromosomes can be almost entirely accounted for by the nucleolar volume.
3) Analysis of wild-type and Ki-67 depleted chromosomes found that the periphery structure comprises 30-47% of the entire chromosome volume and more than 33%
Segmenting Epithelial Cells in High-Throughput RNAi Screens (Miaab 2011)Kevin Keraudren
This document summarizes a proposed method for segmenting epithelial cells in high-throughput RNAi screens using image analysis. The method uses a pipeline that includes pre-processing images using filters to reduce noise and enhance cell structures, segmenting nuclei, generating an edge map of cell-cell contacts, and performing an adaptive watershed segmentation to extract three structures: cell-cell contacts, nuclei, and cell walls. The method is shown to accurately segment these structures and provide reliable quantification of markers in different experimental conditions, distinguishing effects of depleting different actin-binding proteins on cell-cell adhesion receptors and the cytoskeleton.
Pugacheva et al. COMPLETE GB_16.1_p.161_publ.online_08_14_2015 2Victor Lobanenkov
CTCF and BORIS are paralogous proteins that bind to DNA through their nearly identical zinc finger domains. The authors performed ChIP-seq experiments in three cancer cell lines to compare genomic binding patterns of CTCF and BORIS. They found that BORIS selectively occupies a subset (~29-38%) of CTCF binding sites that contain clustered CTCF motifs, termed 2xCTSes. In contrast, the majority of CTCF binding sites contain a single CTCF motif (1xCTSes) and are not occupied by BORIS. 2xCTSes are preferentially located at active promoters and enhancers in cancer cells, and are also enriched in regions retaining histones in sperm. The results suggest there are two
Making effective use of graphics processing units (GPUs) in computationsOregon State University
Graphics processing units (GPUs) are specialized computer processors used in computers and video game systems to accelerate the creation and display of images. Due to their inherent parallel structure, they also have great potential to speed up computations in many scientific and engineering applications. GPUs are attractive for their ability to perform a large number of computations in parallel at an attractive price. Many of the world¹s largest supercomputers use GPUs to achieve their high performance, and personal computers and laptops use them for graphics displays and image processing. This seminar will explore the use of GPUs in general, describe examples of the use of GPUs in computations, and introduce some best practices for GPU computing.
This document summarizes research on mitochondrial DNA (mtDNA) and its mutation rate. It discusses how mtDNA is inherited maternally and generally does not recombine. Two methods for estimating mtDNA mutation rates are pedigree analysis and phylogenetic analysis, which produce rates that differ by around 3 times. Both rates provide accurate estimates of divergence times depending on how closely or distantly sequences are related. The document also explores evidence of mtDNA recombination in one individual who inherited mitochondria from both parents.
Single Molecule Sequence Detection Via Microfluidic Planar Extensional FlowUniv of Cincinnati
1) 164 transcription factors (TFs) are responsible for 277 human diseases or syndromes.
2) The document suggests detecting TF binding sites on DNA using microfluidic planar extensional flow at a stagnation point to stretch DNA for single-molecule detection of TFs.
3) Three additional suggestions for stretching DNA for TF detection include using nanochannels, laminar flow, or stretching DNA in a casting film.
This document summarizes an experiment aiming to knockout the CTNNB1 gene in mouse embryonic stem cells using CRISPR-Cas9 genome editing. It describes designing a guide RNA targeting exon 10 of CTNNB1, cloning it into a vector, transforming E. coli, and testing primers for detecting knockout via PCR and qPCR. Prior studies showed CTNNB1 knockout embryos had defects in ectoderm and mesoderm development. The authors hypothesized knocking out CTNNB1 in stem cells would produce inviable embryos, similar to prior findings.
Advances in Molecular Cytogenetics: Potential for Crop Improvement.pptxKanshouwaModunshim
Title: Exploring Advances in Cytogenetics and Molecular Cytogenetics
Description:
Delve into the intricate world of cytogenetics and its cutting-edge counterpart, molecular cytogenetics, through this insightful presentation. Understand the profound relationship between chromosome structure, behavior, and gene function, with a particular focus on their relevance to crop improvement programs.
Key Points:
Introduction to Cytogenetics: Explore the fundamental principles of cytogenetics, its historical significance, and the recent influence of molecular tools, leading to the emergence of molecular cytogenetics.
Importance in Crop Improvement: Uncover the pivotal role of molecular cytogenetics in crop improvement programs, offering insights into the structural and functional organization of genomes within chromosomes.
Karyotyping: Gain a comprehensive understanding of karyotyping, its significance in identifying chromosomal abnormalities, and its applications in studying evolutionary relationships among different taxa.
Chromosome Identification and Sorting: Learn about the techniques involved in the identification and sorting of individual chromosomes, crucial steps in cytogenetics research for various crops.
Chromosome Banding Techniques: Explore different chromosome banding techniques, such as G-Banding and C-Banding, and understand their applications in detecting structural rearrangements.
CHIAS (Chromosome Image Analyzing System): Get insights into the CHIAS software and its role in mapping and identifying chromosomes automatically.
Flow Cytometry: Discover the applications of flow cytometry in detecting and measuring physical and chemical characteristics of cells, with a focus on its relevance in chromosome research.
In Situ Hybridization: Explore the technique of in situ hybridization, particularly the fluorescent variant, and its applications in precise localization of specific DNA segments.
Genomics and Whole Genome Sequencing: Delve into the realm of genomics and whole-genome sequencing, understanding the approaches like BAC to BAC and Whole Genome Shotgun.
Case Study: Uncover a case study involving the identification of a Wheat-Psathyrostachys huashanica ditelosomic addition line, showcasing the practical applications of the discussed techniques.
Conclusion: Summarize the key takeaways from the presentation, emphasizing the role of these techniques in advancing precision breeding and crop improvement.
Structure and genesis of mitochondrial and chloroplast, DNA replication , tra...Khalid Mukhtar
Presence of precise organelle DNA in mitochondria and chloroplasts became recognized over 3 years ago, proliferation of chloroplast DNA was first validated by the means of Chun et al, illustration of nuclear manipulation of the human mitochondrial genome chloroplast gene transcription managed transcription of cpDNA genes via the means of various factors from the nuclear basis, the number one elements affecting the transcription of cpDNA genes are NEP polymerase and non-intermediate subunits of PEP polymerase, where we explain the mechanism transporting barrel proteins from the outer mitochondrial membrane (OMM) through the TOM complex, and associated with chaperones TIM small cells within the IMS side and inserted into the OMM via sorting means and meeting equipment (SAM), we additionally annotate the chloroplast genome genes for some proteins required for the transcription and translation of encoded genes and, at the extreme, genes for photosynthesis, the locus of these repeats determines the site of unpaired reproduction the short (SSC) and extended unpaired reproductive site (LSC) in the chloroplast genome, leuco = white; plast = living) are colorless plastids that are identified in embryonic and germ cells.
Discussion of latest work on simulating "evolve and resequence" experiments. Covers issues brought up by Burke et al.'s 2010 paper and how the simulations in Baldwin-Brown et al. (2014) address them.
Single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression at the individual cell level, exposing heterogeneity that is hidden in bulk tissue analysis. There are various platforms for scRNA-seq that differ in throughput and customizability. Experimental design considerations include the number of cells to sequence, desired sequencing depth, and controlling for batch effects. The analysis workflow generally involves processing and filtering data, normalization, clustering, differential expression analysis, and trajectory inference to reconstruct cellular responses.
Data Con LA 2022 - Early cancer detection using higher-order genome architectureData Con LA
My (Angela) Chung, Data Enthusiast, San Jose State University
Cancer is a complex disease which requires interactions between cell-intrinsic alterations and tumor microenvironment. The connection between epigenetics and genomic structure plays a key role in chromatin interactions and enhancer-promoter communications for transcriptional activities. Alterations of these components in oncogenic signaling pathway potentially cause cancer cell-intrinsic changes and inappropriate instructions to normal cell cycles, leading to abnormal cell growth.
' Topologically associating domains (TADs) and A/B compartments are the main structures of higher-order chromatin structure. These contact domains, chromatin states, super-enhancers, and histone modifications together regulate transcription and gene expression for normal/abnormal cell cycles.
