Non-backtracking walks reveal compartments in sparse chromatin interaction networks

Polovnikov, K.; Gorsky, A.; Nechaev, S.; Razin, S.V.; Ulianov, S.V.

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: 24 сентября 2020 г.

Авторы: Polovnikov K., Gorsky A., Nechaev S., Razin S.V., Ulianov S.V.
Журнал: Scientific reports
Том: 10
Номер: 1
Год издания: 2020
Издательство: Nature Publishing Group
Местоположение издательства: United Kingdom
Номер статьи: 11398
DOI: 10.1038/s41598-020-68182-0
Аннотация: Chromatin communities stabilized by protein machinery play essential role in gene regulation and refine global polymeric folding of the chromatin fiber. However, treatment of these communities in the framework of the classical network theory (stochastic block model, SBM) does not take into account intrinsic linear connectivity of the chromatin loci. Here we propose the polymer block model, paving the way for community detection in polymer networks. On the basis of this new model we modify the non-backtracking flow operator and suggest the first protocol for annotation of compartmental domains in sparse single cell Hi-C matrices. In particular, we prove that our approach corresponds to the maximum entropy principle. The benchmark analyses demonstrates that the spectrum of the polymer non-backtracking operator resolves the true compartmental structure up to the theoretical detectability threshold, while all commonly used operators fail above it. We test various operators on real data and conclude that the sizes of the non-backtracking single cell domains are most close to the sizes of compartments from the population data. Moreover, the found domains clearly segregate in the gene density and correlate with the population compartmental mask, corroborating biological significance of our annotation of the chromatin compartmental domains in single cells Hi-C matrices.
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Non-backtracking walks reveal compartments in sparse chromatin interaction networksстатья

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