This document discusses epigenetic regulation in plants. It begins by outlining the benefits of studying epigenetics in plants, including their haploid stage and ability to tolerate polyploidy. It then describes the molecular components that regulate chromatin structure in plants, including DNA methyltransferases, histone-modifying enzymes, and other chromatin proteins. Next, it examines the RNA interference pathways involved in epigenetic gene silencing in plants. The document also notes that some epigenetic regulation occurs without RNA involvement, such as paramutation. Finally, it discusses how studying plant epigenetics can provide insights into human evolution and epigenetic reprogramming.
Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. With decreasing time and cost to generate these datasets, omics data integration has created both exciting opportunities and immense challenges for biologists, computational biologists, biostatisticians and biomathematicians. Genomics, transcriptomics, proteomics, and metabolomics together they help to bring out the best of characters in plants.
Access to large-scale omics datasets i.e. genomics, transcriptomics, proteomics, metabolomics, phenomics, etc. has revolutionized biology and led to the emergence of systems approaches to advance our understanding of biological processes. With decreasing time and cost to generate these datasets, omics data integration has created both exciting opportunities and immense challenges for biologists, computational biologists, biostatisticians and biomathematicians. Genomics, transcriptomics, proteomics, and metabolomics together they help to bring out the best of characters in plants.
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Whole genome sequencing of arabidopsis thalianaBhavya Sree
arabidopsis is the representative of plant kingdom or the 'model plant'.it is the first plant genome sequenced. the sequences lead to the overall understanding of the plant kingdom, better understanding of various genes,the important metabolic pathways, evolution etc
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
RNA interference (RNAi): Cellular process by which an mRNA is targeted for degradation by a dsRNA with a strand complementary to a fragment of such mRNA.
in-planta transformation technology is used to transform the desired gene into the plant without using tissue culture step is called in-planta transformation.it is useful for those plants that lack the tissue culture and regeneration system.
Plant epigenetic memory in plant growth behavior and stress response. Sally M...CIAT
Speaker: Sally Mackenzie, Lloyd and Dottie Huck Chair for Functional Genomics, Department of Biology, Pennsylvania State University. Fellow in the American Society of Plant Biologists and the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”.
http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
A concise and well fabricated presentation the current techniques used for plant genome editing including CRISPER/cas9 system, TALENS, TELES, ZINC FINGER NUCLEASES(ZFN), HEJ (homologous endjoing) and many other high throughout techniques along references.
Whole genome sequencing of arabidopsis thalianaBhavya Sree
arabidopsis is the representative of plant kingdom or the 'model plant'.it is the first plant genome sequenced. the sequences lead to the overall understanding of the plant kingdom, better understanding of various genes,the important metabolic pathways, evolution etc
Molecular Breeding in Plants is an introduction to the fundamental techniques...UNIVERSITI MALAYSIA SABAH
This slide describe the process of molecular breeding in plants which involves the application of molecular markers for Marker Assisted Selection and Marker Assisted Breeding.
Introduction
Transcriptome analysis
Goal of functional genomics
Why we need functional genomics
Technique
1. At DNA level
2.At RNA level
3. At protein level
4. loss of function
5. functional genomic and bioinformatics
Application
Latest research and reviews
Websites of functional genomics
Conclusions
Reference
RNA interference (RNAi): Cellular process by which an mRNA is targeted for degradation by a dsRNA with a strand complementary to a fragment of such mRNA.
in-planta transformation technology is used to transform the desired gene into the plant without using tissue culture step is called in-planta transformation.it is useful for those plants that lack the tissue culture and regeneration system.
Plant epigenetic memory in plant growth behavior and stress response. Sally M...CIAT
Speaker: Sally Mackenzie, Lloyd and Dottie Huck Chair for Functional Genomics, Department of Biology, Pennsylvania State University. Fellow in the American Society of Plant Biologists and the American Association for the Advancement of Science (AAAS).
Event: Robert D. Havener Seminar on “Innovations for Crop Productivity”.
http://ciat.cgiar.org/event/robert-d-havener-seminar-on-innovations-for-crop-productivity/
How novel compute technology transforms life science researchDenis C. Bauer
Unprecedented data volumes and pressure on turnaround time driven by commercial applications require bioinformatics solutions to evolve to meed these new demands. New compute paradigms and cloud-based IT solutions enable this transition. Here I present two solution capable of meeting these demands for genomic variant analysis, VariantSpark, as well as genome engineering applications, GT-Scan2.
