CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells

Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited...

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Autores principales: Perez-Rathke, Alan, Sun, Qiu, Wang, Boshen, Boeva, Valentina, Shao, Zhifeng, Liang, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966897/
https://www.ncbi.nlm.nih.gov/pubmed/31948478
http://dx.doi.org/10.1186/s13059-019-1904-z
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author Perez-Rathke, Alan
Sun, Qiu
Wang, Boshen
Boeva, Valentina
Shao, Zhifeng
Liang, Jie
author_facet Perez-Rathke, Alan
Sun, Qiu
Wang, Boshen
Boeva, Valentina
Shao, Zhifeng
Liang, Jie
author_sort Perez-Rathke, Alan
collection PubMed
description Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore unsuitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, which reconstructs ensembles of single-cell chromatin structures by deconvolving Hi-C data and identifies significant many-body interactions. For a diverse set of highly active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions.
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spelling pubmed-69668972020-01-27 CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells Perez-Rathke, Alan Sun, Qiu Wang, Boshen Boeva, Valentina Shao, Zhifeng Liang, Jie Genome Biol Method Chromatin interactions are important for gene regulation and cellular specialization. Emerging evidence suggests many-body spatial interactions play important roles in condensing super-enhancer regions into a cohesive transcriptional apparatus. Chromosome conformation studies using Hi-C are limited to pairwise, population-averaged interactions; therefore unsuitable for direct assessment of many-body interactions. We describe a computational model, CHROMATIX, which reconstructs ensembles of single-cell chromatin structures by deconvolving Hi-C data and identifies significant many-body interactions. For a diverse set of highly active transcriptional loci with at least 2 super-enhancers, we detail the many-body functional landscape and show DNase accessibility, POLR2A binding, and decreased H3K27me3 are predictive of interaction-enriched regions. BioMed Central 2020-01-16 /pmc/articles/PMC6966897/ /pubmed/31948478 http://dx.doi.org/10.1186/s13059-019-1904-z Text en © The Author(s) 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Perez-Rathke, Alan
Sun, Qiu
Wang, Boshen
Boeva, Valentina
Shao, Zhifeng
Liang, Jie
CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
title CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
title_full CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
title_fullStr CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
title_full_unstemmed CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
title_short CHROMATIX: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
title_sort chromatix: computing the functional landscape of many-body chromatin interactions in transcriptionally active loci from deconvolved single cells
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966897/
https://www.ncbi.nlm.nih.gov/pubmed/31948478
http://dx.doi.org/10.1186/s13059-019-1904-z
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