Genome-wide identification of autosomal genes with allelic imbalance of chromatin state.

Abstract

In mammals, monoallelic gene expression can result from X-chromosome inactivation, genomic imprinting, and random monoallelic expression (RMAE). Epigenetic regulation of RMAE is not fully understood. Here we analyze allelic imbalance in chromatin state of autosomal genes using ChIP-seq in a clonal cell line. We identify approximately 3.7% of autosomal genes that show significant differences between chromatin states of two alleles. Allelic regulation is represented among several functional gene categories including histones, chromatin modifiers, and multiple early developmental regulators. Most cases of allelic skew are produced by quantitative differences between two allelic chromatic states that belong to the same gross type (active, silent, or bivalent). Combinations of allelic states of different types are possible but less frequent. When different chromatin marks are skewed on the same gene, their skew is coordinated as a result of quantitative relationships between these marks on each individual allele. Finally, combination of allele-specific densities of chromatin marks is a quantitative predictor of allelic skew in gene expression.

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Published Version (Please cite this version)

10.1371/journal.pone.0182568

Publication Info

Savol, Andrej J, Peggy I Wang, Yesu Jeon, David Colognori, Eda Yildirim, Stefan F Pinter, Bernhard Payer, Jeannie T Lee, et al. (2017). Genome-wide identification of autosomal genes with allelic imbalance of chromatin state. PloS one, 12(8). 10.1371/journal.pone.0182568 Retrieved from https://hdl.handle.net/10161/17153.

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Scholars@Duke

Yildirim

Eda Yildirim

Assistant Professor of Cell Biology

1. Epigenetic mechanisms regulated by long noncoding RNAs: their regulatory roles in gene expression, genome stability and cell fate decisions.
2. Nuclear structure: its role in gene expression and genome function.


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