1
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Ding W, Li X, Zhang J, Ji M, Zhang M, Zhong X, Cao Y, Liu X, Li C, Xiao C, Wang J, Li T, Yu Q, Mo F, Zhang B, Qi J, Yang JC, Qi J, Tian L, Xu X, Peng Q, Zhou WZ, Liu Z, Fu A, Zhang X, Zhang JJ, Sun Y, Hu B, An NA, Zhang L, Li CY. Adaptive functions of structural variants in human brain development. Sci Adv 2024; 10:eadl4600. [PMID: 38579006 DOI: 10.1126/sciadv.adl4600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/01/2024] [Indexed: 04/07/2024]
Abstract
Quantifying the structural variants (SVs) in nonhuman primates could provide a niche to clarify the genetic backgrounds underlying human-specific traits, but such resource is largely lacking. Here, we report an accurate SV map in a population of 562 rhesus macaques, verified by in-house benchmarks of eight macaque genomes with long-read sequencing and another one with genome assembly. This map indicates stronger selective constrains on inversions at regulatory regions, suggesting a strategy for prioritizing them with the most important functions. Accordingly, we identified 75 human-specific inversions and prioritized them. The top-ranked inversions have substantially shaped the human transcriptome, through their dual effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots at the inverted regions. As a proof of concept, we linked APCDD1, located on one of these inversions and down-regulated specifically in humans, to neuronal maturation and cognitive ability. We thus highlight inversions in shaping the human uniqueness in brain development.
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Affiliation(s)
- Wanqiu Ding
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiangshang Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Mengling Zhang
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Xiaoming Zhong
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Center of Excellence for Leukemia Studies, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yong Cao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, 119S Fourth Ring Rd W, Fengtai District, Beijing, China
| | - Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunqiong Li
- Chinese Institute for Brain Research, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jiaxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Ting Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qing Yu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jianhuan Qi
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jie-Chun Yang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Juntian Qi
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Lu Tian
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Qi Peng
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Aisi Fu
- Wuhan Dgensee Clinical Laboratory, Wuhan, China
| | - Xiuqin Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jian-Jun Zhang
- Shanxi Key Laboratory of Chinese Medicine Encephalopathy, National International Joint Research Center for Molecular Chinese Medicine, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- National Biomedical Imaging Center, College of Future Technology, Peking University, Beijing, China
- Southwest United Graduate School, Kunming 650092, China
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2
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Liu X, Xiao C, Xu X, Zhang J, Mo F, Chen JY, Delihas N, Zhang L, An NA, Li CY. Origin of functional de novo genes in humans from "hopeful monsters". Wiley Interdiscip Rev RNA 2024; 15:e1845. [PMID: 38605485 DOI: 10.1002/wrna.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Southwest United Graduate School, Kunming, China
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3
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Zhang J, Peng Q, Ma C, Wang J, Xiao C, Li T, Liu X, Zhou L, Xu X, Zhou WZ, Ding W, An NA, Zhang L, Liu Y, Li CY. 6mA-Sniper: Quantifying 6mA sites in eukaryotes at single-nucleotide resolution. Sci Adv 2023; 9:eadh7912. [PMID: 37862411 PMCID: PMC10588941 DOI: 10.1126/sciadv.adh7912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/18/2023] [Indexed: 10/22/2023]
Abstract
While N6-methyldeoxyadenine (6mA) modification is a fundamental regulation in prokaryotes, its prevalence and functions in eukaryotes are controversial. Here, we report 6mA-Sniper to quantify 6mA sites in eukaryotes at single-nucleotide resolution, and delineate a 6mA profile in Caenorhabditis elegans with 2034 sites. Twenty-six of 39 events with Mnl I restriction endonuclease sites were verified, demonstrating the feasibility of this method. The levels of 6mA sites pinpointed by 6mA-Sniper are generally increased after Pseudomonas aeruginosa infection, but decreased in strains with the removal of METL-9, the dominant 6mA methyltransferase. The enrichment of these sites on specific motif of [GC]GAG, the selective constrains on them, and their coordinated changes with METL-9 levels thus support an active shaping of the 6mA profile by methyltransferase. Moreover, for regions marked by 6mA sites that emerged after infection, an enrichment of up-regulated genes was detected, possibly mediated through a mutual exclusive cross-talk between 6mA and H3K27me3 modification. We thus highlight 6mA regulation as a previously neglected regulator in eukaryotes.
