Alternative splicing is a deviation from the conventional splicing as it removes introns in a different manner. It has a lot of significance in the development of diseases like cancers and in plants adapting to various stress conditions.
RNA splicing is a biological process where a newly synthesized pre-mRNA transcript is processed and transformed into mRNA. It involves the removing of non-coding regions of RNA (introns) and the joining of the coding regions (exons).
Hello everyone, I am Dr. Ujwalkumar Trivedi, Head of Biotechnology Department at Marwadi University Rajkot. I teach Molecular Biology to the students of M.Sc. Microbiology and Biotechnology.
The current presentation describes various co-transcriptional and post-transcriptional RNA modifications in eukaryotic cells. The following processes are described in detail:
1. 5' mRNA Capping
2. Splicing
3. Alternative Splicing
4. 3' Polyadenylation
5. RNA Editing
Enjoy Reading.
Alternative splicing is a deviation from the conventional splicing as it removes introns in a different manner. It has a lot of significance in the development of diseases like cancers and in plants adapting to various stress conditions.
RNA splicing is a biological process where a newly synthesized pre-mRNA transcript is processed and transformed into mRNA. It involves the removing of non-coding regions of RNA (introns) and the joining of the coding regions (exons).
Hello everyone, I am Dr. Ujwalkumar Trivedi, Head of Biotechnology Department at Marwadi University Rajkot. I teach Molecular Biology to the students of M.Sc. Microbiology and Biotechnology.
The current presentation describes various co-transcriptional and post-transcriptional RNA modifications in eukaryotic cells. The following processes are described in detail:
1. 5' mRNA Capping
2. Splicing
3. Alternative Splicing
4. 3' Polyadenylation
5. RNA Editing
Enjoy Reading.
RNA splicing is a form of RNA processing in which a newly made precursor messenger RNA (mRNA) is transformed into a mature RNA by removing the non-coding sequences termed introns.
The process of RNA splicing involves the removal of non-coding sequences or introns and joining of the coding sequences or exons.
RNA splicing takes place during or immediately after transcription within the nucleus in the case of nucleus-encoded genes.
In eukaryotic cells, RNA splicing is crucial as it ensures that an immature RNA molecule is converted into a mature molecule that can then be translated into proteins. The post-transcriptional modification is not necessary for prokaryotic cells.
2 a. RNA polymerase II that is actively transcribing a gene (activel.pdfabhinavbhatnagar201
2 a. RNA polymerase II that is actively transcribing a gene (actively progressing along the DNA
polymerizing an RNA molecule) is phosphorylated. Researchers evaluated the abundance (the
frequency of occupancy) of RNA PolII at difference positions along a gene, and correlated that
with the introns and exons of the gene. The figure represents a portion of one gene that is
transcribed from left to right. The X axis corresponds to position along the DNA, and the boxes
below the figure illustrate where the exons are (with the lines between them representing the
introns). The Y axis represents the relative frequency of occupancy (relative abundance of active
RNA PolII using two different measures [pSer2 and pSer5]). A high the value on this axis means
that, when they sample whether RNA polII is present at the given position, they find the enzyme
present more frequently than at positions where the value is low.
a. With respect to intron/exon boundaries, what positions does the (transcribing) RNA PolII
occupy most?
b. How do you interpret this observation (i.e., does it say anything about how fast or how slow
RNA PolII is moving at different positions across the gene)? Does it suggest anything about the
relationship between transcription and splicing?
2b. You characterize the sequence of a full-length cDNA and the corresponding genomic DNA
for a particular intron-containing gene from mouse cells. When you align them to each other
using a computer program, the exons of the cDNA align perfectly in some regions with pieces of
the genomic DNA, whereas other exons appear to have a small number of specific nucleotide
differences compared to the genomic DNA. Assume this genomic DNA and cDNA come from
the same individual, and there are no sequencing mistakes. What might account for these
differences? ,241 132 15 98 459605 719M850 1341/1417 Ratio pser relative to RNAPI
Solution
2a RNA polymerase II at first recognizes and binds to the promoter DNA forming a state termed
as the closed complex. Following this the DNA surrounding the transcription start site is
unwound and the template strand is positioned in the Polymerase active site, forming the open
complex. Transcription initiation then commences, initially producing short RNA products.
b Alternative splicing is a crucial mechanism for gene regulation and for generating genomic
diversity. Recent studies indicate that the expression of nearly 95% of human multi-exon genes
involves alternative splicing. In metazoans, alternative splicing plays an important role in
generating different protein products that function in diverse cellular processes including cell
growth, differentiation and death.
