DOI: 10.1101/505503Dec 23, 2018Paper

Revealing Hi-C subcompartments by imputing high-resolution inter-chromosomal chromatin interactions

BioRxiv : the Preprint Server for Biology
Kyle Xiong, Jian Ma


The higher-order genome organization and its variation in different cellular conditions remains poorly understood. Recent high-resolution genome-wide mapping of chromatin interactions using Hi-C has revealed that chromosomes in the human genome are spatially segregated into distinct subcompartments. However, due to the requirement on sequencing coverage of the Hi-C data to define subcompartments, to date subcompartment annotation is only available in the GM12878 cell line, making it impractical to compare Hi-C subcompartment patterns across multiple cell types. Here we develop a new computational approach, named SNIPER, based on an autoencoder and multilayer perceptron classifier to infer subcompartments using typical Hi-C datasets with moderate coverage. We demonstrated that SNIPER can accurately reveal subcompartments based on Hi-C datasets with moderate coverage and can significantly outperform an existing method that uses numerous epigenomic datasets as input features in GM12878. We applied SNIPER to eight additional cell lines to identify the variation of Hi-C subcompartments across different cell types. SNIPER revealed that chromosomal regions with conserved and more dynamic subcompartment annotations across cell types ha...Continue Reading

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