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HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution.

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.

SUBMITTER: Cameron CJ

PROVIDER: S-EPMC6961295 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution.

Cameron Christopher Jf CJ Dostie Josée J Blanchette Mathieu M

Genome biology 20200114 1

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 neigh ...[more]

PMID: 31937349

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