hiHMM: Bayesian non-parametric joint inference of chromatin state maps

Bioinformatics
Kyung-Ah SohnJu Han Kim

Abstract

Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications. Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets. The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chrom...Continue Reading

References

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Citations

Mar 17, 2016·Briefings in Bioinformatics·Ryuichiro Nakato, Katsuhiko Shirahige
Apr 21, 2016·Nucleic Acids Research·Yu ZhangRoss C Hardison
Nov 12, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Chandler ZuoSündüz Keleş
Apr 8, 2017·Nature Communications·Eugenio MarcoGuo-Cheng Yuan
Sep 22, 2017·Nucleic Acids Research·Enrique Carrillo-de-Santa-PauUNKNOWN BLUEPRINT Consortium
Feb 14, 2018·Bioinformatics·Selin Jessa, Claudia L Kleinman
Apr 15, 2020·Scientific Data·Kristen UptonJo Lynne Rokita
Mar 27, 2018·Briefings in Functional Genomics·Shan Jiang, Ali Mortazavi
Nov 10, 2017·Nature Protocols·Jason Ernst, Manolis Kellis
Jun 15, 2019·Nucleic Acids Research·Evan D Tarbell, Tao Liu
Feb 6, 2020·Frontiers in Genetics·Yanglan GanGuobing Zou
Oct 15, 2021·PLoS Computational Biology·Maxwell W LibbrechtMichael M Hoffman
Oct 31, 2017·Current Opinion in Systems Biology·Deborah Chasman, Sushmita Roy

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Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
ChIP
RNA-seq

Software Mentioned

custom
DAVID
hiHMM1
ChromHMM
iHMM
Genome
R script
Oamb
hiHMM
Segway

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