An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data Journal Article
| Authors: | Carty, M.; Zamparo, L.; Sahin, M.; González, A.; Pelossof, R.; Elemento, O.; Leslie, C. S. |
| Article Title: | An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data |
| Abstract: | Here we present HiC-DC, a principled method to estimate the statistical significance (P values) of chromatin interactions from Hi-C experiments. HiC-DC uses hurdle negative binomial regression account for systematic sources of variation in Hi-C read counts - for example, distance-dependent random polymer ligation and GC content and mappability bias - and model zero inflation and overdispersion. Applied to high-resolution Hi-C data in a lymphoblastoid cell line, HiC-DC detects significant interactions at the sub-topologically associating domain level, identifying potential structural and regulatory interactions supported by CTCF binding sites, DNase accessibility, and/or active histone marks. CTCF-associated interactions are most strongly enriched in the middle genomic distance range (-1/4700 kb-1.5 Mb), while interactions involving actively marked DNase accessible elements are enriched both at short (<500 kb) and longer (>1.5 Mb) genomic distances. There is a striking enrichment of longer-range interactions connecting replication-dependent histone genes on chromosome 6, potentially representing the chromatin architecture at the histone locus body. © The Author(s) 2017. |
| Journal Title: | Nature Communications |
| Volume: | 8 |
| ISSN: | 2041-1723 |
| Publisher: | Nature Publishing Group |
| Date Published: | 2017-05-17 |
| Start Page: | 15454 |
| Language: | English |
| DOI: | 10.1038/ncomms15454 |
| PROVIDER: | scopus |
| PMCID: | PMC5442359 |
| PUBMED: | 28513628 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 3 July 2017 -- Source: Scopus |
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