VariantSpark classifies 3000 individuals with 80 Million genomic variants each in under 30 minutes. This Hadoop/Spark solution for machine learning application on genomic data is hence capable to scale up to population size cohorts.
GT-Scan2, identifies CRISPR target sites by minimizing off-target effects and maximizing on-target efficiency. This optimization is powered by AWS Lambda functions, which offer an “always-on” web service that can instantaneously recruit enough compute resources keep runtime stable even for queries with several thousand of potential target sites.
Chromosomes and molecular cytogenetics of oil palm: impact for breeding and g...Pat (JS) Heslop-Harrison
See also related talk Crops, Climate Change and Super-domestication Heslop-Harrison for Oil Palm Breeders symposium on Gearing Oil Palm Breeding and Agronomy for Climate Change: Keynote opening address MPOB PIPOC and PIPOC ISOPB ISOPA
http://www.slideshare.net/PatHeslopHarrison/heslop-harrisoncrops-climatechangesuperdomestication
Molecular cytogenetic analysis of the chromosomes of oil palm allows us to understand their evolution, genetics and segregation, genetic recombination and karyotypic stability. The cytogenetic manipulation of genomes and their chromosomes is often valuable for plant breeders to introduce and exploit new variation. Cytological landmarks such as centromeres, telomeres, heterochromatin and nucleolar organizer regions are important for the integration of physical chromosomes with the DNA sequence information. This linkage of the genetic, chromosomal and physical maps is particularly useful in a long-lived tree crop where genetic mapping requires decades of preparation and the mapping crosses may not be directly relevant to DxP commercial plantings. Repetitive DNA is often the most rapidly evolving genomic component, but is poorly understood from sequence assemblies; molecular cytogenetic studies allow its organization and variation to be studied, and the exploitation of repetitive sequences as markers and, by the amplification and mobility of transposable elements or satellite repeats, in generation of new variation.
Molecular cytogenetic approaches provide tools for oil palm genomic research, comparative genomics and evolutionary studies and further facilitate understanding the inheritance of specific traits in oil palm, including DNA methylation, epigenetics, and somaclonal variation, allowing work with hybrids, haploids and polyploids. Knowledge of the structures and organization of the chromosomes of oil palm, as in many crop species, is valuable for development of new lines, making hybrids, understanding the causes of some abnormalities or infertility, and exploiting variation and biodiversity found in related species or breeding lines.
Further information and slides from the talk will be on our website www.molcyt.com.
Brian D. Strahl's lecture presented in the BIOTECHNIQUES VIRTUAL SYMPOSIUM on "The Cell Landscape: From Genotype to Phenotype" Wednesday, October 3, 2012
Triacylglycerols produced by plants are one of the most energy-rich and abundant forms of reduced carbon available from nature. Given their chemical similarities, plant oils represent a logical substitute for conventional diesel, a non-renewable energy source. However, as plant oils are too viscous for use in modern diesel engines, they are converted to fatty acid esters. Apart from seed oil vegetative tissue is potential source as bio mass for biofuel production, taking 15 tonnes per hectare as an average dry matter yield for a perennial grass, an oil content of 20– 25% by weight will produce about 3400 l of biodiesel (Heaton et al., 2004). There is growing interest in engineering green biomass to expand the production of plant oils as feed and biofuels. Here, we show that PHOSPHOLIPID: DIACYLGLYCEROL ACYLTRANSFERASE1 (PDAT1) is a critical enzyme involved in triacylglycerol (TAG) synthesis in leaves. Overexpression of PDAT1 increases leaf TAG accumulation, leading to oil droplet overexpansion through fusion. Ectopic expression of oleosin promotes the clustering of small oil droplets. Coexpression of PDAT1 with oleosin boosts leaf TAG content by up to 6.4% of the dry weight without affecting membrane lipid composition and plant growth. PDAT1 overexpression stimulates fatty acid synthesis (FAS) and increases fatty acid flux toward the prokaryotic glycerolipid pathway (Julian at al..2013). First, an Arabidopsis thaliana gene diacylglycerol acyltransferase (DGAT) coding for a key enzyme in triacylglycerol (TAG) biosynthesis, was expressed in tobacco under the control of a strong ribulose-biphosphate carboxylase small subunit promoter. This modification led to up to a 20-fold increase in TAG accumulation in tobacco leaves and translated into an overall of about a twofold increase in extracted fatty acids (FA) up to 5.8% of dry biomass in Nicotiana tabacum cv Wisconsin, and up to 6% in high-sugar tobacco variety NC-55 ( Andrianovet al 2010). Therefore Biotechnology has important and perhaps critical part to play in large-scale development of Biodiesel.
