Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus

Nature Communications
Yan ZhangFeng Yue

Abstract

Although Hi-C technology is one of the most popular tools for studying 3D genome organization, due to sequencing cost, the resolution of most Hi-C datasets are coarse and cannot be used to link distal regulatory elements to their target genes. Here we develop HiCPlus, a computational approach based on deep convolutional neural network, to infer high-resolution Hi-C interaction matrices from low-resolution Hi-C data. We demonstrate that HiCPlus can impute interaction matrices highly similar to the original ones, while only using 1/16 of the original sequencing reads. We show that the models learned from one cell type can be applied to make predictions in other cell or tissue types. Our work not only provides a computational framework to enhance Hi-C data resolution but also reveals features underlying the formation of 3D chromatin interactions.

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Citations

Dec 21, 2018·Biophysics Reviews·Koustav PalFrancesco Ferrari
Dec 10, 2019·Briefings in Bioinformatics·Yu-Chiao ChiuYidong Chen
Feb 23, 2020·PLoS Computational Biology·Hao HongXiaochen Bo
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Apr 24, 2020·Frontiers in Genetics·Zhilan Li, Zhiming Dai
Nov 18, 2018·Nucleic Acids Research·Xianfeng LiFengbiao Mao
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Oct 14, 2018·BMC Bioinformatics·Pau FarréEldon Emberly
Dec 19, 2019·Nature Reviews. Genetics·Rieke Kempfer, Ana Pombo
Mar 23, 2019·Genome Biology·Linh Huynh, Fereydoun Hormozdiari
Oct 14, 2020·Nature Methods·Ron SchwessingerJim R Hughes
Sep 23, 2020·Genome Génome / Conseil National De Recherches Canada·Ian C TobiasJennifer A Mitchell
Apr 30, 2020·Trends in Biochemical Sciences·Ruth NussinovHyunbum Jang
Mar 10, 2021·Journal of Bioinformatics and Computational Biology·Zhe ChengXin Jin
May 18, 2021·Computational and Structural Biotechnology Journal·Haiyan GongXiaotong Zhang
Jun 3, 2021·International Journal of Molecular Sciences·Mengsheng ZhaZheng Wang
Sep 9, 2021·Animal Genetics·C MacPhillamyW Y Low

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Datasets Mentioned

BETA
GM12878
GSE63525

Methods Mentioned

BETA
Hi-C
Capture
Capture Hi-C

Software Mentioned

chromHMM
HiCPlus
Capture
Sklearn
Hi
ConvNet
Fit

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