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

ABSTRACT: Chromatin 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.

SUBMITTER: Cao F 

PROVIDER: S-EPMC8365954 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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

Cao Fan F   Zhang Yu Y   Cai Yichao Y   Animesh Sambhavi S   Zhang Ying Y   Akincilar Semih Can SC   Loh Yan Ping YP   Li Xinya X   Chng Wee Joo WJ   Tergaonkar Vinay V   Kwoh Chee Keong CK   Fullwood Melissa J MJ   Fullwood Melissa J MJ  

Genome biology 20210816 1

Chromatin 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  ...[more]

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