Abstract:
:High-throughput chromosome conformation capture (3C) technologies, such as Hi-C, have made it possible to survey 3D genome structure. However, obtaining 3D profiles at kilobase resolution at low cost remains a major challenge. Therefore, we herein present an algorithm for precise identification of 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 interactions (CCIs) from low-resolution Hi-C data. 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. The validity of CISD/CISD_loop was further supported by a 3C assay at about 5 kb resolution. Finally, we demonstrate that only modest amounts of MNase-seq and Hi-C data are sufficient to achieve ultrahigh resolution CCI maps. Our results suggest that CCIs may result in characteristic nucleosomes arrangement patterns flanking the interaction sites, and our algorithms may facilitate precise and systematic investigations of CCIs on a larger scale than hitherto have been possible.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Zhang H,Li F,Jia Y,Xu B,Zhang Y,Li X,Zhang Zdoi
10.1093/nar/gkx885subject
Has Abstractpub_date
2017-12-15 00:00:00pages
12739-12751issue
22eissn
0305-1048issn
1362-4962pii
4316106journal_volume
45pub_type
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