' Several bioinformatics tools were utilized ' FANC for processing raw FASTQ data to Hi-C contact matrices, JuicerTools for obtaining the locations of contact domains on the entire genome, and CoolBox for visualizing chromatin contacts in different cell lines.
' High-resolution chromatin contacts showed dynamic interactions among chromosomal regions in different cell lines.
' Qualitative and quantitative features were comprehensively engineered from 3D chromatin folding and epigenetic regulators using available packages (scikit learn, pytorch, pandas, numpy, matplotlib, etc.).
' XGBoost multi-class classifier achieved the highest accuracy of 80.90% in classifying normal and cancer cell lines based on chromatin interactions, followed by Random Forest at 73.76% and TabNet classifier at 70.00%.
Multi-molecular views of a stellar nurserySérgio Sacani
New detectors for radio telescopes can map emissions from many different molecules simultaneously across interstellar clouds. One such pioneering study has probed a wide area of a star-forming cloud in the Orion constellation
SYNTHETIC CHROMOSOME PLATFORMs IN PLANTS: CONCEPTS & APPLICATIONskundan Jadhao
This document outlines a seminar on synthetic/artificial chromosomes. It begins by discussing the need for synthetic chromosomes due to limitations of traditional genetic engineering approaches. It then describes various methods that have been used to develop artificial chromosomes, including the bottom-up and top-down methods. Several case studies are presented where telomere-mediated truncation was used to produce engineered minichromosomes in plants with endogenous centromeres. The document concludes by discussing ways that engineered minichromosomes can be amended in planta, such as through site-specific recombination systems and zinc finger nucleases.
Computational Biophysics in the Petascale Computing Erainside-BigData.com
In this deck from the Blue Waters Symposium, Dr. Rommie E. Amaro from UC San Diego presents: Computational Biophysics in the Petascale Computing Era.
"Advances in structural, chemical, and biophysical data acquisition (e.g., protein structures via X-ray crystallography and near atomic cryoEM, isothermal calorimetry, etc.), coupled with the continued exponential growth in computing power and advances in the underlying algorithms are opening a new era for the simulation of biological systems at the molecular level, and at scales never before reached. In this talk I will discuss how the BlueWaters Petascale computing architecture forever altered the landscape and potential of computational biophysics. In particular, new and emerging capabilities for multiscale dynamic simulations that cross spatial scales from the molecular (angstrom) to cellular ultrastructure (near micron), and temporal scales from the picoseconds of macromolecular dynamics to the physiologically important time scales of organelles and cells (milliseconds to seconds) are now possible. These efforts are driven by the outstanding and persistent advances in peta- and exascale computing and availability of multimodal biological datasets, as well as by gaps in current abilities to connect across scales where it is already clear that new approaches will result in novel fundamental understanding of biological phenomena or open new therapeutic avenues."
Watch the video: https://wp.me/p3RLHQ-j1u
Learn more: https://bluewaters.ncsa.illinois.edu/blue-waters-symposium-2018
Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter
This document discusses organizational heterogeneity in the human genome. It finds significant variation in recombination rates of 100 kbp sequences within different GC content ranges. Various methods are used to analyze genome heterogeneity, detect organizational patterns of segments, and estimate heterogeneity between organizational pattern groups. Certain oligonucleotides are found to be important in classifying segments by recombination rate. Functionally related genes tend to reside in organizationally similar genomic regions. The work is supported by the Israeli Ministry of Immigrant Absorption and Israel Council for Higher Education.
This is Best Search Engine Better Than Google (ABSOLUTELY FREE) ATUSIUBATOCHUKWU1
This letter discusses a controversy in the field of membrane mechanics regarding how cholesterol affects the bending modulus of DOPC bilayers. While previous studies using techniques like tube pulling and X-ray scattering found no increase in bending modulus, a recent study using neutron spin echo and NMR relaxation claimed a threefold increase. However, the letter argues this controversy is unnecessary because the different techniques actually measure different properties - relaxation versus mean-square fluctuations. Specifically, the letter contends neutron spin echo is sensitive to viscosity effects rather than directly measuring the Helfrich bending modulus. The letter concludes insisting a single theory applies to all systems prevents a deeper understanding of membrane mechanics.
Similar to Genome folding by loop extrusion and compartmentalization (20)
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...Travis Hills MN
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
The technology uses reclaimed CO₂ as the dyeing medium in a closed loop process. When pressurized, CO₂ becomes supercritical (SC-CO₂). In this state CO₂ has a very high solvent power, allowing the dye to dissolve easily.
3. HiGlass.io
by Nils Gehlenborg, Peter Karpedjiev, Nezar Abdennur, and others
Harvard University and MIT
HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps
https://www.biorxiv.org/content/early/2017/10/30/121889
4. Outline
Compartments and TADs
1. Emerging evidence of loop extrusion!
2. Compartmentalization by phase separation
3. Phase separation vs extrusion
Emerging Evidence of Chromosome Folding by Loop Extrusion
https://www.biorxiv.org/content/early/2018/02/16/264648
5. Model
36 domains=10MbC
D
Loop extrusion with boundaries => TADs
e
Formation of Chromosomal Domains by Loop Extrusion!
bioRxiv Aug 14 (2015)!
Fudenberg, Imakaev et al.!
DOI: 10.1101/024620
Article
Formation of Chromosomal Domains by Loop
(2016)
6. Model
36 domains=10MbC
D
Loop extrusion with boundaries => TADs
genomic distance, s (bp)
104
105
1
normalized
C
10-2
D
e
Formation of Chromosomal Domains by Loop Extrusion!
bioRxiv Aug 14 (2015)!
Fudenberg, Imakaev et al.!
DOI: 10.1101/024620
Article
Formation of Chromosomal Domains by Loop
(2016)
8. b
00.0100.0200.035
ContactProbability(simulations)
= 13
5’-GGCGGAGACCACAAGGTGGCGCCAGATCCC-3’
17.417.6
1 kb resolution
CTCF
RAD21
SMC3
Chr 1
Chr1
17.6 Mb17.4
0 0.5 1 1.5 2 2.5 3 3.5 4
Number of PeaksD
Forwardmotif
FoldChange
0
0.5
1.0
1.5
0% 20% 40% 60% 80% 100%
Percentage of peak loci bound
YY1
CTCF
RAD21
(2%)(3%)(3%)(92%)
CCACNAGGTGGCAGconsensus
x 1000
CTCF anchor
(arrowhead indicates
motif orientation)
Loop domain
Ordinary domain
290 Kb
110
Kb
190 Kb
350 Kb
270 Kb
130 Kb
450 Kb
170
Kb
F
Figure 6. Many Loops Demarcate Contact Domains; The Vast Majority of Loops Are Anchored at a Pair of Convergent CTCF/RAD21/SMC3
Binding Sites
(A) Histograms of corner scores for peak pixels versus random pixels with an identical distance distribution.
(B) Contact matrix for chr4:20.55 Mb–22.55 Mb in GM12878, showing examples of transitive and intransitive looping behavior.
(C) Percent of peak loci bound versus fold enrichment for 76 DNA-binding proteins.
(D) The pairs of CTCF motifs that anchor a loop are nearly all found in the convergent orientation.
(legend continued on next page)
1674 Cell 159, 1665–1680, December 18, 2014 ª2014 Elsevier Inc.
Border-to-border loops
cannot reproduce Hi-C data
9. b
00.0100.0200.035
ContactProbability(simulations)
= 13
5’-GGCGGAGACCACAAGGTGGCGCCAGATCCC-3’
17.417.6
1 kb resolution
CTCF
RAD21
SMC3
Chr 1
Chr1
17.6 Mb17.4
0 0.5 1 1.5 2 2.5 3 3.5 4
Number of PeaksD
Forwardmotif
FoldChange
0
0.5
1.0
1.5
0% 20% 40% 60% 80% 100%
Percentage of peak loci bound
YY1
CTCF
RAD21
(2%)(3%)(3%)(92%)
CCACNAGGTGGCAGconsensus
x 1000
CTCF anchor
(arrowhead indicates
motif orientation)
Loop domain
Ordinary domain
290 Kb
110
Kb
190 Kb
350 Kb
270 Kb
130 Kb
450 Kb
170
Kb
F
Figure 6. Many Loops Demarcate Contact Domains; The Vast Majority of Loops Are Anchored at a Pair of Convergent CTCF/RAD21/SMC3
Binding Sites
(A) Histograms of corner scores for peak pixels versus random pixels with an identical distance distribution.