This ppts is based upon the recent adavancement and methodology about mitochondrial transformation. What is organellar transformation and what is the importance in contemporary time.
A transplastomic plant is a genetically modified plant in which the new genes have not been inserted in the nuclear DNA but in the DNA of the chloroplasts.
Micro RNA genes and their likely influence in rice (Oryza sativa L.) dynamic ...Open Access Research Paper
Micro RNAs (miRNAs) are small non-coding RNAs molecules having approximately 18-25 nucleotides, they are present in both plants and animals genomes. MiRNAs have diverse spatial expression patterns and regulate various developmental metabolisms, stress responses and other physiological processes. The dynamic gene expression playing major roles in phenotypic differences in organisms are believed to be controlled by miRNAs. Mutations in regions of regulatory factors, such as miRNA genes or transcription factors (TF) necessitated by dynamic environmental factors or pathogen infections, have tremendous effects on structure and expression of genes. The resultant novel gene products presents potential explanations for constant evolving desirable traits that have long been bred using conventional means, biotechnology or genetic engineering. Rice grain quality, yield, disease tolerance, climate-resilience and palatability properties are not exceptional to miRN Asmutations effects. There are new insights courtesy of high-throughput sequencing and improved proteomic techniques that organisms’ complexity and adaptations are highly contributed by miRNAs containing regulatory networks. This article aims to expound on how rice miRNAs could be driving evolution of traits and highlight the latest miRNA research progress. Moreover, the review accentuates miRNAs grey areas to be addressed and gives recommendations for further studies.
Welcome to TechSoup New Member Orientation and Q&A (May 2024).pdfTechSoup
In this webinar you will learn how your organization can access TechSoup's wide variety of product discount and donation programs. From hardware to software, we'll give you a tour of the tools available to help your nonprofit with productivity, collaboration, financial management, donor tracking, security, and more.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Students, digital devices and success - Andreas Schleicher - 27 May 2024..pptxEduSkills OECD
Andreas Schleicher presents at the OECD webinar ‘Digital devices in schools: detrimental distraction or secret to success?’ on 27 May 2024. The presentation was based on findings from PISA 2022 results and the webinar helped launch the PISA in Focus ‘Managing screen time: How to protect and equip students against distraction’ https://www.oecd-ilibrary.org/education/managing-screen-time_7c225af4-en and the OECD Education Policy Perspective ‘Students, digital devices and success’ can be found here - https://oe.cd/il/5yV
How to Create Map Views in the Odoo 17 ERPCeline George
The map views are useful for providing a geographical representation of data. They allow users to visualize and analyze the data in a more intuitive manner.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
We all have good and bad thoughts from time to time and situation to situation. We are bombarded daily with spiraling thoughts(both negative and positive) creating all-consuming feel , making us difficult to manage with associated suffering. Good thoughts are like our Mob Signal (Positive thought) amidst noise(negative thought) in the atmosphere. Negative thoughts like noise outweigh positive thoughts. These thoughts often create unwanted confusion, trouble, stress and frustration in our mind as well as chaos in our physical world. Negative thoughts are also known as “distorted thinking”.
Palestine last event orientationfvgnh .pptxRaedMohamed3
An EFL lesson about the current events in Palestine. It is intended to be for intermediate students who wish to increase their listening skills through a short lesson in power point.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
Unit 8 - Information and Communication Technology (Paper I).pdf
Epigenetic regulation in plants
1. Epigenetic Regulation in Plants Ryza Aditya Priatama (리자 아디티아) Plant Developmental Genetics Laboratory Gyeongsang National University, Korea
2. Outline Benefits of Plants in Epigenetic Research Molecular Components of Chromatin in Plants Molecular Components of RNAi-mediated Gene Silencing Pathways Epigenetic Regulation without RNA Involvement Outlook
3. Benefit of Plants in Epigenetic Research Plants and Mammals are Similar in Terms of (epi)Genome Organization Plants Provide Additional Topics for Epigenetics Research Plants have Haploid (gametophyte) stage between meiosis and fertilization (Fig 1.) Somatic Embryogenesis Differentiation; somaclonal variation Higher tolerance of Polyploidy Plants Tolerate Methodological Approach that are difficult in Mamals Plants efficient in mutagenesis & rapid growing insertion mutants collection Plants have a Proven Record of Contributing to Epigenetic Research Distinction of Euchromation and Heterochromatin (1928) Pioneering work on transposable Element (B. McClintock)
4.
