Open Access
March 2016 Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains
Mengjie Chen, Haifan Lin, Hongyu Zhao
Ann. Appl. Stat. 10(1): 506-526 (March 2016). DOI: 10.1214/16-AOAS905


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 a similar enrichment pattern of histone modification, which leads to orchestrated regulation of expression of genes with relevant biological 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 with a zero-inflated Gaussian mixture, our partitions capture local BLOCKs that manifest a relatively homogeneous enrichment pattern of histone marks. 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 a strong relevance with physical domains, which suggest their important roles in chromatin organization and coordinated gene regulation.


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Mengjie Chen. Haifan Lin. Hongyu Zhao. "Change point analysis of histone modifications reveals epigenetic blocks linking to physical domains." Ann. Appl. Stat. 10 (1) 506 - 526, March 2016.


Received: 1 May 2014; Revised: 1 August 2015; Published: March 2016
First available in Project Euclid: 25 March 2016

zbMATH: 1358.62088
MathSciNet: MR3480505
Digital Object Identifier: 10.1214/16-AOAS905

Keywords: Bayesian change point model , chromosomal domain , Histone modification

Rights: Copyright © 2016 Institute of Mathematical Statistics

Vol.10 • No. 1 • March 2016
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