title: Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.
abstract: Next-generation RNA sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Dong-Dong
authors.initials: DD
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Ling-Qun
authors.initials: LQ
authors.lastname: Ye
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Yan-Bo
authors.initials: YB
authors.lastname: Sun
authors.affiliation: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Shao
authors.affiliation: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Chen
authors.affiliation: Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China.
authors.forename: Zhu
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhong
authors.affiliation: Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China.
authors.forename: Lu
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada Banting and Best Diabetes Centre, University of Toronto, Toronto, Canada.
authors.forename: David M
authors.initials: DM
authors.lastname: Irwin
authors.affiliation: Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
authors.forename: Yong E
authors.initials: YE
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, China zhangyp@mail.kiz.ac.cn.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000596:Amino Acids / Q000235:genetics; D001921:Brain / Q000378:metabolism*; D004843:Epistasis, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008954:Models, Biological; D016366:Open Reading Frames / Q000235:genetics; D017393:RNA Editing / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D000596:Amino Acids
keywords: RNA editing; human brain evolution; human brain transcriptome; young gene