(B) Contact matrix for chr4:20.55 Mb–22.55 Mb in GM12878, showing examples of transitive and intransitive looping behavior.
(C) Percent of peak loci bound versus fold enrichment for 76 DNA-binding proteins.
(D) The pairs of CTCF motifs that anchor a loop are nearly all found in the convergent orientation.
(legend continued on next page)
1674 Cell 159, 1665–1680, December 18, 2014 ª2014 Elsevier Inc.
TAD ≠ border-to-border loop
Border-to-border loops
cannot reproduce Hi-C data
10.
Domain — systems of actively extruded loops
youtube mirnylab
http://mirnylab.mit.edu/projects/emerging-evidence-for-loop-extrusion/
https://www.youtube.com/watch?v=8FW6gOx5lPI
11. increased LEF
density & processivity
WT LEF depletion weakened barriers
genomic separation s, bp
WT
10
0
10
1
P(s)
10
2
10
5
10
6
genomic separation s, bp
10
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genomic separation s, bp
10
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300kb
A B C D
Testing loop extrusion
!
Predictions
12. Testing loop extrusion
!
Experiments
control
46Mb
51Mb
46Mb
51Mb
19Mb
23Mb1 Mb 1 Mb 1 Mb
chr5 chr5 chr11
contactfrequency
0.008
0
Elphege Nora
Benoit G. Bruneau
UCSF
Francois Spitz!
Wibke Schwarzer!
!
Article
The Cohesin Release Factor WAPL
Restricts Chromatin Loop Extension
Judith H.I. Haarhuis,1,6 Robin H. van der Weide,2,6 Vincent A. Blomen,3 J. Omar Ya´ n˜ ez-Cuna,2 Mario Amendola,2,7
Marjon S. van Ruiten,1 Peter H.L. Krijger,4 Hans Teunissen,2 Rene´ H. Medema,1 Bas van Steensel,2
Thijn R. Brummelkamp,3,5 Elzo de Wit,2,* and Benjamin D. Rowland1,8,*
1Division of Cell Biology, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
2Division of Gene Regulation, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
3Division of Biochemistry, the Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
4Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
5Cancer Genomics Center, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
6These authors contributed equally
7Present address: UMR_S951, Genethon, 91000 Evry, France
8Lead Contact
*Correspondence: e.d.wit@nki.nl (E.d.W.), b.rowland@nki.nl (B.D.R.)
http://dx.doi.org/10.1016/j.cell.2017.04.013
SUMMARY
The spatial organization of chromosomes influences
many nuclear processes including gene expression.
The cohesin complex shapes the 3D genome by
looping together CTCF sites along chromosomes.
We show here that chromatin loop size can be
increased and that the duration with which cohesin
embraces DNA determines the degree to which
loops are enlarged. Cohesin’s DNA release factor
the SCC2/SCC4 complex (also known as NIPBL and
respectively), and DNA release is driven by cohesin’s anta
WAPL (Ciosk et al., 2000; Gandhi et al., 2006; Kueng et al.,
The cohesin complex consists of three core subunits,
SMC3, and SCC1 (also known as RAD21 or Mcd1), that to
form a ring-shaped structure that can entrap DNA ins
lumen (Haering et al., 2008). WAPL drives cohesin’s r
from chromatin by opening up a distinct DNA exit gate
interface connecting cohesin’s SMC3 and SCC1 subunits
oue¨ t et al., 2016; Murayama and Uhlmann, 2015). In the ab
ARTICLE doi:10.1038/nature24281
Two independent modes of chromatin
organization revealed by cohesin removal
Wibke Schwarzer1
*, Nezar Abdennur2
*, Anton Goloborodko3
*, Aleksandra Pekowska4
, Geoffrey Fudenberg5
, Yann Loe-Mie6,7
,
Nuno A Fonseca8
, Wolfgang Huber4
, Christian H. Haering9
, Leonid Mirny3,5
& Francois Spitz1,4,6,7
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization,
Article
Targeted Degradation of CTCF Decouples
Local Insulation of Chromosome Domains
from Genomic Compartmentalization
Elphe` ge P. Nora,1,2,* Anton Goloborodko,3 Anne-Laure Valton,4 Johan H. Gibcus,4 Alec Uebersohn,1,2,7 Nezar Abdennur,3
Job Dekker,4 Leonid A. Mirny,3 and Benoit G. Bruneau1,2,5,6,8,*
1Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
2Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
3Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge,
MA 02139, USA
4Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of
Massachusetts Medical School, Worcester, MA 01605-0103, USA
5
regulator of chromosomal structure. Using the
auxin-inducible degron system in mouse embryonic
stem cells, we show that CTCF is absolutely and
dose-dependently required for looping between
CTCF target sites and insulation of topologically
associating domains (TADs). Restoring CTCF rein-
states proper architecture on altered chromosomes,
indicating a powerful instructive function for CTCF
in chromatin folding. CTCF remains essential for
TAD organization in non-dividing cells. Surprisingly,
active and inactive genome compartments remain
properly segregated upon CTCF depletion, revealing
that compartmentalization of mammalian chromo-
somes emerges independently of proper insulation
of TADs. Furthermore, our data support that CTCF
mediates transcriptional insulator function through
enhancer blocking but not as a direct barrier to het-
erochromatin spreading. Beyond defining the func-
tions of CTCF in chromosome folding, these results
provide new fundamental insights into the rules
governing mammalian genome organization.
INTRODUCTION
Chromosomes meet the dual challenge of packaging DNA into
the nucleus and, at the same time, enabling access to genetic in-
formation. Decades of work on chromosome organization have
tackled the link between chromosome structure and genetic
Potts et al., 20
but here we foc
Mammalian c
Euchromatin c
rich regions (G
is condensed, g
highlights the
ical, biochemic
somes. Chromo
belonging to tw
vealed by high-
(3C), with chro
loci of the same
chromosomes (
on linear genom
types forms a d
with regional c
2013; Bonev an
ment contains
B compartmen
lamina-associat
et al., 2015), wh
At a more loc
megabase segm
relatively insulat
cally associatin
et al., 2012). Th
by the binding
et al., 2012; Phi
zinc-finger nucl
930 Cell 169, 930–944, May 18, 2017 ª 2017 Elsevier Inc.
16. Same results from direct targeting of cohesinArticle
Cohesin Loss Eliminates All Loop Domains
Suhas S.P. Rao,1,2,3 Su-Chen Huang,1,2 Brian Glenn St Hilaire,1,2,4 Jesse M. Engreitz,5 Elizabeth M. Perez,5
Kyong-Rim Kieffer-Kwon,6 Adrian L. Sanborn,1,4,7 Sarah E. Johnstone,5,8 Gavin D. Bascom,9 Ivan D. Bochkov,1,2
Xingfan Huang,1,10 Muhammad S. Shamim,1,2,10,11 Jaeweon Shin,1,10 Douglass Turner,1,12 Ziyi Ye,1,10 Arina D. Omer,1,2
James T. Robinson,1,5,12 Tamar Schlick,9,13,14 Bradley E. Bernstein,5,8 Rafael Casellas,6,15 Eric S. Lander,5,16,17
and Erez Lieberman Aiden1,2,4,5,10,18,*
1The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
3Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
4Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
5Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
6Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
7Department of Computer Science, Stanford University, Stanford, CA 94305, USA
8Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston,
MA 02114, USA
9Department of Chemistry, New York University, New York, NY 10003, USA
10Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA
11Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
12Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
13Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
14NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
15Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
16Department of Biology, MIT, Cambridge, MA 02139, USA
17Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
18Lead Contact
*Correspondence: erez@erez.com
https://doi.org/10.1016/j.cell.2017.09.026
SUMMARY
The human genome folds to create thousands of
intervals, called ‘‘contact domains,’’ that exhibit
enhanced contact frequency within themselves.
