Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data

Kos, P.; Galitsyna, A.; Ulianov, S.; Gelfand, M.; Razin, S.; Chertovich, A.

Статья опубликована в высокорейтинговом журнале

Информация о цитировании статьи получена из Web of Science, Scopus
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 4 марта 2022 г.

Авторы: Kos PI, Galitsyna AA, Ulianov SV, Gelfand MS, Razin SV, Chertovich AV
Журнал: PLoS Computational Biology
Том: 17
Номер: 11
Год издания: 2021
Издательство: Public Library of Science
Местоположение издательства: United States
Первая страница: e1009546
DOI: 10.1371/journal.pcbi.1009546
Аннотация: Construction of chromosomes 3D models based on single cell Hi-C data constitute an important challenge. We present a reconstruction approach, DPDchrom, that incorporates basic knowledge whether the reconstructed conformation should be coil-like or globular and spring relaxation at contact sites. In contrast to previously published protocols, DPDchrom can naturally form globular conformation due to the presence of explicit solvent. Benchmarking of this and several other methods on artificial polymer models reveals similar reconstruction accuracy at high contact density and DPDchrom advantage at low contact density. To compare 3D structures insensitively to spatial orientation and scale, we propose the Modified Jaccard Index. We analyzed two sources of the contact dropout: contact radius change and random contact sampling. We found that the reconstruction accuracy exponentially depends on the number of contacts per genomic bin allowing to estimate the reconstruction accuracy in advance. We applied DPDchrom to model chromosome configurations based on single-cell Hi-C data of mouse oocytes and found that these configurations differ significantly from a random one, that is consistent with other studies.
Добавил в систему: Разин Сергей Владимирович

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Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C dataстатья

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