Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle

Abstract How chromosomes fold into 3D structures and how genome functions are affected or even controlled by their spatial organization remain challenging questions. Hi-C experiment has provided important structural insights for chromosome, and Hi-C data are used here to construct the 3D chromatin s...

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Autores principales:	Wen Jun Xie, Luming Meng, Sirui Liu, Ling Zhang, Xiaoxia Cai, Yi Qin Gao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/37867cf56480463fb8f78b81b1cbcf9e
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spelling	oai:doaj.org-article:37867cf56480463fb8f78b81b1cbcf9e2021-12-02T15:05:46ZStructural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle10.1038/s41598-017-02923-62045-2322https://doaj.org/article/37867cf56480463fb8f78b81b1cbcf9e2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-02923-6https://doaj.org/toc/2045-2322Abstract How chromosomes fold into 3D structures and how genome functions are affected or even controlled by their spatial organization remain challenging questions. Hi-C experiment has provided important structural insights for chromosome, and Hi-C data are used here to construct the 3D chromatin structure which are characterized by two spatially segregated chromatin compartments A and B. By mapping a plethora of genome features onto the constructed 3D chromatin model, we show vividly the close connection between genome properties and the spatial organization of chromatin. We are able to dissect the whole chromatin into two types of chromatin domains which have clearly different Hi-C contact patterns as well as different sizes of chromatin loops. The two chromatin types can be respectively regarded as the basic units of chromatin compartments A and B, and also spatially segregate from each other as the two chromatin compartments. Therefore, the chromatin loops segregate in the space according to their sizes, suggesting the excluded volume or entropic effect in chromatin compartmentalization as well as chromosome positioning. Taken together, these results provide clues to the folding principles of chromosomes, their spatial organization, and the resulted clustering of many genome features in the 3D space.Wen Jun XieLuming MengSirui LiuLing ZhangXiaoxia CaiYi Qin GaoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wen Jun Xie Luming Meng Sirui Liu Ling Zhang Xiaoxia Cai Yi Qin Gao Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle
description	Abstract How chromosomes fold into 3D structures and how genome functions are affected or even controlled by their spatial organization remain challenging questions. Hi-C experiment has provided important structural insights for chromosome, and Hi-C data are used here to construct the 3D chromatin structure which are characterized by two spatially segregated chromatin compartments A and B. By mapping a plethora of genome features onto the constructed 3D chromatin model, we show vividly the close connection between genome properties and the spatial organization of chromatin. We are able to dissect the whole chromatin into two types of chromatin domains which have clearly different Hi-C contact patterns as well as different sizes of chromatin loops. The two chromatin types can be respectively regarded as the basic units of chromatin compartments A and B, and also spatially segregate from each other as the two chromatin compartments. Therefore, the chromatin loops segregate in the space according to their sizes, suggesting the excluded volume or entropic effect in chromatin compartmentalization as well as chromosome positioning. Taken together, these results provide clues to the folding principles of chromosomes, their spatial organization, and the resulted clustering of many genome features in the 3D space.
format	article
author	Wen Jun Xie Luming Meng Sirui Liu Ling Zhang Xiaoxia Cai Yi Qin Gao
author_facet	Wen Jun Xie Luming Meng Sirui Liu Ling Zhang Xiaoxia Cai Yi Qin Gao
author_sort	Wen Jun Xie
title	Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle
title_short	Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle
title_full	Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle
title_fullStr	Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle
title_full_unstemmed	Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle
title_sort	structural modeling of chromatin integrates genome features and reveals chromosome folding principle
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/37867cf56480463fb8f78b81b1cbcf9e
work_keys_str_mv	AT wenjunxie structuralmodelingofchromatinintegratesgenomefeaturesandrevealschromosomefoldingprinciple AT lumingmeng structuralmodelingofchromatinintegratesgenomefeaturesandrevealschromosomefoldingprinciple AT siruiliu structuralmodelingofchromatinintegratesgenomefeaturesandrevealschromosomefoldingprinciple AT lingzhang structuralmodelingofchromatinintegratesgenomefeaturesandrevealschromosomefoldingprinciple AT xiaoxiacai structuralmodelingofchromatinintegratesgenomefeaturesandrevealschromosomefoldingprinciple AT yiqingao structuralmodelingofchromatinintegratesgenomefeaturesandrevealschromosomefoldingprinciple
_version_	1718388696677351424

Structural Modeling of Chromatin Integrates Genome Features and Reveals Chromosome Folding Principle

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