Putative promoters within gene bodies control exon expression via TET1‐mediated H3K36 methylation

2020 ◽  
Vol 235 (10) ◽  
pp. 6711-6724
Author(s):  
Ling Ma ◽  
Tahir Muhammad ◽  
Hongyang Wang ◽  
Guangyuan Du ◽  
Ali Sakhawat ◽  
...  
Keyword(s):  
H3k36 Methylation ◽  
Exon Expression

scholarly journals Modeling Exon Expression Using Histone Modifications

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e67448 ◽  
Author(s):  
Shijia Zhu ◽  
Guohua Wang ◽  
Bo Liu ◽  
Yadong Wang
Keyword(s):  
Histone Modifications ◽  
Exon Expression

scholarly journals Integrative Visual Analysis of the Effects of Alternative Splicing on Protein Domain Interaction Networks

2008 ◽  
Vol 5 (2) ◽  
Author(s):  
Dorothea Emig ◽  
Melissa S. Cline ◽  
Karsten Klein ◽  
Anne Kunert ◽  
Petra Mutzel ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Protein Interactions ◽  
Visual Analysis ◽  
Protein Isoforms ◽  
Interaction Networks ◽  
Protein Domain ◽  
Domain Interaction ◽  
Exon Arrays ◽  
Exon Expression ◽  
Splicing Patterns

SummaryProteins and their interactions are essential for the functioning of all organisms and for understanding biological processes. Alternative splicing is an important molecular mechanism for increasing the protein diversity in eukaryotic cells. Splicing events that alter the protein structure and the domain composition can be responsible for the regulation of protein interactions and the functional diversity of different tissues. Discovering the occurrence of splicing events and studying protein isoforms have become feasible using Affymetrix Exon Arrays. Therefore, we have developed the versatile Cytoscape plugin DomainGraph that allows for the visual analysis of protein domain interaction networks and their integration with exon expression data. Protein domains affected by alternative splicing are highlighted and splicing patterns can be compared.

scholarly journals Combinatorial Genetic Control of Rpd3S Through Histone H3K4 and H3K36 Methylation in Budding Yeast

2018 ◽  
Vol 8 (11) ◽  
pp. 3411-3420 ◽  
Author(s):  
Kwan Yin Lee ◽  
Mathieu Ranger ◽  
Marc D. Meneghini
Keyword(s):  
Genetic Control ◽  
Budding Yeast ◽  
H3k36 Methylation ◽  
Histone H3k4

scholarly journals The RNA Polymerase II Kinase Ctk1 Regulates Positioning of a 5′ Histone Methylation Boundary along Genes

2006 ◽  
Vol 27 (2) ◽  
pp. 721-731 ◽  
Author(s):  
Tiaojiang Xiao ◽  
Yoichiro Shibata ◽  
Bhargavi Rao ◽  
R. Nicholas Laribee ◽  
Rose O'Rourke ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Histone Deacetylation ◽  
H3k4 Methylation ◽  
H3k36 Methylation ◽  
Transcriptional Initiation ◽  
Spurious Transcription ◽  
Transcriptional Stress ◽  
Rnap Ii

ABSTRACT In yeast and other eukaryotes, the histone methyltransferase Set1 mediates methylation of lysine 4 on histone H3 (H3K4me). This modification marks the 5′ end of transcribed genes in a 5′-to-3′ tri- to di- to monomethyl gradient and promotes association of chromatin-remodeling and histone-modifying enzymes. Here we show that Ctk1, the serine 2 C-terminal domain (CTD) kinase for RNA polymerase II (RNAP II), regulates H3K4 methylation. We found that CTK1 deletion nearly abolished H3K4 monomethylation yet caused a significant increase in H3K4 di- and trimethylation. Both in individual genes and genome-wide, loss of CTK1 disrupted the H3K4 methylation patterns normally observed. H3K4me2 and H3K4me3 spread 3′ into the bodies of genes, while H3K4 monomethylation was diminished. These effects were dependent on the catalytic activity of Ctk1 but are independent of Set2-mediated H3K36 methylation. Furthermore, these effects are not due to spurious transcription initiation in the bodies of genes, to changes in RNAP II occupancy, to changes in serine 5 CTD phosphorylation patterns, or to “transcriptional stress.” These data show that Ctk1 acts to restrict the spread of H3K4 methylation through a mechanism that is independent of a general transcription defect. The evidence presented suggests that Ctk1 controls the maintenance of suppressive chromatin in the coding regions of genes by both promoting H3K36 methylation, which leads to histone deacetylation, and preventing the 3′ spread of H3K4 trimethylation, a mark associated with transcriptional initiation.

scholarly journals The Structure of NSD1 Reveals an Autoregulatory Mechanism Underlying Histone H3K36 Methylation

2010 ◽  
Vol 286 (10) ◽  
pp. 8361-8368 ◽  
Author(s):  
Qi Qiao ◽  
Yan Li ◽  
Zhi Chen ◽  
Mingzhu Wang ◽  
Danny Reinberg ◽  
...  
Keyword(s):  
H3k36 Methylation ◽  
Autoregulatory Mechanism

Abstract 08: Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas

2017 ◽  
Author(s):  
Chao Lu ◽  
Simon Papillon-Cavanagh ◽  
Tenzin Gayden ◽  
Leonie G. Mikael ◽  
Denise Bechet ◽  
...  
Keyword(s):  
Head And Neck ◽  
Squamous Cell ◽  
Squamous Cell Carcinomas ◽  
H3k36 Methylation

scholarly journals Quantitative visualization of alternative exon expression from RNA-seq data

2015 ◽  
Vol 31 (14) ◽  
pp. 2400-2402 ◽  
Author(s):  
Yarden Katz ◽  
Eric T. Wang ◽  
Jacob Silterra ◽  
Schraga Schwartz ◽  
Bang Wong ◽  
...  
Keyword(s):  
Alternative Exon ◽  
Rna Seq ◽  
Exon Expression ◽  
Quantitative Visualization

Gene- and exon-expression profiling reveals an extensive LPS-induced response in immune cells in patients with cirrhosis

2013 ◽  
Vol 58 (5) ◽  
pp. 936-948 ◽  
Author(s):  
Sonia Gandoura ◽  
Emmanuel Weiss ◽  
Pierre-Emmanuel Rautou ◽  
Magali Fasseu ◽  
Thierry Gustot ◽  
...  
Keyword(s):  
Immune Cells ◽  
Expression Profiling ◽  
Induced Response ◽  
Exon Expression
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