Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex

TitleHi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex
Publication TypeJournal Article
Year of Publication2015
AuthorsBabaei, S, Mahfouz, AE, Hulsman, M, Lelieveldt, BPF, de Ridder, J, Reinders, MJT
JournalPLoS Comput Biol
Volume11
Issue5
Paginatione1004221
Date Published2015 May
ISSN1553-7358
Abstract

The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains challenging. We address this by characterizing the topology of the cortical chromatin interaction network using scale-aware topological measures. We demonstrate that based on these characterizations it is possible to accurately predict spatial co-expression between genes in the mouse cortex. Consistent with previous findings, we find that the chromatin interaction profile of a gene-pair is a good predictor of their spatial co-expression. However, the accuracy of the prediction can be substantially improved when chromatin interactions are described using scale-aware topological measures of the multi-resolution chromatin interaction network. We conclude that, for co-expression prediction, it is necessary to take into account different levels of chromatin interactions ranging from direct interaction between genes (i.e. small-scale) to chromatin compartment interactions (i.e. large-scale).

DOI10.1371/journal.pcbi.1004221
Custom 1

http://www.ncbi.nlm.nih.gov/pubmed/25965262?dopt=Abstract

Alternate JournalPLoS Comput. Biol.
PubMed ID25965262