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

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...

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Autores principales:	Pavel I Kos, Aleksandra A Galitsyna, Sergey V Ulianov, Mikhail S Gelfand, Sergey V Razin, Alexander V Chertovich
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/bf9ef8a3ca1c4ad0bd894ed8ee553a32
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spelling	oai:doaj.org-article:bf9ef8a3ca1c4ad0bd894ed8ee553a322021-12-02T19:57:56ZPerspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.1553-734X1553-735810.1371/journal.pcbi.1009546https://doaj.org/article/bf9ef8a3ca1c4ad0bd894ed8ee553a322021-11-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.1009546https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Construction 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.Pavel I KosAleksandra A GalitsynaSergey V UlianovMikhail S GelfandSergey V RazinAlexander V ChertovichPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 17, Iss 11, p e1009546 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Pavel I Kos Aleksandra A Galitsyna Sergey V Ulianov Mikhail S Gelfand Sergey V Razin Alexander V Chertovich Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
description	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.
format	article
author	Pavel I Kos Aleksandra A Galitsyna Sergey V Ulianov Mikhail S Gelfand Sergey V Razin Alexander V Chertovich
author_facet	Pavel I Kos Aleksandra A Galitsyna Sergey V Ulianov Mikhail S Gelfand Sergey V Razin Alexander V Chertovich
author_sort	Pavel I Kos
title	Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
title_short	Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
title_full	Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
title_fullStr	Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
title_full_unstemmed	Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
title_sort	perspectives for the reconstruction of 3d chromatin conformation using single cell hi-c data.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/bf9ef8a3ca1c4ad0bd894ed8ee553a32
work_keys_str_mv	AT pavelikos perspectivesforthereconstructionof3dchromatinconformationusingsinglecellhicdata AT aleksandraagalitsyna perspectivesforthereconstructionof3dchromatinconformationusingsinglecellhicdata AT sergeyvulianov perspectivesforthereconstructionof3dchromatinconformationusingsinglecellhicdata AT mikhailsgelfand perspectivesforthereconstructionof3dchromatinconformationusingsinglecellhicdata AT sergeyvrazin perspectivesforthereconstructionof3dchromatinconformationusingsinglecellhicdata AT alexandervchertovich perspectivesforthereconstructionof3dchromatinconformationusingsinglecellhicdata
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Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.

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