Differential chromatin marking of introns and expressed exons by H3K36me3

By P. Kolasinska-Zwierz, Thomas A. Down, I. Latorre, Tao Liu, X. S. Liu, J. Ahringer. 2009

727 citations recorded by the source corpus.

Variation in patterns of methylations of histone tails reflects and modulates chromatin structure and function. To provide a framework for the analysis of chromatin function in Caenorhabditis elegans, we generated a genome-wide map of histone H3 tail methylations. We find that C. elegans genes show distributions of histone modifications that are similar to those of other organisms, with H3K4me3 near transcription start sites, H3K36me3 in the body of genes and H3K9me3 enriched on silent genes. We also observe a novel pattern: exons are preferentially marked with H3K36me3 relative to introns. H3K36me3 exon marking is dependent on transcription and is found at lower levels in alternatively spliced exons, supporting a splicing-related marking mechanism. We further show that the difference in H3K36me3 marking between exons and introns is evolutionarily conserved in human and mouse. We propose that H3K36me3 exon marking in chromatin provides a dynamic link between transcription and splicing.

Subfields: Molecular Biology

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Citations in the corpus

Iterative random forests to discover predictive and stable high-order interactions (2017, positive): “Studies, initially in model organisms, have revealed that the chromatin mark H3K36me3, the DNA binding protein CTCF, and a few other factors all play splice-enhancing roles (Kolasinska-Zwierz et al., 2009; Sims Iii and Reinberg, 2009; Kornblihtt, 2012).”
Cistrome: an integrative platform for transcriptional regulation studies (2011, background): “For instance, H3K4me3 is enriched in the promoter regions of active genes [21], and H3K36me3 is enriched in transcribed exons [22].”
Epigenetics in alternative pre-mRNA splicing (2011, neutral): “…along genes and are particularly enriched at intron-exon junctions, thus marking exons (Andersson et al., 2009; Chodavarapu et al., 2010; Dhami et al., 2010; Kolasinska-Zwierz et al., 2009; Nahkuri et al., 2009; Ponts et al., 2008; Schwartz et al., 2009; Spies et al., 2009; Tilgner et al., 2009).”
Modeling gene expression using chromatin features in various cellular contexts (2012, neutral): “Z, H3K9ac and H3K27ac as promoter marks [5,24], H3K36me3 and H3K79me2 as structural marks [25,26], H3K27me3 and H3K9me3 as repressive marks [6], and H3K4me1, H4K20me1 and H3K9me1 as distal/other marks [4,6].”
Histone Lysine Methylation Dynamics: Establishment, Regulation, and Biological Impact (2012, neutral): “…demarcation of expressed exons by H3K36me3 is conserved in worm and fly, but it remains unclear if expressed exons in these organisms are also preferentially marked by H2BK5me1, H4K20me1, and H3K79me1 (Kharchenko et al., 2011; Kolasinska-Zwierz et al., 2009; Liu et al., 2011; Riddle et al., 2011).”
ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases (2014, background): “Exons and their neighbouring regions are known to contain chromatin modifications that may facilitate exon recognition and influence alternative splicing [30-32].”
Discovery and characterization of chromatin states for systematic annotation of the human genome (2010, background): “Spliced exons were previously reported to be enriched in several individual mark”