5. Figure 1. Specialties of the Plant life Cycle Plants can propagate sexually (gametogenesis, fertilization, and seed formation, right) as well as somatically (vegetative sprigs, de- and re-differentiation or embryogenesis, left). The body of higher plants, with roots, stem, leaves, and flowers, is the diploid sporophyte. During meiosis, the chromosome number is reduced to half. Whereas in animals the meiotic products form the gametes without further division and fuse directly to produce the diploid embryo, plants form haploid male or female gametophytes by two or three mitotic divisions, respectively. The pollen tube ultimately contains one vegetative (white) and two generative (black) nuclei. The two generative nuclei fertilize the egg cell (black) and the central cell, which has a diploid nucleus derived from fusion of the two polar nuclei (yellow). This double fertilization gives rise to the diploid embryo and the triploid endosperm, which provides a nutrient source for the developing embryo. After seed germination, the embryo will grow into a new sporophyte. In addition, most plants have the potential for vegetative propagation through activation of quiescent lateral meristems, outgrowth of specialized root structures such as tubers, amplification in tissue culture, and even regeneration from individual somatic cells after removal of the cell wall (protoplasts). Endoreduplication is frequent in plants, producing polyploid cells or tissues. Plants can be grafted to produce chimeras. In summary, genetic and epigenetic information in plants therefore passes a much less well-defined germ line than in animals.
10. Active DNA demethylation and its function in plants. The plant 5-methylcytosine DNA glycosylases ROS1, DME, DML2, and DML3 function as active DNA demethylases. Cell Research (2011) 21:442-465.
11. MatteiMG et al (2003 .)URL : http://AtlasGeneticsOncology.org/Educ/HeterochromEng.html
12. Histone-modifying Enzyme Histone Deacetylases (HAT) and Histone Acetyltransferases (HDACs) The histone switch. Targeted modifications under the control of histone methylases (HMTs), histone acetyltransferases (HATs) and histone deacetylases (HDACs) alter the histone code at gene regulatory regions. Deacetylation, frequently followed by histone methylation, establishes a base for highly repressive structures, such as heterochromatin. Acetylated histone tails are shown as yellow stars. Methylation (Me) is shown to recruit heterochromatin protein 1 (HP-1). Adcock et al.Respiratory Research 2006 7:21 doi:10.1186/1465-9921-7-21
13. Histone-modifying Enzyme Histone Methyl Transferases Protein are able to methylated lysine residues in Histone and other proteins contain a common SET domain(SU(VAR)/E(Z)/TRX) Through their ability to methylate histone H3 or H4 at various lysine residues, different complexes containing SET domain proteins play roles in promoting or inhibiting the transcription of specific genes and in forming heterochromatin Some SET domain proteins are members of the Polycomb group (PcG) or trithorax group (trxG), which maintain transcriptionally repressed or active states, respectively, of homeotic genes during plant and animal development (see Chapters 11 and 12). Other SET domain proteins, such as SU(VAR)3-9, participate in maintaining condensed heterochromatin, often inrepetitiveregions, by methylating H3 at lysine 9 (H3K9). Schematic of the nucleosome, illustrating the types of post-translational modifications that can occur on the histone tails and the enzymes responsible for these modification reactions.
