Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data

Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Measuring nucleosome positioning in cells is crucial for the analysis of epigenetic gene regulation. Reconstruction of nucleosome profiles of individual cells or subpopulations of cells remains challenging because most genome-wide assays measure nucleosome positioning and DNA accessibility for thousands of cells using bulk sequencing. Here we use characteristics of the NOMe-sequencing assay to derive a new approach, called ChromaClique, for deconvolution of different nucleosome profiles (chromatypes) from cell subpopulations of one NOMe-seq measurement. ChromaClique uses a maximal clique enumeration algorithm on a newly defined NOMe read graph that is able to group reads according to their nucleosome profiles. We show that the edge probabilities of that graph can be efficiently computed using Hidden Markov Models. We demonstrate using simulated data that ChromaClique is more accurate than a related method and scales favorably, allowing genome-wide analyses of chromatypes in cell subpopulations. Software is available at https://github.com/shounak1990/ChromaClique under MIT license.

Original languageEnglish (US)
Title of host publicationResearch in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings
EditorsBenjamin J. Raphael
PublisherSpringer Verlag
Pages21-36
Number of pages16
ISBN (Print)9783319899282
DOIs
StatePublished - 2018
Event22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018 - Paris, France
Duration: Apr 21 2018Apr 24 2018

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10812 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other22nd International Conference on Research in Computational Molecular Biology, RECOMB 2018
Country/TerritoryFrance
CityParis
Period4/21/184/24/18

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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