ChromTime: modeling spatio-temporal dynamics of chromatin marks

Petko Fiziev; Jason Ernst

doi:10.1186/s13059-018-1485-2

ChromTime: modeling spatio-temporal dynamics of chromatin marks

Genome Biol. 2018 Aug 10;19(1):109. doi: 10.1186/s13059-018-1485-2.

Authors

Petko Fiziev^{1

2

3}, Jason Ernst^{4

5

6

7

8

9}

Affiliations

¹ Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA.
² Department of Biological Chemistry, University of California, Los Angeles, CA, USA.
³ Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA.
⁴ Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA. [email protected].
⁵ Department of Biological Chemistry, University of California, Los Angeles, CA, USA. [email protected].
⁶ Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, Los Angeles, CA, USA. [email protected].
⁷ Computer Science Department, University of California, Los Angeles, CA, USA. [email protected].
⁸ Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA. [email protected].
⁹ Molecular Biology Institute, University of California, Los Angeles, CA, USA. [email protected].

Abstract

To model spatial changes of chromatin mark peaks over time we develop and apply ChromTime, a computational method that predicts peaks to be either expanding, contracting, or holding steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provide information about gene expression changes beyond localized signal density changes. ChromTime detects asymmetric expansions and contractions, which for some marks associate with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.

Keywords: Chromatin marks; Epigenomics; Histone modifications; Spatial dynamics; Time course.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromatin / metabolism*
Databases, Genetic
Deoxyribonuclease I / metabolism
Gene Expression Regulation
Histones / metabolism
Methylation
Models, Genetic
Protein Binding
Reproducibility of Results
Software*
Time Factors
Transcription Factors / metabolism
Transcription, Genetic

Substances

Chromatin
Histones
Transcription Factors
Deoxyribonuclease I

Abstract

Publication types

MeSH terms

Substances

Grants and funding