14. Other Chromatin Proteins Other Polycomb Proteins Component of Imprinting Chromatin-remodelling Proteins Chromatin Assembling Factor Heterochromatin-like Proteins
15. Model for activation and repression. a, In the off state, the DNA-bound repressor (REP) at the upstream repressor site (URS) recruits negative modifiers, such as histone deacetylase (HDAC), which remove acetyl (ac) groups from histones. b, In the on state, DNA-bound activator (ACT) at the upstream activator site (UAS) recruits positive modifiers, such as histone acetylases (HAT), at the promoter, while DNA-bound RNA polymerase (POL) recruits histone methylases at the ORF. Early during elongation, the C-terminal domain (CTD) polymerase repeat is phosphorylated at serine 5 (S5ph), leading to recruitment of the COMPASS complex (Set1, part of the COMPASS complex, methylates H3K4) and DOT1 (which methylates H3K79). Later in elongation the CTD repeat is phosphorylated at serine 2 (S2ph), leading to recruitment of Set2 (which methylates H3K36) Shelley L. Berger Nature 447, 407-412(24 May 2007)
16. Molecular Components of RNAi-mediated Gene Silencing Pathways Elaboration of RNAi-mediated Silencing in Plants Transgene-related Posttranscriptional and Virus-induced Silencing (PTGS/VIGS) Regulation of Plant Development by RNAs and Trans-acting siRNAs, Transgene-related Transcriptional Silencing, RNA-directed DNA Methylation, and Heterochromatin Formation
17. RNAi and related types of gene silencing represent cellular responses to double-stranded RNA (dsRNA). The proliferation of RNAi-mediated gene-silencing pathways in plants is illustrated by 1. the expansion and functional diversification of gene families encoding core components of RNAi: the Arabidopsis genome encodes four DICER-LIKE (DCL) proteins and ten Argonaute (AGO) proteins 2. the heterogeneity in length and functional diversity of small RNAs, including the 21-nucleotide short interfering RNAs (siRNA) derived from transgenes and viruses, and several types of endogenous small RNAs, such as 21- to 24-nucleotide microRNAs; 21-nucleotide trans-acting siRNAs, and 24- to 26nucleotide heterochromatic siRNAs 3. the various modes of gene silencing elicited by different small RNAs: PTGS involves mRNA degradation or repression of translation, and TGS is associated with epigenetic modifications such as DNA cytosine methylation and histone methylation 4. the importance of PTGS in antiviral defense, which can be countered by a variety of plant viral proteins that repress silencing at different steps of the pathway 5. the existence of processes, such as non-cellautonomous silencing and transitivity (see Section 3.2, Non-ceil-autonomous silencing and transitivity),that rely on RNA-dependent RNA polymerases, six of which are encoded in the Arabidopsis genome
18.
19. The RNA-directed DNA methylation pathway in plants. In transposons and other DNA repeat regions, aberrant single-stranded RNAs are proposed to be produced by DNA-dependent RNA polymerase IV (Pol IV). The chromatin remodeling protein CLSY may facilitate Pol IV transcription. RNA-dependent RNA polymerase RDR2 converts the aberrant single-stranded RNAs to double-stranded RNAs, which are then cleaved into 24-nt siRNAs by the Dicer-like protein DCL3. The 24-nt siRNAs are bound by an ARGONAUTE protein AGO4, AGO6, or AGO9. In intergenic non-coding (IGN) regions, DNA-dependent RNA polymerase V (Pol V) generates single-stranded scaffold RNA transcripts. Generation of Pol V RNA transcripts requires RDM4/DMS4, DRD1, DMS3, and RDM1. RDM1 may bind single-stranded methylated DNA and help recruit Pol V and Pol II to appropriate chromatin regions. DRD1, DMS3, and RDM1 form a stable protein complex, named DDR. KTF1 is an RNAbinding protein, which tethers AGO4 to nascent Pol V or Pol II RNA transcripts to form the RNA-directed DNA methylation effector complex. IDN2 may stabilize the base-pairing between the nascent scaffold transcripts and 24-nt siRNAs. The effector complex directs the de novo DNA methyltransferase DRM2 to specific chromatin regions to catalyze new DNA methylation. Cell Research (2011) 21:442-465
21. Despite the specificity provided by small RNAs, they probably do not induce all epigenetic modifications in plants. For example, MOM, a protein with a partial SNF2 domain, has not yet been implicated in RNAi-mediated TGS. There is also no evidence that PcG proteins in plants are directed to their target genes by small RNAs. Other types of signal, such as homologous pairing of non-transcribed repetitive sequences or special sequence compositions, might nucleate heterochromatin formation or attract DNA methyltransferases. The RNAi machinery, for instance, is dispensable for DNA methylation and histone methylation in Neurospora, where Tarich segments are preferentially targeted for modification
22. An unusual epigenetic phenomenon in plants that has not yet been shown to involve RNAi is paramutation. Paramutationoccurs when certain alleles, termed paramutagenic, impose an epigenetic imprint on susceptible (paramutable) alleles. The epigenetic imprint is inherited through meiosis and persists even after the two interacting alleles segregate in progeny. Paramutation represents a violation of Mendel's law, which stipulates that alleles segregate unchanged from a heterozygote. Paramutation was first observed decades ago in maize and tomato, but the mechanism(s) has remained enigmatic. The B locus in maize, one of the most intensively studied cases of paramutation, contains a series of direct repeats almost 100 kb from the transcription start site that mediate paramutation in an unknown manner. Although RNA-based silencing has not been fully ruled out, alternate mechanisms relying on pairing of alleles are still under consideration.