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Affiliation(s)
- Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Qi Peng
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chengchuan Ma
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100871, China
| | - Jiaxin Wang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Ting Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Liankui Zhou
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wanqiu Ding
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Bioinformatics Core, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Ni A. An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Ying Liu
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100871, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
- Chinese Institute for Brain Research, Beijing, China
- Southwest United Graduate School, Kunming 650092, China
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4
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Qi J, Mo F, An NA, Mi T, Wang J, Qi J, Li X, Zhang B, Xia L, Lu Y, Sun G, Wang X, Li C, Hu B. A Human-Specific De Novo Gene Promotes Cortical Expansion and Folding. Adv Sci (Weinh) 2023; 10:e2204140. [PMID: 36638273 PMCID: PMC9982566 DOI: 10.1002/advs.202204140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Newly originated de novo genes have been linked to the formation and function of the human brain. However, how a specific gene originates from ancestral noncoding DNAs and becomes involved in the preexisting network for functional outcomes remains elusive. Here, a human-specific de novo gene, SP0535, is identified that is preferentially expressed in the ventricular zone of the human fetal brain and plays an important role in cortical development and function. In human embryonic stem cell-derived cortical organoids, knockout of SP0535 compromises their growth and neurogenesis. In SP0535 transgenic (TG) mice, expression of SP0535 induces fetal cortex expansion and sulci and gyri-like structure formation. The progenitors and neurons in the SP0535 TG mouse cortex tend to proliferate and differentiate in ways that are unique to humans. SP0535 TG adult mice also exhibit improved cognitive ability and working memory. Mechanistically, SP0535 interacts with the membrane protein Na+ /K+ ATPase subunit alpha-1 (ATP1A1) and releases Src from the ATP1A1-Src complex, allowing increased level of Src phosphorylation that promotes cell proliferation. Thus, SP0535 is the first proven human-specific de novo gene that promotes cortical expansion and folding, and can function through incorporating into an existing conserved molecular network.
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Affiliation(s)
- Jianhuan Qi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
| | - Ni A. An
- Laboratory of Bioinformatics and Genomic MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking UniversityBeijing100871China
| | - Tingwei Mi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
| | - Jiaxin Wang
- Laboratory of Bioinformatics and Genomic MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking UniversityBeijing100871China
| | - Jun‐Tian Qi
- Laboratory of Bioinformatics and Genomic MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking UniversityBeijing100871China
| | - Xiangshang Li
- Laboratory of Bioinformatics and Genomic MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking UniversityBeijing100871China
| | - Boya Zhang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
| | - Longkuo Xia
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
| | - Yingfei Lu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
| | - Gaoying Sun
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xinyue Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
| | - Chuan‐Yun Li
- Laboratory of Bioinformatics and Genomic MedicineInstitute of Molecular MedicineCollege of Future TechnologyPeking UniversityBeijing100871China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijing100101China
- Savaid Medical SchoolUniversity of Chinese Academy of SciencesBeijing100049China
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijing100101China
- Beijing Institute for Stem Cell and Regenerative MedicineBeijing100101China
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5
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An NA, Zhang J, Mo F, Luan X, Tian L, Shen QS, Li X, Li C, Zhou F, Zhang B, Ji M, Qi J, Zhou WZ, Ding W, Chen JY, Yu J, Zhang L, Shu S, Hu B, Li CY. De novo genes with an lncRNA origin encode unique human brain developmental functionality. Nat Ecol Evol 2023; 7:264-278. [PMID: 36593289 PMCID: PMC9911349 DOI: 10.1038/s41559-022-01925-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 10/04/2022] [Indexed: 01/03/2023]
Abstract
Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA-mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.
