Multiscale Identification of Topological Domains in Chromatin

TL;DR

This paper presents a new multiscale algorithm for identifying topological domains in chromatin, revealing novel domains that are enriched for key regulatory markers and exist across multiple length scales.

Contribution

The authors introduce an efficient multiscale method that captures persistent chromatin domains at various resolutions, uncovering novel domains with biological significance.

Findings

Identified novel chromatin domains enriched for CTCF binding.

Domains are conserved across cell types and species.

Method captures domains at multiple length scales.

Abstract

Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated with a number of chromatin markers and have since been included in a number of analyses. However, functionally-relevant domains may exist at multiple length scales. We introduce a new and efficient algorithm that is able to capture persistent domains across various resolutions by adjusting a single scale parameter. The identified novel domains are substantially different from domains reported previously and are highly enriched for insulating factor CTCF binding and histone modfications at the boundaries.