‘‘Loop domains’’ form because of tethering between
two loci—almost always bound by CTCF and cohe-
sin—lying on the same chromosome. ‘‘Compartment
domains’’ form when genomic intervals with similar
histone marks co-segregate. Here, we explore the ef-
fects of degrading cohesin. All loop domains are
eliminated, but neither compartment domains nor
histone marks are affected. Loss of loop domains
(Wendt et al., 2008) and lie at the anchors of loops (Rao et al.,
2014; Splinter et al., 2006) and the boundaries of contact do-
mains (also called ‘‘topologically constrained domains,’’ ‘‘topo-
logically associated domains,’’ or ‘‘physical domains’’) (Dixon
et al., 2012; Lieberman-Aiden et al., 2009; Nora et al., 2012;
Rao et al., 2014). This suggests that these proteins help regulate
genome folding (Merkenschlager and Nora, 2016). Consistent
with this, deletion of CTCF sites interferes with loop and contact
domain formation (Guo et al., 2015; Sanborn et al., 2015; de Wit
et al., 2015). However, initial, low-resolution experiments exam-
ining genome-wide depletion of CTCF and cohesin observed
only limited effects, reporting that compartments and contact
domains still appear to be present (Seitan et al., 2013; Sofueva
et al., 2013; Zuin et al., 2014). These results have made it difficult
A
= 42
= 114
= 111
134.6133.842.140.8
42.140.8
91.995.8
91.9 95.8 Mb
134.6133.8
HCT116-RAD21-mAC
- auxin
HCT116-RAD21-mAC
+ auxin, 6hr
Chr4
Chr 4
Chr 1
Chr1Chr8
Chr 8
134.6 Mb133.8
Chr 8
= 38
= 111
42.1 Mb40.8
Chr 4
= 107
91.9 95.8 Mb
Chr 1
E
H3K27ac
H3K4me3
H3K4me1
NIPBL
Fast
+ auxin, 6hr withdraw, 20
Withdraw
68.467.6Mb68.2
= 107 = 34= 116
Chr18Chr14
0
7
0
25
0
100
0
50
Chr18
Rao et al., 2017, Cell 171, 305–320
October 5, 2017 ª 2017 Elsevier Inc.
https://doi.org/10.1016/j.cell.2017.09.026
Article
Topologically associating domains and chromatin
loops depend on cohesin and are regulated by
CTCF, WAPL, and PDS5 proteins
Gordana Wutz1,†
, Csilla Várnai2,†
, Kota Nagasaka1,†
, David A Cisneros1,†,‡
, Roman R Stocsits1
,
Wen Tang1
, Stefan Schoenfelder2
, Gregor Jessberger1
, Matthias Muhar1
, M Julius Hossain3
,
Nike Walther3
, Birgit Koch3
, Moritz Kueblbeck3
, Jan Ellenberg3
, Johannes Zuber1
,
Peter Fraser2,4
& Jan-Michael Peters1,*
Abstract
Mammalian genomes are spatially organized into compartments,
topologically associating domains (TADs), and loops to facilitate
gene regulation and other chromosomal functions. How compart-
ments, TADs, and loops are generated is unknown. It has been
proposed that cohesin forms TADs and loops by extruding chro-
matin loops until it encounters CTCF, but direct evidence for this
hypothesis is missing. Here, we show that cohesin suppresses
compartments but is required for TADs and loops, that CTCF
defines their boundaries, and that the cohesin unloading factor
WAPL and its PDS5 binding partners control the length of loops. In
the absence of WAPL and PDS5 proteins, cohesin forms extended
loops, presumably by passing CTCF sites, accumulates in axial
chromosomal positions (vermicelli), and condenses chromosomes.
Unexpectedly, PDS5 proteins are also required for boundary func-
tion. These results show that cohesin has an essential genome-
wide function in mediating long-range chromatin interactions and
support the hypothesis that cohesin creates these by loop extru-
sion, until it is delayed by CTCF in a manner dependent on PDS5
proteins, or until it is released from DNA by WAPL.
Introduction
Duplicated DNA molecules become physically connected with each
other during DNA replication. This sister chromatid cohesion is
essential for bi-orientation of chromosomes on the mitotic or
meiotic spindle and thus enables their symmetrical segregation
during cell division (Dewar et al, 2004). Cohesion is mediated by
cohesin complexes (Guacci et al, 1997; Michaelis et al, 1997;
Losada et al, 1998) which are thought to perform this function by
entrapping both sister DNA molecules inside a ring structure that is
formed by the cohesin subunits SMC1, SMC3, and SCC1 (also
known as RAD21 and Mcd1) (Haering et al, 2008).
Cohesin is present at centromeres and on chromosome arms (re-
viewed in Peters et al, 2008). At centromeres, cohesin resists the
pulling force of spindle microtubules, a function that is required
both for stabilization of microtubule–kinetochore attachments and
for chromosome bi-orientation. On chromosome arms, however, the
precise location of cohesin would not be expected to matter if cohe-
sin’s only function was to mediate cohesion. But contrary to this
expectation, cohesin is enriched at thousands of well-defined loci on
chromosome arms. In mammalian genomes, ~90% of these are
Published online: December 7, 2017
Article
A mechanism of cohesin-dependent loop extrusion
organizes zygotic genome architecture
Johanna Gassler1,†
, Hugo B Brandão2,†
, Maxim Imakaev3,4
, Ilya M Flyamer5
, Sabrina Ladstätter1
,
Wendy A Bickmore5
, Jan-Michael Peters6
, Leonid A Mirny2,3,*
& Kikuë Tachibana1,**
Abstract Introduction
Published online: December 7, 2017
Zp3-Cre
∆/∆ ∆/∆fl/flfl/fl
B
I
R
T
H
+
B
A
1.43
Scc1fl
combined
1.14
A
B
1.03
Scc1∆
combined
1.03
Average loop
-100kb
0 kb
+90kb
activeinactive
TAD
Average TAD Com
A
B
-100kb
0 kb
+90kb
TAD
activeinactivee
The EMBO Journal
Published online: December 7, 2017
G
190 Mb0 Mb
Chromosome 4
0 min auxin
190
15 min auxin 180 min auxin
J
0
10 kb 100 kb 1 Mb 10 Mb100 Mb
c
genomic distance
88 Mb 94.5 Mbchromosome 12
8
0 min auxin 15 min auxin 180 min auxin
a-tubulin
H3
0 20 40
0.0
0.2
time (min)
nor
10 30
H I
log2(observed/expected)
1.6
0.8
0
-0.8
-1.6
1 50
0 min auxin 15 min auxin 180 min auxin
1
50
-450 kb 0 450 kb
0 min auxin 15 min auxin 180 min auxin
chromosome 4
471 377
5 6
2
0
-2
log2enrichment
Figure 1.
17. SMC is a motor!
Cite as: M. Ganji et al., Science
10.1126/science.aar7831 (2018).
REPORTS
The spatial organization of chromosomes is of paramount
importance to cell biology. Members of the SMC family of
protein complexes, including condensin, cohesin, and the
Smc5/6 complex, play vital roles in restructuring genomes
during the cellular life cycle (1–3). The principles by which
SMC complexes achieve these fundamental tasks are still
incompletely understood. Models based on random cross-
linking of DNA by pairwise interactions or conformational
changes in the DNA superhelicity have been proposed (4, 5).
An alternative hypothesis suggested that SMC protein com-
plexes bind to small loops in the genome to then processive-
ly enlarge them (6). More recently, the idea emerged that
condensin can start and subsequently extrude DNA loops,
which would elegantly explain how condensin mediates the
formation of mitotic chromosomes structures observed in
electron micrographs and deduced from Hi-C experiments
(7, 8). Indeed, polymer simulations showed that loop extru-
sion can, in principle, result in the efficient disentanglement
and compaction of chromatin fibers (9–11). The recent dis-
covery that condensin exhibits DNA translocase activity (12)
was consistent with, but did not provide conclusive evidence
for (13), DNA loop extrusion.
