Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences

Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences

Genome Biology

10.1186/s13059-021-02453-5

http://dx.doi.org/10.1186/s13059-021-02453-5

Fan Cao, Yu Zhang, Yichao Cai, Sambhavi Animesh, Ying Zhang, Semih Can AKINCILAR, Yan Ping Loh, Xinya Li, Wee Joo Chng, Vinay Tergaonkar, Chee Keong Kwoh, Melissa J. Fullwood

16 August 2021

Cao, F., Zhang, Y., Cai, Y., Animesh, S., Zhang, Y., Akincilar, S. C., Loh, Y. P., Li, X., Chng, W. J., Tergaonkar, V., Kwoh, C. K., & Fullwood, M. J. (2021). Chromatin interaction neural network (ChINN): a machine learning-based method for predicting chromatin interactions from DNA sequences. Genome Biology, 22(1). https://doi.org/10.1186/s13059-021-02453-5

AbstractChromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited. We develop a computational method, chromatin interaction neural network (ChINN), to predict chromatin interactions between open chromatin regions using only DNA sequences. ChINN predicts CTCF- and RNA polymerase II-associated and Hi-C chromatin interactions. ChINN shows good across-sample performances and captures various sequence features for chromatin interaction prediction. We apply ChINN to 6 chronic lymphocytic leukemia (CLL) patient samples and a published cohort of 84 CLL open chromatin samples. Our results demonstrate extensive heterogeneity in chromatin interactions among CLL patient samples.

Attribution 4.0 International (CC BY 4.0)

This research / project is supported by the NRF - NRF Fellowship
Grant Reference no. : NRF-NRFF2012-054

This research / project is supported by the Singapore Ministry of Education - Academic Research Fund Tier 3
Grant Reference no. : MOE2014-T3-1-006

This research / project is supported by the National Research Foundation - Competitive Research Programme
Grant Reference no. : NRF-CRP17-2017-02

This research / project is supported by the Ministry of Education - Tier II grant
Grant Reference no. : T2EP30120-0020

This research / project is supported by the Nanyang Technological University (NTU) - Start-Up Grant
Grant Reference no. : #001220-00001

This research / project is supported by the National Research Foundation / Singapore Ministry of Education - Research Centres of Excellence initiative
Grant Reference no. : N.A

https://oar.a-star.edu.sg/communities-collections/articles/18202

1474-760X

Institute of Molecular and Cell Biology

https://doi.org/10.1186/s13059-021-02453-5