24. Plants clearly share a number of features of epigenetic control with other organisms, yet they have also evolved a number of plant-specific variations and innovations. These likely underpin the unique aspects of plant development and their extraordinary ability to survive and reproduce successfully in unpredictable environments. Plants able to induce or erase repressive modifications in nondividing cells-the former through RdDM and histone modifications, and the latter through the activity of DNA glycosylases such as DME and ROS1-allows epigenetic reprogramming without intervening cycles of DNA replication. Unraveling the mechanisms of meiotic inheritance of epigenetic marks in plants could eventually permit scientists to manipulate this feature for improvements in horticulture and agriculture.
25. The origin of heterosis, the superior performance of hybrids compared to that of inbred parent lines, is still unknown, but it is likely to involve epigenetic alterations triggered by combining two related but distinct genomes. Similarly, polyploidization combines and/or multiplies whole genomes, with innumerable possibilities for epigenetic changes. Learning the epigenetic consequences of polyploidization in plants would also help to understand our own evolutionary history Clearly, even at this scale of inquiry, plant epigenetics can be informative for human biology, justifying their reputation as "masters of epigenetic regulation.
31. Abbreviation H3Kxx : histone 3 lysine xx CpG: C-phosphate-G RNAi :RNA interference PTGS : Post Transcriptional Gen Silencing TGS : Transcriptional Gen Silencing RNA-directed DNA Methylation
Editor's Notes
In mammals, genetic approaches are limited by demanding procedures for generating mutations and by the requirement for mating in order to establish homozygous genotypes, which are mandatory for revealing recessive traits.
(A) ROS1 was discovered by screening for repressor of silencing in Arabidopsis plants expressing the RD29A promoter-driven luciferase reportergene. ROS1 prevents transgene silencing that is caused by RNA-directed DNA methylation. ROS1 also functions to prevent over-methylation and alleviate the silencing of some endogenous genes and transposons. ROS3 is an RNA-binding protein that may direct ROS1 to specific genome targets. (B) DME is preferentially expressed in endosperms, and is responsible for genome-wide DNA demethylation and gene imprinting. GenomewideDNA demethylation activates transposons and other repetitiveDNA sequences, leading to the enhanced production ofsiRNAs in endosperms. These siRNAs might be transported intoembryos, and contribute to DNA hypermethylation, to ensuregenome stability in embryos. Black and white circles representmethylated and unmethylatedcytosines, respectively
The RNA-directed DNA methylation pathway in plants. In transposons and other DNA repeat regions, aberrant single-stranded RNAs are proposed to be produced by DNA-dependent RNA polymerase IV (Pol IV). The chromatin remodelingprotein CLSY may facilitate Pol IV transcription. RNA-dependent RNA polymerase RDR2 converts the aberrant single-strandedRNAs to double-stranded RNAs, which are then cleaved into 24-nt siRNAs by the Dicer-like protein DCL3. The 24-nt siRNAsare bound by an ARGONAUTE protein AGO4, AGO6, or AGO9. In intergenic non-coding (IGN) regions, DNA-dependentRNA polymerase V (Pol V) generates single-stranded scaffold RNA transcripts. Generation of Pol V RNA transcripts requiresRDM4/DMS4, DRD1, DMS3, and RDM1. RDM1 may bind single-stranded methylated DNA and help recruit Pol V and Pol IIto appropriate chromatin regions. DRD1, DMS3, and RDM1 form a stable protein complex, named DDR. KTF1 is an RNAbindingprotein, which tethers AGO4 to nascent Pol V or Pol II RNA transcripts to form the RNA-directed DNA methylation effectorcomplex. IDN2 may stabilize the base-pairing between the nascent scaffold transcripts and 24-nt siRNAs. The effectorcomplex directs the de novo DNA methyltransferase DRM2 to specific chromatin regions to catalyze new DNA methylation.