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Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation
Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and RNA polymerase II (RNAPII)-associated promoter–promoter interactions and H3K9me2-marked heterochromatin...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692402/ https://www.ncbi.nlm.nih.gov/pubmed/31409785 http://dx.doi.org/10.1038/s41467-019-11535-9 |
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author | Zhao, Lun Wang, Shuangqi Cao, Zhilin Ouyang, Weizhi Zhang, Qing Xie, Liang Zheng, Ruiqin Guo, Minrong Ma, Meng Hu, Zhe Sung, Wing-Kin Zhang, Qifa Li, Guoliang Li, Xingwang |
author_facet | Zhao, Lun Wang, Shuangqi Cao, Zhilin Ouyang, Weizhi Zhang, Qing Xie, Liang Zheng, Ruiqin Guo, Minrong Ma, Meng Hu, Zhe Sung, Wing-Kin Zhang, Qifa Li, Guoliang Li, Xingwang |
author_sort | Zhao, Lun |
collection | PubMed |
description | Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and RNA polymerase II (RNAPII)-associated promoter–promoter interactions and H3K9me2-marked heterochromatin interactions at nucleotide/gene resolution in rice. The chromatin architecture is separated into different independent spatial interacting modules with distinct transcriptional potential and covers approximately 82% of the genome. Compared to inactive modules, active modules possess the majority of active loop genes with higher density and contribute to most of the transcriptional activity in rice. In addition, promoter–promoter interacting genes tend to be transcribed cooperatively. In contrast, the heterochromatin-mediated loops form relative stable structure domains in chromatin configuration. Furthermore, we examine the impact of genetic variation on chromatin interactions and transcription and identify a spatial correlation between the genetic regulation of eQTLs and e-traits. Thus, our results reveal hierarchical and modular 3D genome architecture for transcriptional regulation in rice. |
format | Online Article Text |
id | pubmed-6692402 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-66924022019-08-15 Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation Zhao, Lun Wang, Shuangqi Cao, Zhilin Ouyang, Weizhi Zhang, Qing Xie, Liang Zheng, Ruiqin Guo, Minrong Ma, Meng Hu, Zhe Sung, Wing-Kin Zhang, Qifa Li, Guoliang Li, Xingwang Nat Commun Article Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and RNA polymerase II (RNAPII)-associated promoter–promoter interactions and H3K9me2-marked heterochromatin interactions at nucleotide/gene resolution in rice. The chromatin architecture is separated into different independent spatial interacting modules with distinct transcriptional potential and covers approximately 82% of the genome. Compared to inactive modules, active modules possess the majority of active loop genes with higher density and contribute to most of the transcriptional activity in rice. In addition, promoter–promoter interacting genes tend to be transcribed cooperatively. In contrast, the heterochromatin-mediated loops form relative stable structure domains in chromatin configuration. Furthermore, we examine the impact of genetic variation on chromatin interactions and transcription and identify a spatial correlation between the genetic regulation of eQTLs and e-traits. Thus, our results reveal hierarchical and modular 3D genome architecture for transcriptional regulation in rice. Nature Publishing Group UK 2019-08-13 /pmc/articles/PMC6692402/ /pubmed/31409785 http://dx.doi.org/10.1038/s41467-019-11535-9 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Zhao, Lun Wang, Shuangqi Cao, Zhilin Ouyang, Weizhi Zhang, Qing Xie, Liang Zheng, Ruiqin Guo, Minrong Ma, Meng Hu, Zhe Sung, Wing-Kin Zhang, Qifa Li, Guoliang Li, Xingwang Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation |
title | Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation |
title_full | Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation |
title_fullStr | Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation |
title_full_unstemmed | Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation |
title_short | Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation |
title_sort | chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692402/ https://www.ncbi.nlm.nih.gov/pubmed/31409785 http://dx.doi.org/10.1038/s41467-019-11535-9 |
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