In this Report, we visualize the formation of DNA loops
by the Saccharomyces cerevisiae condensin complex in real
(ATP), we observed the accumulation of fluorescence densi-
ty at one spot along the length of the DNA (Fig. 1, D and E,
fig. S1, and movie S2). This finding shows that condensin
induces local compaction of DNA.
To visualize the compacted DNA structures in the imag-
ing plane of the microscope, we applied flow at a large angle
with respect to the double-tethered DNA. This revealed that
the bright spots were made up of extended pieces of DNA,
consistent with single large DNA loops (Fig. 1, F and G, fig.
S2, and movie S3). Importantly, we observed no DNA loop
formation by wild-type condensin in the absence of either
ATP or Mg2+
, when we replaced ATP by the non-
hydrolyzable analogs ATP S or AMPPNP, or when we used a
mutant condensin that is unable to bind ATP. Condensin
hence creates DNA loops in a strictly ATP-hydrolysis-
dependent manner, either by gradually extruding DNA or by
randomly grabbing and linking two DNA loci.
To distinguish between these two possibilities, we moni-
tored the looping process by real-time imaging of the DNA
while applying constant flow. This revealed the gradual ap-
pearance of an initially weak increase in fluorescence inten-
sity at a local spot that grew into an extended loop over time
(Fig. 2A, fig. S3, and movies S4 and S5), providing direct
visual evidence of loop extrusion and ruling out the random
Real-time imaging of DNA loop extrusion by condensin
Mahipal Ganji,1
Indra A. Shaltiel,2
* Shveta Bisht,2
* Eugene Kim,1
Ana Kalichava,1
Christian H. Haering,2
† Cees Dekker1
†
1
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands. 2
Cell Biology and Biophysics Unit,
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
*These authors contributed equally to this work.
†Corresponding author. Email: christian.haering@embl.de (C.H.H.); c.dekker@tudelft.nl (C.D.)
It has been hypothesized that Structural Maintenance of Chromosomes (SMC) protein complexes such as
condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. Here, we
provide unambiguous evidence for loop extrusion by directly visualizing the formation and processive
extension of DNA loops by yeast condensin in real-time. We find that a single condensin complex is able to
extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1,500 base pairs per second,
using the energy of ATP hydrolysis. Condensin-induced loop extrusion is strictly asymmetric, which
demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop
extrusion by SMC complexes may provide the universal unifying principle for genome organization.
Cite as: M. Ganji et al., Science
10.1126/science.aar7831 (2018).
REPORTS
First release: 22 February 2018 www.sciencemag.org (Page numbers not final at time of first release) 1
The spatial organization of chromosomes is of paramount
importance to cell biology. Members of the SMC family of
protein complexes, including condensin, cohesin, and the
Smc5/6 complex, play vital roles in restructuring genomes
during the cellular life cycle (1–3). The principles by which
SMC complexes achieve these fundamental tasks are still
incompletely understood. Models based on random cross-
linking of DNA by pairwise interactions or conformational
changes in the DNA superhelicity have been proposed (4, 5).
An alternative hypothesis suggested that SMC protein com-
plexes bind to small loops in the genome to then processive-
ly enlarge them (6). More recently, the idea emerged that
condensin can start and subsequently extrude DNA loops,
which would elegantly explain how condensin mediates the
formation of mitotic chromosomes structures observed in
electron micrographs and deduced from Hi-C experiments
(7, 8). Indeed, polymer simulations showed that loop extru-
sion can, in principle, result in the efficient disentanglement
and compaction of chromatin fibers (9–11). The recent dis-
covery that condensin exhibits DNA translocase activity (12)
was consistent with, but did not provide conclusive evidence
for (13), DNA loop extrusion.
In this Report, we visualize the formation of DNA loops
by the Saccharomyces cerevisiae condensin complex in real
time (Fig. 1A). We tethered both ends of a double-stranded
48.5-kilobase pair (kbp) -DNA molecule to a passivated
surface (14, 15), using flow to adjust the DNA end-to-end
length to a distance much shorter than its contour length
(Fig. 1B). We then imaged DNA after staining with Sytox
Orange (SxO; Fig. 1C and movie S1). Upon flushing in 1 nM
of condensin (12) and 5 mM of adenosine triphosphate
(ATP), we observed the accumulation of fluorescence densi-
ty at one spot along the length of the DNA (Fig. 1, D and E,
fig. S1, and movie S2). This finding shows that condensin
induces local compaction of DNA.
To visualize the compacted DNA structures in the imag-
ing plane of the microscope, we applied flow at a large angle
with respect to the double-tethered DNA. This revealed that
the bright spots were made up of extended pieces of DNA,
consistent with single large DNA loops (Fig. 1, F and G, fig.
S2, and movie S3). Importantly, we observed no DNA loop
formation by wild-type condensin in the absence of either
ATP or Mg2+
, when we replaced ATP by the non-
hydrolyzable analogs ATP S or AMPPNP, or when we used a
mutant condensin that is unable to bind ATP. Condensin
hence creates DNA loops in a strictly ATP-hydrolysis-
dependent manner, either by gradually extruding DNA or by
randomly grabbing and linking two DNA loci.
To distinguish between these two possibilities, we moni-
tored the looping process by real-time imaging of the DNA
while applying constant flow. This revealed the gradual ap-
pearance of an initially weak increase in fluorescence inten-
sity at a local spot that grew into an extended loop over time
(Fig. 2A, fig. S3, and movies S4 and S5), providing direct
visual evidence of loop extrusion and ruling out the random
cross-linking model. The extruded loops were in general
stable (fig. S4), but occasionally disrupted spontaneously in
a single step (Fig. 2A and movie S6). Such a single-step dis-
ruption suggests that the DNA loop had been extruded by a
single condensin unit that spontaneously let go of the loop,
instead of a multi-step relaxation of the loop due to multiple
units.
Real-time imaging of DNA loop extrusion by condensin
Mahipal Ganji,1
Indra A. Shaltiel,2
* Shveta Bisht,2
* Eugene Kim,1
Ana Kalichava,1
Christian H. Haering,2
† Cees Dekker1
†
1
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands. 2
Cell Biology and Biophysics Unit,
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
*These authors contributed equally to this work.
†Corresponding author. Email: christian.haering@embl.de (C.H.H.); c.dekker@tudelft.nl (C.D.)
It has been hypothesized that Structural Maintenance of Chromosomes (SMC) protein complexes such as
condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. Here, we
provide unambiguous evidence for loop extrusion by directly visualizing the formation and processive
extension of DNA loops by yeast condensin in real-time. We find that a single condensin complex is able to
extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1,500 base pairs per second,
using the energy of ATP hydrolysis. Condensin-induced loop extrusion is strictly asymmetric, which
demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop
extrusion by SMC complexes may provide the universal unifying principle for genome organization.
onFebruary23,2018http://science.sciencemag.org/Downloadedfrom
~8 Kb/min
for two motors
~40Kb/min on nucleosomal fiber
g. 2.
peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint (which was not.http://dx.doi.org/10.1101/137711doi:preprint first posted online May. 13, 2017;
Speed =4 Kb/min
Cite as: T. Terakawa et al., Science
10.1126/science.aan6516 (2017).
REPORTS
First release: 7 September 2017 www.sciencemag.org (Page numbers not final at time of first release) 1
Structural maintenance of chromosomes (SMC) complexes
are the major organizers of chromosomes in all living organ-
isms (1, 2). These protein complexes play essential roles in
sister chromatid cohesion, chromosome condensation and
segregation, DNA replication, DNA damage repair, and gene
expression. A distinguishing feature of SMC complexes is
their large ring-like architecture, the circumference of which
is made up of two SMC protein coiled-coil proteins and a sin-
gle kleisin subunit (Fig. 1A) (1–4). The ~50-nm long antipar-
allel coiled-coils are connected at one end by a stable
dimerization interface, referred to as the hinge domain, and
at the other end by globular ATP-binding cassette (ABC) fam-
ily ATPase domains (5). The ATPase domains are bound by a
protein of the kleisin family, along with additional accessory
subunits, which vary for different types of SMC complexes
(Fig. 1A). The relationship between SMC structures and their
functions in chromosome organization is not completely un-
derstood (6), but many models envision that the coiled-coil
domains allow the complexes to topologically embrace DNA
(1–4). Given the general resemblance to myosin and kinesin,
some early models postulated that SMC proteins might be
mechanochemical motors (7–10).
