Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains

DOI10.1214/16-AOAS905zbMATH Open1358.62088arXiv1309.5337OpenAlexW2963860487WikidataQ41815695 ScholiaQ41815695MaRDI QIDQ288617FDOQ288617

Authors: Mengjie Chen, Haifan Lin, Hongyu Zhao 

Publication date: 27 May 2016

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Histone modification is a vital epigenetic mechanism for transcriptional control in eukaryotes. High-throughput techniques have enabled whole-genome analysis of histone modifications in recent years. However, most studies assume one combination of histone modification invariantly translates to one transcriptional output regardless of local chromatin environment. In this study we hypothesize that, the genome is organized into local domains that manifest similar enrichment pattern of histone modification, which leads to orchestrated regulation of expression of genes with relevant bio- logical functions. We propose a multivariate Bayesian Change Point (BCP) model to segment the Drosophila melanogaster genome into consecutive blocks on the basis of combinatorial patterns of histone marks. By modeling the sparse distribution of histone marks across the chromosome with a zero-inflated Gaussian mixture, our partitions capture local BLOCKs that manifest relatively homogeneous enrichment pattern of histone modifications. We further characterized BLOCKs by their transcription levels, distribution of genes, degree of co-regulation and GO enrichment. Our results demonstrate that these BLOCKs, although inferred merely from histone modifications, reveal strong relevance with physical domains, which suggest their important roles in chromatin organization and coordinated gene regulation.

Full work available at URL: https://arxiv.org/abs/1309.5337

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zbMATH Keywords

Bayesian change point modelchromosomal domainhistone modification

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) Non-Markovian processes: hypothesis testing (62M07)

Cites Work

• Product partition models for change point problems
• A Bayesian Analysis for Change Point Problems
• Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains
• Sequence alignment in bioinformatics
• A branching process model for flow cytometry and budding index measurements in cell synchrony experiments

Cited In (5)

• Prediction of gene expression level based on generalized linear model
• Modeling epigenetic modifications under multiple treatment conditions
• Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains
• Efficient detection and classification of epigenomic changes under multiple conditions
• Nonparametric Bayesian bi-clustering for next generation sequencing count data

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