Splicing is carried out by the spliceosome. A massive structure in which five small nuclear
ribonucleoprotein particles (snRNPs) and a large number of auxiliary proteins cooperate to
accurately recognize the splice sites and catalyse the two steps of the splicing reaction.
2b There is consistent evidence that both proce.
Graduate level educational lectures on innate and adaptive immune signaling mechanisms in two parts. Part 1 focuses on Antigen Receptor Signaling with focus on TCR singaling & the Immunological Synapse. Part 2 focuses on Cytokine Receptor, Notch and Innate Immunoreceptor Signaling as well as Regulation of signal dynamics. This material is taught as part of Immunobiology (BIOM514) at the University of New Mexico School of Medicine.
Introduction
What RNA Splicing???
Discovery
Types
Alternative Splicing
Mechanism
Regulatory element And protein
Splicing repression
Splicing activation
Significance
Diseases
Conclusion
Refrences
This PowerPoint is applicable for the medical, paramedical, and all the life science students who read the mechanism of gene expression. This is equally useful for teachers as well. This is the comprehensive coverage on the aforementioned topic.
REGULATION OF
GENE EXPRESSION
IN PROKARYOTES & EUKARYOTES .
This presentation is enriched with lots of information of gene expression with many pictures so that anyone can understand gene expression easily.
Gene expression is the process by which the information encoded in a gene is used to direct the assembly of a protein molecule.
Gene expression is explored through a study of protein structure and function, transcription and translation, differentiation and stem cells.
It is the process by which information from a gene is used in the synthesis of a functional gene product.
These products are often proteins, but in non-protein coding genes such as ribosomal RNA (rRNA), transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA.
The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea)
Regulation of gene expression:
Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA).
Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed.
CLASSIFICATION OF GENE WITH RESPECT TO THEIR EXPRESSION:
Constitutive ( house keeping) genes:
Are expressed at a fixed rate, irrespective to the cell condition.
Their structure is simpler.
Controllable genes:
Are expressed only as needed. Their amount may increase or decrease with respect to their basal level in different condition.
Their structure is relatively complicated with some response elements.
TYPES OF REGULATION OF GENE:
positive & negative regulation.
Steps involving gene regulation of prokaryotes & eukaryotes.
Operon-structure,classification of mechanisms- lac operon,tryptophan operon ,
and many things related to gene expression.
This is a video slide so anyone can understand this topic easily by seeing pictures included in this slide.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
RNA splicing is a form of RNA processing in which a newly made precursor messenger RNA (mRNA) is transformed into a mature RNA by removing the non-coding sequences termed introns.
The process of RNA splicing involves the removal of non-coding sequences or introns and joining of the coding sequences or exons.
RNA splicing takes place during or immediately after transcription within the nucleus in the case of nucleus-encoded genes.
In eukaryotic cells, RNA splicing is crucial as it ensures that an immature RNA molecule is converted into a mature molecule that can then be translated into proteins. The post-transcriptional modification is not necessary for prokaryotic cells.
2 a. RNA polymerase II that is actively transcribing a gene (activel.pdfabhinavbhatnagar201
2 a. RNA polymerase II that is actively transcribing a gene (actively progressing along the DNA
polymerizing an RNA molecule) is phosphorylated. Researchers evaluated the abundance (the
frequency of occupancy) of RNA PolII at difference positions along a gene, and correlated that
with the introns and exons of the gene. The figure represents a portion of one gene that is
transcribed from left to right. The X axis corresponds to position along the DNA, and the boxes
below the figure illustrate where the exons are (with the lines between them representing the
introns). The Y axis represents the relative frequency of occupancy (relative abundance of active
RNA PolII using two different measures [pSer2 and pSer5]). A high the value on this axis means
that, when they sample whether RNA polII is present at the given position, they find the enzyme
present more frequently than at positions where the value is low.
a. With respect to intron/exon boundaries, what positions does the (transcribing) RNA PolII
occupy most?
b. How do you interpret this observation (i.e., does it say anything about how fast or how slow
RNA PolII is moving at different positions across the gene)? Does it suggest anything about the
relationship between transcription and splicing?
2b. You characterize the sequence of a full-length cDNA and the corresponding genomic DNA
for a particular intron-containing gene from mouse cells. When you align them to each other
using a computer program, the exons of the cDNA align perfectly in some regions with pieces of
the genomic DNA, whereas other exons appear to have a small number of specific nucleotide
differences compared to the genomic DNA. Assume this genomic DNA and cDNA come from
the same individual, and there are no sequencing mistakes. What might account for these
differences? ,241 132 15 98 459605 719M850 1341/1417 Ratio pser relative to RNAPI
Solution
2a RNA polymerase II at first recognizes and binds to the promoter DNA forming a state termed
as the closed complex. Following this the DNA surrounding the transcription start site is
unwound and the template strand is positioned in the Polymerase active site, forming the open
complex. Transcription initiation then commences, initially producing short RNA products.
b Alternative splicing is a crucial mechanism for gene regulation and for generating genomic
diversity. Recent studies indicate that the expression of nearly 95% of human multi-exon genes
involves alternative splicing. In metazoans, alternative splicing plays an important role in
generating different protein products that function in diverse cellular processes including cell
growth, differentiation and death.
