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HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution
- Source :
- Genome Biology; December 2020, Vol. 21 Issue: 1
- Publication Year :
- 2020
-
Abstract
- Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C’s resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability. We present the Hi-C Interaction Frequency Inference (HIFI) algorithms that accurately estimate restriction-fragment resolution Hi-C matrices by exploiting dependencies between neighboring fragments. Cross-validation experiments and comparisons to 5C data and known regulatory interactions demonstrate HIFI’s superiority to existing approaches. In addition, HIFI’s restriction-fragment resolution reveals a new role for active regulatory regions in structuring topologically associating domains.
Details
- Language :
- English
- ISSN :
- 14747596 and 1474760X
- Volume :
- 21
- Issue :
- 1
- Database :
- Supplemental Index
- Journal :
- Genome Biology
- Publication Type :
- Periodical
- Accession number :
- ejs52096666
- Full Text :
- https://doi.org/10.1186/s13059-019-1913-y