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Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain
The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains. We id...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981234/ https://www.ncbi.nlm.nih.gov/pubmed/31980617 http://dx.doi.org/10.1038/s41467-020-14368-z |
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author | Yin, Senlin Lu, Keying Tan, Tao Tang, Jie Wei, Jingkuan Liu, Xu Hu, Xinlei Wan, Haisu Huang, Wei Fan, Yong Xie, Dan Yu, Yang |
author_facet | Yin, Senlin Lu, Keying Tan, Tao Tang, Jie Wei, Jingkuan Liu, Xu Hu, Xinlei Wan, Haisu Huang, Wei Fan, Yong Xie, Dan Yu, Yang |
author_sort | Yin, Senlin |
collection | PubMed |
description | The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains. We identify gene modules associated with specific brain regions like the cerebral cortex, pituitary, and thalamus. In addition, we discover 9703 novel intergenic transcripts, including 1701 coding transcripts and 2845 lncRNAs. Most of the novel transcripts are only expressed in specific brain regions or cortical regions of specific individuals. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Our results add to the growing body of knowledge regarding the baseline transcriptomic and open chromatin profiles in the brain of the rhesus macaque. |
format | Online Article Text |
id | pubmed-6981234 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-69812342020-01-27 Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain Yin, Senlin Lu, Keying Tan, Tao Tang, Jie Wei, Jingkuan Liu, Xu Hu, Xinlei Wan, Haisu Huang, Wei Fan, Yong Xie, Dan Yu, Yang Nat Commun Article The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains. We identify gene modules associated with specific brain regions like the cerebral cortex, pituitary, and thalamus. In addition, we discover 9703 novel intergenic transcripts, including 1701 coding transcripts and 2845 lncRNAs. Most of the novel transcripts are only expressed in specific brain regions or cortical regions of specific individuals. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Our results add to the growing body of knowledge regarding the baseline transcriptomic and open chromatin profiles in the brain of the rhesus macaque. Nature Publishing Group UK 2020-01-24 /pmc/articles/PMC6981234/ /pubmed/31980617 http://dx.doi.org/10.1038/s41467-020-14368-z Text en © The Author(s) 2020 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 Yin, Senlin Lu, Keying Tan, Tao Tang, Jie Wei, Jingkuan Liu, Xu Hu, Xinlei Wan, Haisu Huang, Wei Fan, Yong Xie, Dan Yu, Yang Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
title | Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
title_full | Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
title_fullStr | Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
title_full_unstemmed | Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
title_short | Transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
title_sort | transcriptomic and open chromatin atlas of high-resolution anatomical regions in the rhesus macaque brain |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6981234/ https://www.ncbi.nlm.nih.gov/pubmed/31980617 http://dx.doi.org/10.1038/s41467-020-14368-z |
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