Splicing is carried out by the spliceosome. A massive structure in which five small nuclear
ribonucleoprotein particles (snRNPs) and a large number of auxiliary proteins cooperate to
accurately recognize the splice sites and catalyse the two steps of the splicing reaction.
2b There is consistent evidence that both proce.
Graduate level educational lectures on innate and adaptive immune signaling mechanisms in two parts. Part 1 focuses on Antigen Receptor Signaling with focus on TCR singaling & the Immunological Synapse. Part 2 focuses on Cytokine Receptor, Notch and Innate Immunoreceptor Signaling as well as Regulation of signal dynamics. This material is taught as part of Immunobiology (BIOM514) at the University of New Mexico School of Medicine.
Introduction
What RNA Splicing???
Discovery
Types
Alternative Splicing
Mechanism
Regulatory element And protein
Splicing repression
Splicing activation
Significance
Diseases
Conclusion
Refrences
This PowerPoint is applicable for the medical, paramedical, and all the life science students who read the mechanism of gene expression. This is equally useful for teachers as well. This is the comprehensive coverage on the aforementioned topic.
REGULATION OF
GENE EXPRESSION
IN PROKARYOTES & EUKARYOTES .
This presentation is enriched with lots of information of gene expression with many pictures so that anyone can understand gene expression easily.
Gene expression is the process by which the information encoded in a gene is used to direct the assembly of a protein molecule.
Gene expression is explored through a study of protein structure and function, transcription and translation, differentiation and stem cells.
It is the process by which information from a gene is used in the synthesis of a functional gene product.
These products are often proteins, but in non-protein coding genes such as ribosomal RNA (rRNA), transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA.
The process of gene expression is used by all known life - eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea)
Regulation of gene expression:
Regulation of gene expression includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA).
Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed.
CLASSIFICATION OF GENE WITH RESPECT TO THEIR EXPRESSION:
Constitutive ( house keeping) genes:
Are expressed at a fixed rate, irrespective to the cell condition.
Their structure is simpler.
Controllable genes:
Are expressed only as needed. Their amount may increase or decrease with respect to their basal level in different condition.
Their structure is relatively complicated with some response elements.
TYPES OF REGULATION OF GENE:
positive & negative regulation.
Steps involving gene regulation of prokaryotes & eukaryotes.
Operon-structure,classification of mechanisms- lac operon,tryptophan operon ,
and many things related to gene expression.
This is a video slide so anyone can understand this topic easily by seeing pictures included in this slide.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
2. Ensuring proper splicing
exon intron T
P
E exon intron exon
P’ E
If conserved sequences dictate splice junctions, what prevents the exon 1 splice donor site from interacting with exon
3, exon 4, etc splice acceptor and branch site?
3. Exons are typically the size of 1 nucleosome
while introns are much larger
100 1000 10000
Nature 409, 860-921 (15 February 2001)
Phys Biol. 2009 Nov 24;6(4):046018.
4. Alternative Splicing can occur in multiple ways
Mol Genet Genomics. 2017 Dec;292(6):1175-1195.
Exons can be skipped or inserted
Exons can be mutually exclusive
Alternative 5’ donor sites
Alternative 5’ acceptor sites
Introns can be retained
5. Introns usually contain multiple potential
splice sites
exon intron T
exon intron exon E
Splice Donor Splice Acceptor
Splice Acceptor
Splice Acceptor
Despite the fact that introns contain multiple possible splice acceptor sites, splicing
occurs in a reproducible and conserved manner.
Other mechanisms beyond RNA sequence must define proper splicing junctions.
6. Defining exons vs. Defining introns
Intron/exon borders need to be identified.
When introns are small, the machinery seems to assemble “around” the intron
When introns are large, the machinery seems to assemble “around” the exon
Most exons are small, however when a large exon is found, it usually flanked by small introns
7. Elements within the RNA sequence can guide
splicing
• 4 Types of Splicing Regulatory Elements (SRE)
• Exonic Splicing Enhancers (ESE)
• Exonic Splicing Silencers (ESS)
• Intronic Splicing Enhancers (ISE)
• Intronic Splicing Silencers (ISS)
• These elements bind RNA binding factors
• 71 known factors that bind these elements to regulate splicing.