SMC complexes are thought to regulate genome architec-
ture by physically linking distal chromosomal loci, but how
these bridging interactions might be formed remains un-
known (1, 2, 11). An early model suggested that many three-
dimensional (3D) features of eukaryotic chromosomes might
be explained by DNA loop extrusion (Fig. 1B) (12, 13), and re-
cent polymer dynamics simulations have shown that loop ex-
trusion can recapitulate the formation of topologically
associating domains (TADs), chromatin compaction, and sis-
ter chromatid segregation (14–18). This loop extrusion model
assumes a central role for SMC complexes in actively creating
the DNA loops (11, 12). Similarly, it has been proposed that
prokaryotic SMC proteins may structure bacterial chromo-
somes through an active loop extrusion mechanism (19–21).
Yet, the loop extrusion model remains hypothetical, in large
part because the motor activity that is necessary for driving
loop extrusion could not be identified (11). Indeed, the ab-
sence of an identifiable motor activity in SMC complexes in-
stead has lent support to alternative models in which DNA
loops are not actively extruded, but instead are captured and
stabilized by stochastic pairwise SMC binding interactions to
bridge distal loci (22).
To help distinguish between possible mechanisms of SMC
protein-mediated chromosomal organization, we examined
the DNA-binding properties of condensin (23). We overex-
pressed the five subunits of the condensin complex in bud-
ding yeast and purified the complex to homogeneity (Fig. 1C
and fig. S1). Electron microscopy images confirmed that the
complexes were monodisperse (Fig. 1D). As previously de-
scribed for electron micrographs of immunopurified Xenopus
laevis or human condensin (24), we observed electron density
that presumably corresponds to the two HEAT-repeat subu-
The condensin complex is a mechanochemical motor that
translocates along DNA
Tsuyoshi Terakawa,1
* Shveta Bisht,2
* Jorine M. Eeftens,3
* Cees Dekker,3
† Christian H. Haering,2
† Eric C.
Greene1
†
1
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. 2
Cell Biology and Biophysics Unit, Structural and Computational Unit,
European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. 3
Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology,
Delft, Netherlands.
*These authors contributed equally to this work.
†Corresponding author. Email: c.dekker@tudelft.nl (C.D.); christian.haering@embl.de (C.H.H.); ecg2108@cumc.columbia.edu (E.C.G.)
Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for
its functions remains obscure. Here, we use single-molecule imaging to demonstrate that Saccharomyces
cerevisiae condensin is a molecular motor capable of ATP hydrolysis-dependent translocation along
double-stranded DNA. Condensin’s translocation activity is rapid and highly processive, with individual
complexes traveling an average distance of 10 kilobases at a velocity of ~60 base pairs per second. Our
results suggest that condensin may take steps comparable in length to its ~50-nanometer coiled-coil
subunits, suggestive of a translocation mechanism that is distinct from any reported DNA motor protein.
The finding that condensin is a mechanochemical motor has important implications for understanding the
mechanisms of chromosome organization and condensation.
onNovember1,2017http://science.sciencemag.org/Downloadedfrom
Speed =36 Kb/min
Theory: speed ~100-200Kb per cohesin residence time (5-20min)
=> 10-40Kb/min
One-sided!?
20. Outline
Compartments and TADs
1. Emerging evidence of loop extrusion
2. Compartmentalization by phase separation!
3. Phase separation vs extrusion
Chromatin Organization by an Interplay of Loop Extrusion and Compartmental
Segregation
https://www.biorxiv.org/content/early/2017/10/03/196261
Heterochromatin drives organization of conventional and inverted nuclei
https://www.biorxiv.org/content/early/2018/01/09/244038
21. Kikue
Tachibana-Konwalski
Ilya M. Flyamer !
Johanna Gassler!
IBMA, Vienna!
!
!
!
!
!
Maxim Imakaev
MIT
Hugo Brandao
Harvard Biophysics
Single-nucleus Hi-C
Flyamer, Gassler, Imakaev et al. Nature 2017!
a
TADs compartments
yesyes
yes no
Compartments and TADs are formed
by separate mechanisms
b
active inactive
0.0 0.5
Log enrichment
-80kbinactive
0.5
Log enrichment
0.32 0.88
Effective
contact probability
-80kb loop +70kb TAD
0.0 0.8
Log enrichment
Compartmentalization Average loop Average TAD
active
24. Compartments and TADs are formed
by separate mechanisms
Compartments become stronger and fragmented
in the absence of loop extrusion
A
B
1.5
1.5
35.0 47.5 60.035.0 47.5 60.0
35.0
47.5
60.0
1.5
1.5
TAM (control)
25. Fine compartments match epigenetic state better than
wild-type compartments
C
D E
Eigenvector
1.5 -
-1.5 _
-0-
H3K4me3
2 -
0 _
H3K4me1
2 -
0 _
H3K36me3
2 -
0 _
H3K27me3
2 -
0 _
25.0 30.0 35.0
10 Mb
H3K27ac
2 -
0 _
Activity
chr15
20.0
30.0
40.0
20.0
30.0
40.0
20.0 30.0 40.0 55.0 70.0 72.0 88.0 103.5
B
C
TAM
chr17
1.5 1.5
26. Conclusions
1. Strong experimental support of the loop extrusion by
cohesin, hindered by CTCF
2. TAD and compartment formation — separate mechanisms
3. Innate compartments (associated with histone marks)
are partially suppressed by loop extrusion
A
1.5
1.5
35.0 47.5 60.035.0 47.5 60.0
35.0
47.5
60.0
1.5
1.5
TAM
27. Published online 04 August 2014 Nucleic Acids Research, 2014, Vol. 42, No. 15 9553–9561
doi: 10.1093/nar/gku698
Modeling epigenome folding: formation and dynamics
of topologically associated chromatin domains
Daniel Jost1
, Pascal Carrivain2
, Giacomo Cavalli2,*
and C´edric Vaillant1,*
1
Laboratoire de Physique, Ecole Normale Sup´erieure de Lyon, CNRS UMR 5672, Lyon 69007, France and 2
Institute
of Human Genetics, CNRS UPR 1142, Montpellier 34000, France
Received April 1, 2014; Revised July 02, 2014; Accepted July 19, 2014
ABSTRACT
Genomes of eukaryotes are partitioned into domains
of functionally distinct chromatin states. These do-
mains are stably inherited across many cell gener-
ations and can be remodeled in response to devel-
opmental and external cues, hence contributing to
the robustness and plasticity of expression patterns
and cell phenotypes. Remarkably, recent studies in-
dicate that these 1D epigenomic domains tend to fold
into 3D topologically associated domains forming
specialized nuclear chromatin compartments. How-
ever, the general mechanisms behind such compart-
mentalization including the contribution of epige-
netic regulation remain unclear. Here, we address
the question of the coupling between chromatin fold-
ing and epigenome. Using polymer physics, we ana-
lyze the properties of a block copolymer model that
accounts for local epigenomic information. Consid-
ering copolymers build from the epigenomic land-
scape of Drosophila, we observe a very good agree-
ment with the folding patterns observed in chro-
mosome conformation capture experiments. More-
over, this model provides a physical basis for the
existence of multistability in epigenome folding at
sub-chromosomal scale. We show how experiments
are fully consistent with multistable conformations
where topologically associated domains of the same
epigenomic state interact dynamically with each
other. Our approach provides a general framework
to improve our understanding of chromatin folding
during cell cycle and differentiation and its relation
to epigenetics.