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Affiliation(s)
- Ni A. An
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Zhang
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Fan Mo
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Xuke Luan
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Lu Tian
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiangshang Li
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Chunqiong Li
- grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, China
| | - Fanqi Zhou
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Boya Zhang
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Mingjun Ji
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jianhuan Qi
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Zhen Zhou
- grid.415105.40000 0004 9430 5605State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wanqiu Ding
- grid.11135.370000 0001 2256 9319Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jia-Yu Chen
- grid.41156.370000 0001 2314 964XState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jia Yu
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Key Laboratory of RNA Regulation and Hematopoiesis, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, CAMS and Peking Union Medical College, Beijing, China
| | - Li Zhang
- grid.510934.a0000 0005 0398 4153Chinese Institute for Brain Research, Beijing, China
| | - Shaokun Shu
- grid.11135.370000 0001 2256 9319Peking University International Cancer Institute, Beijing, China
| | - Baoyang Hu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China. .,Chinese Institute for Brain Research, Beijing, China.
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6
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Li Y, Shen QS, Peng Q, Ding W, Zhang J, Zhong X, An NA, Ji M, Zhou WZ, Li CY. Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. Brief Bioinform 2021; 22:6273384. [PMID: 33973996 PMCID: PMC8574621 DOI: 10.1093/bib/bbab157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/22/2021] [Accepted: 04/04/2021] [Indexed: 11/26/2022] Open
Abstract
Rhesus macaque is a unique nonhuman primate model for human evolutionary and translational study, but the error-prone gene models critically limit its applications. Here, we de novo defined full-length macaque gene models based on single molecule, long-read transcriptome sequencing in four macaque tissues (frontal cortex, cerebellum, heart and testis). Overall, 8 588 227 poly(A)-bearing complementary DNA reads with a mean length of 14 106 nt were generated to compile the backbone of macaque transcripts, with the fine-scale structures further refined by RNA sequencing and cap analysis gene expression sequencing data. In total, 51 605 macaque gene models were accurately defined, covering 89.7% of macaque or 75.7% of human orthologous genes. Based on the full-length gene models, we performed a human–macaque comparative analysis on polyadenylation (PA) regulation. Using macaque and mouse as outgroup species, we identified 79 distal PA events newly originated in humans and found that the strengthening of the distal PA sites, rather than the weakening of the proximal sites, predominantly contributes to the origination of these human-specific isoforms. Notably, these isoforms are selectively constrained in general and contribute to the temporospatially specific reduction of gene expression, through the tinkering of previously existed mechanisms of nuclear retention and microRNA (miRNA) regulation. Overall, the protocol and resource highlight the application of bioinformatics in integrating multilayer genomics data to provide an intact reference for model animal studies, and the isoform switching detected may constitute a hitherto underestimated regulatory layer in shaping the human-specific transcriptome and phenotypic changes.
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Affiliation(s)
- Yumei Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qing Sunny Shen
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Qi Peng
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Xiaoming Zhong
