Annotation and cluster analysis of spatiotemporaland sex-related lncRNA expression in rhesus macaque brain

Siling Liu; Yi Zhang; Xiangting Wang; Zhengbo Wang; Dong Chen; Bowen Zhang; Ren Rong Tian; Jing Wu; Ying Zhang; Kaiyu Xu; Liu Meng Yang; Chao Cheng; Jian Ma; Longbao Lv; Yong Tang Zheng; Xintian Hu; Jiali Li

doi:10.1101/gr.217463.116

Annotation and cluster analysis of spatiotemporaland sex-related lncRNA expression in rhesus macaque brain

Siling Liu
, Yi Zhang
, Xiangting Wang
, Zhengbo Wang
, Dong Chen
, Bowen Zhang
, Ren Rong Tian
, Jing Wu
, Ying Zhang
, Kaiyu Xu
, Liu Meng Yang
, Chao Cheng
, Jian Ma
, Longbao Lv
, Yong Tang Zheng
, Xintian Hu
, Jiali Li

School of Medicine

CAS - Kunming Institute of Zoology
University of Chinese Academy of Sciences
ABLife Inc.
University of Science and Technology of China
CAS - Center for Excellence in Molecular Cell Science
Chinese Academy of Sciences
Center for Excellence in Brain Science and Intelligence Technology

Research output: Contribution to journal › Article › peer-review

98 Scopus citations

Abstract

Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes and diseases. We applied comprehensive analyses of RNA-seq and CAGE-seq (cap analysis of gene expression and sequencing) to characterize the dynamic changes in lncRNA expression in rhesus macaque (Macaca mulatta) brain in four representative age groups. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age, and sex specificities. Spatiotemporal-and sex-biased changes in lncRNA expression were generally higher than those observed in mRNA expression. A negative correlation between lncRNA and mRNA expression in cerebral cortex was observed and functionally validated. Our findings offer a fresh insight into spatial-, age-, and sex-biased changes in lncRNA expression in macaque brain and suggest that the changes represent a previously unappreciated regulatory system that potentially contributes to brain development and aging.

Original language	English
Pages (from-to)	1608-1620
Number of pages	13
Journal	Genome Research
Volume	27
Issue number	9
DOIs	https://doi.org/10.1101/gr.217463.116
State	Published - Sep 2017

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10.1101/gr.217463.116

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title = "Annotation and cluster analysis of spatiotemporaland sex-related lncRNA expression in rhesus macaque brain",

abstract = "Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes and diseases. We applied comprehensive analyses of RNA-seq and CAGE-seq (cap analysis of gene expression and sequencing) to characterize the dynamic changes in lncRNA expression in rhesus macaque (Macaca mulatta) brain in four representative age groups. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age, and sex specificities. Spatiotemporal-and sex-biased changes in lncRNA expression were generally higher than those observed in mRNA expression. A negative correlation between lncRNA and mRNA expression in cerebral cortex was observed and functionally validated. Our findings offer a fresh insight into spatial-, age-, and sex-biased changes in lncRNA expression in macaque brain and suggest that the changes represent a previously unappreciated regulatory system that potentially contributes to brain development and aging.",

author = "Siling Liu and Yi Zhang and Xiangting Wang and Zhengbo Wang and Dong Chen and Bowen Zhang and Tian, \{Ren Rong\} and Jing Wu and Ying Zhang and Kaiyu Xu and Yang, \{Liu Meng\} and Chao Cheng and Jian Ma and Longbao Lv and Zheng, \{Yong Tang\} and Xintian Hu and Jiali Li",

note = "Publisher Copyright: {\textcopyright} 2017 Liu et al.",

year = "2017",

month = sep,

doi = "10.1101/gr.217463.116",

language = "English",

volume = "27",

pages = "1608--1620",

journal = "Genome Research",

issn = "1088-9051",

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TY - JOUR

T1 - Annotation and cluster analysis of spatiotemporaland sex-related lncRNA expression in rhesus macaque brain

AU - Liu, Siling

AU - Zhang, Yi

AU - Wang, Xiangting

AU - Wang, Zhengbo

AU - Chen, Dong

AU - Zhang, Bowen

AU - Tian, Ren Rong

AU - Wu, Jing

AU - Zhang, Ying

AU - Xu, Kaiyu

AU - Yang, Liu Meng

AU - Cheng, Chao

AU - Ma, Jian

AU - Lv, Longbao

AU - Zheng, Yong Tang

AU - Hu, Xintian

AU - Li, Jiali

PY - 2017/9

Y1 - 2017/9

N2 - Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes and diseases. We applied comprehensive analyses of RNA-seq and CAGE-seq (cap analysis of gene expression and sequencing) to characterize the dynamic changes in lncRNA expression in rhesus macaque (Macaca mulatta) brain in four representative age groups. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age, and sex specificities. Spatiotemporal-and sex-biased changes in lncRNA expression were generally higher than those observed in mRNA expression. A negative correlation between lncRNA and mRNA expression in cerebral cortex was observed and functionally validated. Our findings offer a fresh insight into spatial-, age-, and sex-biased changes in lncRNA expression in macaque brain and suggest that the changes represent a previously unappreciated regulatory system that potentially contributes to brain development and aging.

AB - Long noncoding RNAs (lncRNAs) mediate important epigenetic regulation in a wide range of biological processes and diseases. We applied comprehensive analyses of RNA-seq and CAGE-seq (cap analysis of gene expression and sequencing) to characterize the dynamic changes in lncRNA expression in rhesus macaque (Macaca mulatta) brain in four representative age groups. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age, and sex specificities. Spatiotemporal-and sex-biased changes in lncRNA expression were generally higher than those observed in mRNA expression. A negative correlation between lncRNA and mRNA expression in cerebral cortex was observed and functionally validated. Our findings offer a fresh insight into spatial-, age-, and sex-biased changes in lncRNA expression in macaque brain and suggest that the changes represent a previously unappreciated regulatory system that potentially contributes to brain development and aging.

UR - https://www.scopus.com/pages/publications/85028763652

U2 - 10.1101/gr.217463.116

DO - 10.1101/gr.217463.116

M3 - Article

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AN - SCOPUS:85028763652

SN - 1088-9051

VL - 27

SP - 1608

EP - 1620

JO - Genome Research

JF - Genome Research

IS - 9

ER -

Annotation and cluster analysis of spatiotemporaland sex-related lncRNA expression in rhesus macaque brain

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