Jul 31, 2016

Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution

BioRxiv : the Preprint Server for Biology
Hui ZhangZhihua Zhang

Abstract

High-throughput chromosome conformation capture technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, the ability to obtain 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein report a computational method to precisely identify chromatin interaction sites at kilobase resolution from MNase-seq data, termed chromatin interaction site detector (CISD), and a CISD-based chromatin loop predictor (CISD\_loop) that predicts chromatin-chromatin interaction (CCI) from low-resolution Hi-C data. The methods are built on a hypothesis that CCIs result in a characteristic nucleosome arrangement pattern flanking the interaction sites. Accordingly, we show that the predictions of CISD and CISD\_loop overlap closely with chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) anchors and loops, respectively. Moreover, the methods trained in one cell type can be applied to other cell types with high accuracy. The validity of the methods was further supported by chromosome conformation capture (3C) experiments at 5kb resolution. Finally, we demonstrate that only modest amounts of MNase-seq and Hi-C data are sufficient to achieve ultrahigh resolution CCI m...Continue Reading

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Mentioned in this Paper

Sex Chromatin Identification Test
Chromatin Loop
Nucleosomes
Patterns
Genome
Positron-Emission Tomography
Three-dimensional
High Throughput Screening
Molecular Probe Techniques
CISD1

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