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A diverse epigenetic landscape at human exons with implication for expression.

Singer M, Kosti I, Pachter L, Mandel-Gutfreund Y - Nucleic Acids Res. (2015)

Bottom Line: Consistent with previous work we found that intragenic methylation is positively correlated with gene expression and that exons are more highly methylated than their neighboring intronic environment.Specifically, we demonstrate that hypo-methylated exons at highly expressed genes are associated with open chromatin and have a characteristic histone code comprised of significantly high levels of histone markings.In particular our results reveal a previously unrecognized diverse and complex role of the epigenetic landscape within the gene body.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of California at Berkeley, Berkeley, CA 94720 USA.

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Graphical summary of the exon methylation and expression analyses. Exons are represented as rectangles. The color of the rectangle frame represents the exon's expression rate, red and blue for high and low expression, respectively. The color of the rectangle represents the methylation level, red and blue for methylated and hypomethylated exons, respectively.
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Figure 1: Graphical summary of the exon methylation and expression analyses. Exons are represented as rectangles. The color of the rectangle frame represents the exon's expression rate, red and blue for high and low expression, respectively. The color of the rectangle represents the methylation level, red and blue for methylated and hypomethylated exons, respectively.

Mentions: We computed DNA methylation rates and expression rates for 31,854 constitutive internal exons, excluding exons that are first or last in any annotated RefSeq transcript (Figure 1, see Materials and Methods section). As previously reported for intragenic regions (3,10,14,16) the exon methylation rates were positively correlated with the gene expression rates (Pearson r = 0.37 for correlation of methylation rates with log of FPKM expression rate, empirical P-value < 0.0001).


A diverse epigenetic landscape at human exons with implication for expression.

Singer M, Kosti I, Pachter L, Mandel-Gutfreund Y - Nucleic Acids Res. (2015)

Graphical summary of the exon methylation and expression analyses. Exons are represented as rectangles. The color of the rectangle frame represents the exon's expression rate, red and blue for high and low expression, respectively. The color of the rectangle represents the methylation level, red and blue for methylated and hypomethylated exons, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402514&req=5

Figure 1: Graphical summary of the exon methylation and expression analyses. Exons are represented as rectangles. The color of the rectangle frame represents the exon's expression rate, red and blue for high and low expression, respectively. The color of the rectangle represents the methylation level, red and blue for methylated and hypomethylated exons, respectively.
Mentions: We computed DNA methylation rates and expression rates for 31,854 constitutive internal exons, excluding exons that are first or last in any annotated RefSeq transcript (Figure 1, see Materials and Methods section). As previously reported for intragenic regions (3,10,14,16) the exon methylation rates were positively correlated with the gene expression rates (Pearson r = 0.37 for correlation of methylation rates with log of FPKM expression rate, empirical P-value < 0.0001).

Bottom Line: Consistent with previous work we found that intragenic methylation is positively correlated with gene expression and that exons are more highly methylated than their neighboring intronic environment.Specifically, we demonstrate that hypo-methylated exons at highly expressed genes are associated with open chromatin and have a characteristic histone code comprised of significantly high levels of histone markings.In particular our results reveal a previously unrecognized diverse and complex role of the epigenetic landscape within the gene body.

View Article: PubMed Central - PubMed

Affiliation: Department of Computer Science, University of California at Berkeley, Berkeley, CA 94720 USA.

Show MeSH