Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain
- Siling Liu1,2,9,
- Zhengbo Wang1,9,
- Dong Chen3,9,
- Bowen Zhang4,9,
- Ren-Rong Tian1,9,
- Jing Wu1,
- Ying Zhang1,
- Kaiyu Xu1,2,
- Liu-Meng Yang1,
- Chao Cheng3,
- Jian Ma1,2,
- Longbao Lv1,5,
- Yong-Tang Zheng1,5,
- Xintian Hu1,5,6,
- Yi Zhang3,7,
- Xiangting Wang4,8 and
- Jiali Li1,5
- 1Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China;
- 2Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650223, China;
- 3Center for Genome Analysis, ABLife Incorporated, Wuhan 430075, China;
- 4School of Life Science, CAS Key Laboratory of Brain Function and Disease, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Hefei, Anhui 230026, China;
- 5Kunming Primate Research Center of the Chinese Academy of Sciences, Kunming, Yunnan 650223, China;
- 6CAS Center for Excellence in Brain Science and Intelligence Technology, Hefei, Anhui 230027, China;
- 7Laboratory for Genome Regulation and Human Health, ABLife Incorporated, Wuhan 430075, China;
- 8CAS Center for Excellence in Molecular Cell Science, Hefei, Anhui 230027, China
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↵9 These authors contributed equally to this work.
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.217463.116.
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Freely available online through the Genome Research Open Access option.
- Received October 20, 2016.
- Accepted June 26, 2017.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