INTRODUCTION
Gene expression is regulated by many sets of proteins that
associate with the genome in a cell-type and condition-
specific manner at specific regulatory elements including
proximal promoters, enhancers and repressors. The packag-
ing of eukaryotic DNA into chromatin contributes to this
regulation via the modulation of the accessibility and speci-
ficity of regulators to their nucleic sites. Locally, the chro-
matin state is characterized by various features like the nu-
cleosome positioning, the covalent modifications of DNA
and histones tails and the insertion of histone variants. This
pattern of chromatin states along the genome, the so-called
‘epigenome’, is itself regulated by the combined action of
different specialized chromatin regulators like chromatin re-
modelers, modifying enzymes and histone chaperones.
The general picture that emerges from the genome-wide
high-resolution profiling of structural and functional chro-
matin marks obtained in various organisms and cell types
(1–4), is that eukaryotic genomes are linearly organized into
distinct epigenomic domains. These domains extend over
few kilobases up to few megabases, are characterized by
a specific type of chromatin and are isolated from their
neighborhood by boundary elements such as insulators.
Euchromatin, less condensed, early replicating and con-
taining most active genes, is generally distinguished from
heterochromatin, typically highly condensed, late replicat-
ing and inhibitory to transcriptional machinery. In many
higher eukaryotes, from plants to mammals, statistical anal-
yses of hundreds of chromatin marks have identified only
a small number of main chromatin types (1,3,5,6), typi-
cally four or five, covering the well-known constitutive HP1-
like heterochromatin or the facultative (developmentally
regulated) Polycomb-like heterochromatin but also a less-
characterized ultra-repressive heterochromatin enriched in
genes that are expressed in very few tissues, the so-called
void or black chromatin (1,7).
Interestingly, within epigenomic domains, regulatory se-
quences such as enhancers may be located far from the tar-
get genes and multiple elements that are distributed over
large regions may collaborate or compete for the regula-
tion of individual genes or gene clusters. This implies the
existence of long-range mechanisms where regulatory ele-
ments could act over large genomic distances up to hun-
dreds of kilobases or more. A possible mechanism regu-
lating such long-range effects is the linear spreading of a
*To whom correspondence should be addressed. Tel: +33 4 72 72 86 34; Fax: +33 4 72 72 89 50; Email: cedric.vaillant@ens-lyon.fr
Correspondence may also be addressed to Giacomo Cavalli. Tel: +33 4 34 35 99 70; Fax: +33 4 34 35 99 01; Email: giacomo.cavalli@igh.cnrs.fr
C⃝ The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Mechanism of compartmentalization
Johannes Nübler
Many problems associated with it are not solved yet, and the potential of its
practical use is far from being exhausted.
Recall that a block copolymer is a chain consisting of consecutively joined
blocks, each of which constitutes a long homopolymer chain. For example, the
chemical structure of a two-block copolymer is A--...--A--B--...--B. The
number of blocks in the molecule, just as the number of links in the block, can
be arbitrary.
What happens when a sufficiently concentrated solution or melt is made from
the chains of a block copolymer? From previous subsections, we know that in a
typical case, the chains of poly-A and poly-B (or in our case, the blocks) are
incompatible. A phase separation in such a system, .however, is impossible
because of the covalent bonding of the blocks into common chains.
As a result, the phase separation, which is impossible on the some of the whole
system, occurs on a certain limited length scale defined by the size of the blocks.
The arising microdomain structure is schematically shown in Figure 5.1.
If the total amount of one of the components (e.g., A) is relatively small, then
the corresponding phase enriched with A component (the A phase) occupies a
small fraction of the total volume, and it constitutes a system of spherically
shaped micelles scattered like "islets>, in a °’sea" of the phase enriched with B
component (the B phase). On increasing the fraction of A links, the spherically
shaped micelles become cylindric ones piercing the B phase like reinforcing
wires. On further increasing the A fraction, a lamellar (or layer), structure
appears, with A and B phases laid out in alternating planar layers. Finally, on
still further increasing the fraction of A links, the so-called in~zerse phases
emerge: first the cylindric phase (B phase cylinders piercing the A phase), then
the spheric one ( B "’raisins" in the A "’pudding").
To conclude, it should be noted that the microdomain (or micellar) structures
are typical not only for block copolymers but also for systems consisting of the
so-called diphilic molecules. One of their blocks has a low molecular weight, but
because of its thermodynamic properties, it cannot mix withthe other block.
Examples include phospholipid molecules consisting of a hydrophilic "head"
and a polymeric (usually not very long) "tail." The dissolution of such mole-
h ~
FIGUItE 5.1. Microdomain structure in a melt of block copolymers. (a), Spheric A phase
micelles in massive B phase. (b), Cylindric micelles. (c), Alternating planar lamellae.
cu
(a
2
.o
(
o
t
t
"
Statistical Physics of Macromolecules 1991
(micro)phase separation
extrusion segregation
counteracts
native compartmentalization
contact frequency
low
high
no loop
extrusion
(nA+nB)
-1 (nA-nB)
(nA+nB)
counts,a.u.
A
B
Chromatin Organization by an Interplay of Loop Extrusion and Compartmental
Segregation
https://www.biorxiv.org/content/early/2017/10/03/196261
28. …..add loop extrusion on top
loop
extrusion
compartmental
segregation
counteracts
native compartmentalization
no loop
extrusion
-1 1(nA-nB)
(nA+nB)
-1 1(nA-nB)
(nA+nB)
counts,a.u.
0.0
0.18
A
B
Eattr(kBT)
5 MB equiv.5 MB equiv.
50 MB equiv.
simul
29. …..add loop extrusion on top
5 MB equiv.
5 MB equiv.
5 MB equiv.
loop
extrusion
compartmental
segregation
counteracts
native compartmentalization
no loop
extrusion
-1 1(nA-nB)
(nA+nB)
-1 1(nA-nB)
(nA+nB)
counts,a.u.
0.0
0.18
A
B
Eattr(kBT)
50 MB equiv.
simul
compaction
1
ofile
rr.
1
50 MB equiv.
modelB
loop
extrusion
compartmental
segregation
counteracts
simulationC
example snapshot A/B number difference
-1 1(nA-nB)
(nA+nB)
counts,a.u.u.
0.0
A
B
30. Active mixing by loop extrusion suppresses small
compartments compartments
Nuebler et al.,
bioRxiv (2017)
Hi-C
Fig. 2
92Mb 97Mb72Mb 122Mbchr6
comp.profile
autocorr.
WTNipbl
experiments (Schwarzer 2017)
31. Active mixing by loop extrusion suppresses small
compartments compartments
Nuebler et al.,
bioRxiv (2017)
Hi-C
Fig. 2
small compartments
are “erased” by
loop extrusion
92Mb 97Mb72Mb 122Mbchr6
comp.profile
autocorr.
WTNipbl
experiments (Schwarzer 2017)
32. Active mixing by loop extrusion suppresses small
compartments compartments
Nuebler et al.,
bioRxiv (2017)
Hi-C
Fig. 2
small compartments
are “erased” by
loop extrusion
92Mb 97Mb72Mb 122Mbchr6
comp.profile
autocorr.
WTNipbl
experiments (Schwarzer 2017)
33. Attractions:
A-A
B-B (direct or mediated, e.g. HP1)
B-Lamina
!
- Can one disentangle these contributions?
- Which ones are more important for compartmentalization?
Mechanism of compartmentalization
Irina
Solovei,
LMU
Yana
Fedorova,
Plovidv U
Hard to disentangle in conventional nuclei
Heterochromatin drives organization of conventional and inverted nuclei
https://www.biorxiv.org/content/early/2018/01/09/244038
42. Correct order: AA<AB<BB<BC<CC; AA≈0!
BB is the only free parameter
Mechanism of compartmentalization
Figure 3. Polymer model reproduces micro
Hi-C features
a, Our approach is to: define a mechanistic mo
interactions; simulate an ensemble of configurati
dynamics; and compare these configurations to Hi-
Correct order: AA<AB<BB<BC<CC; AA≈0!
BB = 0.5-0.6 kT
46. Summary
Active loop extrusion!
by cohesin!
!
!
!
!
!
1. Loop extrusion can be
universal mechanism!
• fold domains
• compacts chromosomes
2. Compartments are formed by
heterochromatin interactions,
and positioned in space
interactions with lamina
Active loop extrusion!
by cohesin!
!
!
!
!
blocked by CTCF!
