Inter-nucleosomal Communication Between Histone Modifications for Nucleosome Phasing

Overview

Journal PLoS Comput Biol

Specialty Biology

Date 2018 Sep 7

PMID 30188887

Citations 2

Authors

Weizhong Chen

Yi Liu

Shanshan Zhu

Guoyu Chen

Jing-Dong J Han

Affiliations

Soon will be listed here.

Abstract

Combinatorial effects of epigenetic modifications on transcription activity have been proposed as "histone codes". However, it is unclear whether there also exist inter-nucleosomal communications among epigenetic modifications at single nucleosome level, and if so, what functional roles they play. Meanwhile, how clear nucleosome patterns, such as nucleosome phasing and depletion, are formed at functional regions remains an intriguing enigma. To address these questions, we developed a Bayesian network model for interactions among different histone modifications across neighboring nucleosomes, based on the framework of dynamic Bayesian network (DBN). From this model, we found that robust inter-nucleosomal interactions exist around transcription start site (TSS), transcription termination sites (TTS) or around CTCF binding sites; and these inter-nucleosomal interactions are often involved in transcription regulation. In addition to these general principles, DBN also uncovered a novel specific epigenetic interaction between H2A.Z and H4K20me1 on neighboring nucleosomes, involved in nucleosome free region (NFR) and nucleosome phasing establishment or maintenance. The level of negative correlation between neighboring H2A.Z and H4K20me1 strongly correlate with the size of NFR and the strength of nucleosome phasing around TSS. Our study revealed inter-nucleosomal communications as important players in signal propagation, chromatin remodeling and transcription regulation.

Citing Articles

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases.

Shi D, Huang Y, Bai C Polymers (Basel). 2023; 15(7).

PMID: 37050377 PMC: 10096840. DOI: 10.3390/polym15071763.

The Effects of Histone H2B Ubiquitylations on the Nucleosome Structure and Internucleosomal Interactions.

Sengupta B, Huynh M, Smith C, McGinty R, Krajewski W, Lee T Biochemistry. 2022; 61(20):2198-2205.

PMID: 36112542 PMC: 9588709. DOI: 10.1021/acs.biochem.2c00422.

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