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 b...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | Genome Biology |
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| Online Access: | https://doi.org/10.1186/s13059-019-1913-y |
| _version_ | 1818723055710502912 |
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| author | Christopher JF Cameron Josée Dostie Mathieu Blanchette |
| author_facet | Christopher JF Cameron Josée Dostie Mathieu Blanchette |
| author_sort | Christopher JF Cameron |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-17T21:04:26Z |
| format | Article |
| id | doaj.art-6f2be5e0bc9c4a4db400423d3ebc5bac |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-17T21:04:26Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-6f2be5e0bc9c4a4db400423d3ebc5bac2022-12-21T21:32:38ZengBMCGenome Biology1474-760X2020-01-0121111510.1186/s13059-019-1913-yHIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolutionChristopher JF Cameron0Josée Dostie1Mathieu Blanchette2School of Computer Science, McGill UniversityDepartment of Biochemistry and Goodman Cancer Research Center, McGill UniversitySchool of Computer Science, McGill UniversityAbstract 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.https://doi.org/10.1186/s13059-019-1913-yChromosome conformation captureHi-C5CChIA-PETTopologically associating domainssubTADs |
| spellingShingle | Christopher JF Cameron Josée Dostie Mathieu Blanchette HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution Genome Biology Chromosome conformation capture Hi-C 5C ChIA-PET Topologically associating domains subTADs |
| title | HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution |
| title_full | HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution |
| title_fullStr | HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution |
| title_full_unstemmed | HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution |
| title_short | HIFI: estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution |
| title_sort | hifi estimating dna dna interaction frequency from hi c data at restriction fragment resolution |
| topic | Chromosome conformation capture Hi-C 5C ChIA-PET Topologically associating domains subTADs |
| url | https://doi.org/10.1186/s13059-019-1913-y |
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