10. SR proteins interact with the Pol II CTD and thus
participate in the coupling of transcription to
splicing
11. SR protein activity is tightly regulated
A series of phosphorylation and
dephosphorylation events regulate
both localization and activity.
Thus, the relative abundance of SR
protein activity can be adjusted
leading to strong vs weak ESE
activity.
12. Intronic Splice Enhancers associate with a
number of splicing factors
FEBS Letters Volume 581, Issue 22, 4 September 2007, Pages 4127-4131
Typically bind within the first couple hundred bases of the
intron.
Tend to promote use of the 5’ splice donor site.
Act as silencers when located closer to the 3’ exon
Thus positional location of these factors may direct activity
13. Exonic Silencing Elements interact with hnRNPs
Heterogeneous Nuclear Ribonucleoproteins have been
shown to act as splicing silencers through a variety of
mechanisms.
A. Steric repression of SR binding to a exonic splicing
enhancer
B. Promotes recruitment of other hnRNPs across the
RNA and thus silencing an enhancer
C. Interaction within an intron can block enhancer
activity or directly cover a splice donor or branch
site.
D. Formation of an RNA loop structure the blocks
recognition of an exon.
14. hnRNPs are factors important in multiple
facets of RNA regulation
• hnRNPs are protein/RNA complexes
• Aid in 3’ RNA processing
• Act as a chaperone molecule for RNA
• Promotes certain RNA structures the
either block or facilitate interactions with
other factors
• Aid in transport of RNA out of nucleus
• Regulate mRNA stability
Biochemical Journal Sep 15, 2010, 430 (3) 379-392;
15. The combination of enhancers and silencers as
well as the associating factors can direct specific
splice patterns
16. Splicing coupled to transcription is a
mechanism of regulation
First come first serve
model.
Pausing at exon borders
allows time for splice
machinery to set up.
When elongation is fast,
exons can be skipped.
Trends in Biochemical Sciences. Volume 35, Issue 9, p497–504, September 2010
17. Regulating elongation Speed: Kinetic Coupling
Nucleosome positioning:
The average exon is roughly 1 nucleosome in length
Exons on average slow transcription by 20-30 seconds
per exon.
Exons with strong splice acceptor sites have less of a
preference for a positioned nucleosome.
Genome Res. 2009 Oct; 19(10): 1732–1741.
Nature Structural & Molecular Biology 16, 996–1001 (2009)
18. Loss of histones causes exon skipping
Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14840-5.
Use of inducible H3 knockdown:
• Decreased histone occupancy at exons
• Increased rate of transcription
• Caused exon skipping
19. H3K36me3 may influence splicing
H3K36me3 is higher in exons that are more often included in the final mRNA.
H3K36me3 has a number of readers that are associated with splicing regulation
Nucleic Acids Res. 2014 Jan; 42(2): 701–713.
PTB is a protein associated with
intronic splicing silencers. It can be
recruited by MRG15, and
H3K36me3 reader
Alternatively, the H3K36me3
reader Psip1 interacts with SP
proteins to promote inclusion of
exons.
20. Histone acetylation is associated with exon
skipping
• Higher levels of histone acetylation associated with alternative exons
suggests that this mark promotes skipping.
• Histone acetylation may reduce pausing at the exon boundary
21. H3K9me3 is associated with exon retention
• H3K9me3 is normally associated with silenced heterochromatin
• Has been detected in coding regions
• Association with variable exons suggests H3K9me3 results in exon
inclusion
22. Chromatin remodeling and Splicing
• The Swi/SNF complex has been shown to interact with spliceosome
components
• Also shown to slow down rate of Pol II elongation
• Loss of Swi/SNF is associated with exon skipping
• CHD1 chromatin remodeler is associated with nucleosome
positioning.
• Loss of CHD1 resulted in decreases in H3K36me3 and intron
retention.
23. Summary of Chromatin influence on Splicing
• Through chromatin remodeling or histone modifications, chromatin
regulated splicing through:
• Altering the rate of Pol II elongation
• Recruiting splicing factors
24. The genome as a regulator of splicing
• Identification of SNPs that alter splicing
• Can impact the strength of splice donor sites,
splice acceptor sites, branch points, splicing
elements, etc …
Front. Genet., 06 July 2012
25. Elongation control does not always depend
upon amino acid abundance
Mechanisms of Microbrial Genetics: OpenStax
Riboswitches use the interaction of
the RNA with small molecules to
stabilize secondary structures.
There are a few identified
eukaryote genes that
seemingly use riboswitches to
govern splicing.