Epigenetic information regulates gene expression and development. However, our understanding of the evolution of epigenetic regulation on brain development in primates is limited. Here, we compared chromatin accessibility landscapes and transcriptomes during fetal prefrontal cortex (PFC) development between rhesus macaques and humans. A total of 304,761 divergent DNase I-hypersensitive sites (DHSs) are identified between rhesus macaques and humans, although many of these sites share conserved DNA sequences. Interestingly, most of the cis-elements linked to orthologous genes with dynamic expression are divergent DHSs. Orthologous genes expressed at earlier stages tend to have conserved cis-elements, whereas orthologous genes specifically expressed at later stages seldom have conserved cis-elements. These genes are enriched in synapse organization, learning and memory. Notably, DHSs in the PFC at early stages are linked to human educational attainment and cognitive performance. Collectively, the comparison of the chromatin epigenetic landscape between rhesus macaques and humans suggests a potential role for regulatory elements in the evolution of differences in cognitive ability between non-human primates and humans.
Publication:
Nature Communications, (2022) 13:3883.
Author:
Xuelong Yao
CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101 Beijing, China
University of Chinese Academy of Sciences, 100049 Beijing, China
Guangzhou Nvwa Life Technology Co., Ltd, Guangzhou 510535, China
Zongyang Lu
University of Chinese Academy of Sciences, 100049 Beijing, China
School of Life Science and Technology, Shanghai Tech University, 100 Haike Rd., Pudong New Area, Shanghai 201210, China
Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
Zhanying Feng
University of Chinese Academy of Sciences, 100049 Beijing, China
CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190 Beijing, China
Lei Gao
CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101 Beijing, China
Xin Zhou
State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
Min Li
University of Chinese Academy of Sciences, 100049 Beijing, China
State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
Suijuan Zhong
State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, 100875 Beijing, China
IDG/McGovern Institute for Brain Research, Beijing Normal University, 100875 Beijing, China
Qian Wu
State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, 100875 Beijing, China
IDG/McGovern Institute for Brain Research, Beijing Normal University, 100875 Beijing, China
Zhenbo Liu
CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101 Beijing, China
Haofeng Zhang
Obstetrics and Gynecology Medical Center of Severe Cardiovascular of Beijing Anzhen Hospital, Capital Medical University, 100029 Beijing, China
Zeyuan Liu
University of Chinese Academy of Sciences, 100049 Beijing, China
State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
Lizhi Yi
CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101 Beijing, China
University of Chinese Academy of Sciences, 100049 Beijing, China
Tao Zhou
School of Life Science and Technology, Shanghai Tech University, 100 Haike Rd., Pudong New Area, Shanghai 201210, China
Shenzhen Key Lab of Drug Addiction; The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
Xudong Zhao
Kunming Primate Research Center, Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
Jun Zhang
Obstetrics and Gynecology Medical Center of Severe Cardiovascular of Beijing Anzhen Hospital, Capital Medical University, 100029 Beijing, China
Yong Wang
University of Chinese Academy of Sciences, 100049 Beijing, China
CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, 100190 Beijing, China
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
Email: yongwang@amss.ac.cn
Xingxu Huang
School of Life Science and Technology, Shanghai Tech University, 100 Haike Rd., Pudong New Area, Shanghai 201210, China
Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
Xiaoqun Wang
University of Chinese Academy of Sciences, 100049 Beijing, China
State Key Laboratory of Brain and Cognitive Science, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Brain-Intelligence Technology (Shanghai), Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101 Beijing, China
Beijing Institute for Brain Disorders, 100069 Beijing, China
Jiang Liu
CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101 Beijing, China
University of Chinese Academy of Sciences, 100049 Beijing, China
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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