Advances in computational ChIA-PET data analysis

Abstract

Genome-wide chromatin interaction analysis has become important for understanding 3D topological structure of a genome as well as for linking distal cis-regulatory elements to their target genes. Compared to the Hi-C method, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) is unique, in that one can interrogate thousands of chromatin interactions (in a genome) mediated by a specific protein of interest at high resolution and reasonable cost. However, because of the noisy nature of the data, efficient analytical tools have become necessary. Here, we review some new computational methods recently developed by us and compare them with other existing methods. Our intention is to help readers to better understand ChIA-PET results and to guide the users on selection of the most appropriate tools for their own projects.

Graphical abstract

References

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ACKNOWLEDGEMENTS

This work is supported by the National Basic Research Program of China (No. 2012CB316503), the National Nature Science Foundation of China (Nos. 91519326, 31361163004 and 31301044) and Tsinghua National Laboratory for Information Science and Technology Cross-discipline Foundation. We thank Zhenyu Liang for help of cover figure design.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Chao He, Guipeng Li, Diekidel M. Nadhir, Yang Chen, Xiaowo Wang and Michael Q. Zhang declare that they have no conflict of interests.

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

Funding

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2016 Higher Education Press and Springer-Verlag Berlin Heidelberg