Non-backtracking walks reveal compartments in sparse chromatin interaction networks

Abstract 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...

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Autores principales:	K. Polovnikov, A. Gorsky, S. Nechaev, S. V. Razin, S. V. Ulianov
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1eed9010b7fb420aacb37971b5773702
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spelling	oai:doaj.org-article:1eed9010b7fb420aacb37971b57737022021-12-02T15:39:40ZNon-backtracking walks reveal compartments in sparse chromatin interaction networks10.1038/s41598-020-68182-02045-2322https://doaj.org/article/1eed9010b7fb420aacb37971b57737022020-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-68182-0https://doaj.org/toc/2045-2322Abstract 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.K. PolovnikovA. GorskyS. NechaevS. V. RazinS. V. UlianovNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-11 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q K. Polovnikov A. Gorsky S. Nechaev S. V. Razin S. V. Ulianov Non-backtracking walks reveal compartments in sparse chromatin interaction networks
description	Abstract 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.
format	article
author	K. Polovnikov A. Gorsky S. Nechaev S. V. Razin S. V. Ulianov
author_facet	K. Polovnikov A. Gorsky S. Nechaev S. V. Razin S. V. Ulianov
author_sort	K. Polovnikov
title	Non-backtracking walks reveal compartments in sparse chromatin interaction networks
title_short	Non-backtracking walks reveal compartments in sparse chromatin interaction networks
title_full	Non-backtracking walks reveal compartments in sparse chromatin interaction networks
title_fullStr	Non-backtracking walks reveal compartments in sparse chromatin interaction networks
title_full_unstemmed	Non-backtracking walks reveal compartments in sparse chromatin interaction networks
title_sort	non-backtracking walks reveal compartments in sparse chromatin interaction networks
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/1eed9010b7fb420aacb37971b5773702
work_keys_str_mv	AT kpolovnikov nonbacktrackingwalksrevealcompartmentsinsparsechromatininteractionnetworks AT agorsky nonbacktrackingwalksrevealcompartmentsinsparsechromatininteractionnetworks AT snechaev nonbacktrackingwalksrevealcompartmentsinsparsechromatininteractionnetworks AT svrazin nonbacktrackingwalksrevealcompartmentsinsparsechromatininteractionnetworks AT svulianov nonbacktrackingwalksrevealcompartmentsinsparsechromatininteractionnetworks
_version_	1718385858508226560

Non-backtracking walks reveal compartments in sparse chromatin interaction networks

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