1. Fundenberg J, Abnennur N, et al bioRxiv 2018
2. Gibcus, Samejima, Goloborodko A et al Science 2018
3. Falk M, et al., bioRxiv 2018
4. Nueber J et al., bioRxiv 2018
http://HiGlass.io
II
47. Emerging Evidence of Chromosome Folding by Loop Extrusion
https://www.biorxiv.org/content/early/2018/02/16/264648
HiGlass: Web-based Visual Exploration and Analysis of Genome
Interaction Maps
https://www.biorxiv.org/content/early/2017/10/30/121889
Chromatin Organization by an Interplay of Loop Extrusion and
Compartmental Segregation
https://www.biorxiv.org/content/early/2017/10/03/196261
Heterochromatin drives organization of conventional and inverted
nuclei
https://www.biorxiv.org/content/early/2018/01/09/244038
bioRxiv
48. Maxim
Imakaev
MIT
Nezar
Abdennur
MIT Comp/Sys
Biology
NSF, NIH: Center of Structure
and Physics of the Genome
Hugo
Brandao
Harvard
Biophysics
Ed
Banigan
MIT
Aafke
Van den Berg
MIT
Carolyn
Lu
MIT senior
Martin
Falk
MIT
Job Dekker
UMass Medical
!
!
John Marko
Northwestern U.
Francois Spitz
Institut Pasteur
Elphege Nora
Benoit G. Bruneau
UCSF
Kick
Tachibana-
Konwalski
IBMA, Vienna
Bill Earnshaw
U of Edinburgh
Irina
Solovei,
LMU
Geoff
Fudenberg
UCSF
Anton
Goloborodko
MIT Physics
Johannes
Nübler
MIT
49. 2-8 molecules (or motors) of cohesin per Mb
each consume ATP at a rate of 2 per sec per motor
< 1e5 ATP/sec!
!
Fibroblast ATP production: 1e9 ATP/sec,
!
!
hence the fraction consumed by cohesins < 0.0001
(very modest: ~1% of the NIH budget in US GDP).
50. How can SMCs extrude loops?
2. From translocation to extrusion
51. How can SMCs extrude loops?
2. From translocation to extrusion
Figure 4.
a. Walking as a possible mechanism of SMC translocation, with SMC arms in yellow and orang
kleisin in blue, creating a shackled walker.
possible implementation of
two-sided
52. Mechanism of loop extrusion
long-range interactions are formed by 1D process
number of sites L ) 1: At time t = 0, M motile element
pairs are dispersed randomly, each pair initially occupying
adjacent sites of this lattice. The DNA-binding motile
elements (referred to below as ‘motors’) then move
along the DNA with rates independent of position; steps
that move a motor away from its partner (‘forward’ steps
that extrude a DNA loop) occur at a rate r+ and steps that
move a motor back toward its partner (‘reverse steps’ that
retract the loop) occur at a rate rÀ (Figure 1). We suppose
the motion to be directed by energy gained from ATP
hydrolysis, with r+ > rÀ (when r+ ¼ rÀ there is 1D diffu-
sion of each motor; when rÀ > r+, the motors are driven
together which is not of interest here). The motor pairs are
assumed to have left/right symmetry, i.e. the left and right
motors move with the same rates.
increment Át to the event is distributed over the
0 Át 1 exponentially, with probability distr
PðÁtÞ ¼ ReÀRt
: The actual realization of Át is
from this continuous distribution. Which of the K
tions actually occurs is determined from their prob
distribution pi ¼ ri=R: This second, discrete, distrib
be used to select which of the K candidates actually
Once Át and i are determined, the state of the sy
changed, and time is increased to t+Át: The algor
then repeated to propagate the system forward from
to event, for as many transition steps as one r
(or for as long a total time as is required). The r
a series of transition events, distributed in time acc
to the rates that define the model. There is no tim
cretization; events can occur separated by arbitraril
Figure 1. Schematic drawing of machine positions on the lattice as time progresses; lattice model equivalent is sketched below each pan
dumbbell shapes (and arrows in the lattice sketch) depict enzymes and green lines show DNA. Panel (a) depicts the starting point and the pro
of infinitely processive machines, while Panel (b) shows machines with lower processivity (disassociation rate is still relatively small,
Panel (c) depicts a single step, with ATP binding, hydrolysis and release associated with extrusion of a small amount of DNA.
Nucleic Acids Research, 2
Self-organization of domain structures by
DNA-loop-extruding enzymes
Elnaz Alipour1,
* and John F. Marko2,
*
1
Center for Cell Analysis and Modeling, University of Connecticut Health Sciences Center, Farmington,
CT 06030 and 2
Departments of Physics and Astronomy and Molecular Biosciences, Northwestern University,
Evanston, IL 60208, USA
Received June 1, 2012; Revised August 17, 2012; Accepted September 13, 2012
ABSTRACT
The long chromosomal DNAs of cells are organized
into loop domains much larger in size than individual
DNA-binding enzymes, presenting the question of
how formation of such structures is controlled. We
present a model for generation of defined chromo-
somal loops, based on molecular machines consist-
ing of two coupled and oppositely directed motile
elements which extrude loops from the double helix
along which they translocate, while excluding one
another sterically. If these machines do not dissoci-
ate from DNA (infinite processivity), a disordered,
exponential steady-state distribution of small loops
is obtained. However, if dissociation and rebinding
of the machines occurs at a finite rate (finite
processivity), the steady state qualitatively changes
to a highly ordered ‘stacked’ configuration with sup-
pressed fluctuations, organizing a single large,
stable loop domain anchored by several machines.
The size of the resulting domain can be simply
regulated by boundary elements, which halt the
progress of the extrusion machines. Possible real-
izations of these types of molecular machines
are discussed, with a major focus on structural main-
tenance of chromosome complexes and also with
discussion of type I restriction enzymes. This mech-
anism could explain the geometrically uniform
folding of eukaryote mitotic chromosomes, through
nucleoids. It has been proposed that chromosomes
might simply occupy maximum-entropy conformations,
in the manner of confined random-coil polymers (1,2).
However, sequence position analyses reveal DNA to be
spatially ordered. Chromosomes of Escherichia coli (3–5)
and Caulobacter crescentus (6) have loci precisely pos-
itioned inside the cell, with fluctuations too small to be
consistent with random-polymer statistics (7). In eukary-
ote cells, interphase chromosomes in differentiated cells
occupy distinct territories (8). Furthermore, analyses of
DNA juxtapositions inside eukaryote nuclei reveal that
loci up to tens of megabases apart along chromosomes
are positioned near one another in the nucleus (9,10),
with statistical properties inconsistent with random-
polymer organization (10).
Detailed characterizations of specific cases of in cis
gene regulation also indicate that chromosomes have a
well-defined ‘loop domain’ organization, with specific
but distant sequences along the same chromosome pos-
itioned to be near one another (11). It is thought that
‘chromatin-bridging’ proteins (12) somehow stabilize
these loop structures, but the processes by which
sequence-defined chromatin loops are established and
maintained are unknown.
Strong correlations of juxtaposed DNA sequences are
especially clear during eukaryote mitosis, when chromo-
somes are compactly folded, following their replication.
Chromosomes are ‘condensed’ by folding along their
length into linear paired-chromatid noodle-like structures,
with a well-defined thickness and strikingly uniform struc-
tural and mechanical properties (13). As mitotic chromo-
Nucleic Acids Research, 2012, 1–11
doi:10.1093/nar/gks925
Nucleic Acids Research Advance Access published October 15, 2012
atMITLibrariesonNovember13,2012http://nar.oxfordjournals.org/Downloadedfrom
Marko 2013
Nasmyth 2001
on July 13, 2010rstb.royalsocietypublishing.orgDownloaded from
doi: 10.1098/rstb.1990.0012
, 285-2973261990Phil. Trans. R. Soc. Lond. B
A. D. Riggs
Folding and Enhancer Function
Memory, and Type 1 DNA Reeling Could Aid Chromosome
DNA Methylation and Late Replication Probably Aid Cell
References http://rstb.royalsocietypublishing.org/content/326/1235/285#related-urls
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