NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality

Kun Fang, Tianbao Li, Yufei Huang, Victor X. Jin

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

We develop a novel computational method, NucHMM, to identify functional nucleosome states associated with cell type-specific combinatorial histone marks and nucleosome organization features such as phasing, spacing and positioning. We test it on publicly available MNase-seq and ChIP-seq data in MCF7, H1, and IMR90 cells and identify 11 distinct functional nucleosome states. We demonstrate these nucleosome states are distinctly associated with the splicing potentiality of skipping exons. This advances our understanding of the chromatin function at the nucleosome level and offers insights into the interplay between nucleosome organization and splicing processes.

Original languageEnglish (US)
Article number250
JournalGenome biology
Volume22
Issue number1
DOIs
StatePublished - Dec 2021

Keywords

  • Hidden Markov model
  • Nucleosome organization
  • Splicing potentiality

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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