A novel method to identify topological domains using Hi-C data

Abstract

Over the last decade the 3C-based (Chromosome Conformation Capture, 3C) approaches have been developed to describe the frequency of chromatin interaction. The invention of Hi-C allows us to obtain genome-wide chromatin interaction map. However, it is challenging to develop efficient and robust analytical tools to interpret the Hi-C data. Here we present a new method called Clustering based Hi-C Domain Finder (CHDF), which is based on the difference of interaction intensity inside/outside domains, to identify Hi-C domains. We also compared CHDF with existing methods including Direction Index (DI) and HiCseg. CHDF can define more chromatin domains validated by higher resolution local chromatin structure data (Chromosome Conformation Capture Carbon Copy (5C) data). Using Hi-C data of lower sequencing depth, chromatin structure identified by CHDF is closer to that discovered by data of higher sequencing depth. Furthermore, the implement of CHDF is faster than the other two. Using CHDF, we are potentially able to discover more hints and clues about chromatin structural elements at domain level.

Graphical abstract

Keywords

chromatin domain / Hi-C / dynamic programming

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ACKNOWLEDGEMENTS

This work is supported by National Key Basic Research Project (973 program, 2012CB316503) and the National Natural Science Foundation of China (Nos. 31361163004 and 91019016).

COMPLIANCE WITH ETHICS GUIDELINES

The authors Yang Wang, Yanjian Li, Juntao Gao and Michael Q. Zhang declare they have no conflict of interest.

This article does not contain any studies with human or animal subjects performed by any of the authors.

RIGHTS & PERMISSIONS

2014 Higher Education Press and Springer-Verlag Berlin Heidelberg