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ni A An
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Mingjun Ji
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
| | - Wei-Zhen Zhou
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Beijing, China
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,College of Future Technology, Peking University, Beijing, China
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Xue Y, Bao Y, Zhang Z, Zhao W, Xiao J, He S, Zhang G, Li Y, Zhao G, Chen R, Song S, Ma L, Zou D, Tian D, Li C, Zhu J, Gong Z, Chen M, Wang A, Ma Y, Li M, Teng X, Cui Y, Duan G, Zhang M, Jin T, Shi C, Du Z, Zhang Y, Liu C, Li R, Zeng J, Hao L, Jiang S, Chen H, Han D, Xiao J, Zhang Z, Zhao W, Xue Y, Bao Y, Zhang T, Kang W, Yang F, Qu J, Zhang W, Bao Y, Liu GH, Liu L, Zhang Y, Niu G, Zhu T, Feng C, Liu X, Zhang Y, Li Z, Chen R, Li Q, Teng X, Ma L, Hua Z, Tian D, Jiang C, Chen Z, He F, Zhao Y, Jin Y, Zhang Z, Huang L, Song S, Yuan Y, Zhou C, Xu Q, He S, Ye W, Cao R, Wang P, Ling Y, Yan X, Wang Q, Zhang G, Li Z, Liu L, Jiang S, Li Q, Feng C, Du Q, Ma L, Zong W, Kang H, Zhang M, Xiong Z, Li R, Huan W, Ling Y, Zhang S, Xia Q, Cao R, Fan X, Wang Z, Zhang G, Chen X, Chen T, Zhang S, Tang B, Zhu J, Dong L, Zhang Z, Wang Z, Kang H, Wang Y, Ma Y, Wu S, Kang H, Chen M, Li C, Tian D, Tang B, Liu X, Teng X, Song S, Tian D, Liu X, Li C, Teng X, Song S, Zhang Y, Zou D, Zhu T, Chen M, Niu G, Liu C, Xiong Y, Hao L, Niu G, Zou D, Zhu T, Shao X, Hao L, Li Y, Zhou H, Chen X, Zheng Y, Kang Q, Hao D, Zhang L, Luo H, Hao Y, Chen R, Zhang P, He S, Zou D, Zhang M, Xiong Z, Nie Z, Yu S, Li R, Li M, Li R, Bao Y, Xiong Z, Li M, Yang F, Ma Y, Sang J, Li Z, Li R, Tang B, Zhang X, Dong L, Zhou Q, Cui Y, Zhai S, Zhang Y, Wang G, Zhao W, Wang Z, Zhu Q, Li X, Zhu J, Tian D, Kang H, Li C, Zhang S, Song S, Li M, Zhao W, Yan J, Sang J, Zou D, Li C, Wang Z, Zhang Y, Zhu T, Song S, Wang X, Hao L, Liu Y, Wang Z, Luo H, Zhu J, Wu X, Tian D, Li C, Zhao W, Jing HC, Chen M, Zou D, Hao L, Zhao L, Wang J, Li Y, Song T, Zheng Y, Chen R, Zhao Y, He S, Zou D, Mehmood F, Ali S, Ali A, Saleem S, Hussain I, Abbasi AA, Ma L, Zou D, Zou D, Jiang S, Zhang Z, Jiang S, Zhao W, Xiao J, Bao Y, Zhang Z, Zuo Z, Ren J, Zhang X, Xiao Y, Li X, Zhang X, Xiao Y, Li X, Tu Y, Xue Y, Wu W, Ji P, Zhao F, Meng X, Chen M, Peng D, Xue Y, Luo H, Gao F, Zhang X, Xiao Y, Li X, Ning W, Xue Y, Lin S, Xue Y, Liu T, Guo AY, Yuan H, Zhang YE, Tan X, Xue Y, Zhang W, Xue Y, Xie Y, Ren J, Wang C, Xue Y, Liu CJ, Guo AY, Yang DC, Tian F, Gao G, Tang D, Xue Y, Yao L, Xue Y, Cui Q, An NA, Li CY, Luo X, Ren J, Zhang X, Xiao Y, Li X. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res 2021; 49:D18-D28. [PMID: 33175170 PMCID: PMC7779035 DOI: 10.1093/nar/gkaa1022] [Citation(s) in RCA: 135] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a suite of database resources to support worldwide research activities in both academia and industry. With the explosive growth of multi-omics data, CNCB-NGDC is continually expanding, updating and enriching its core database resources through big data deposition, integration and translation. In the past year, considerable efforts have been devoted to 2019nCoVR, a newly established resource providing a global landscape of SARS-CoV-2 genomic sequences, variants, and haplotypes, as well as Aging Atlas, BrainBase, GTDB (Glycosyltransferases Database), LncExpDB, and TransCirc (Translation potential for circular RNAs). Meanwhile, a series of resources have been updated and improved, including BioProject, BioSample, GWH (Genome Warehouse), GVM (Genome Variation Map), GEN (Gene Expression Nebulas) as well as several biodiversity and plant resources. Particularly, BIG Search, a scalable, one-stop, cross-database search engine, has been significantly updated by providing easy access to a large number of internal and external biological resources from CNCB-NGDC, our partners, EBI and NCBI. All of these resources along with their services are publicly accessible at https://bigd.big.ac.cn.
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An NA, Ding W, Yang XZ, Peng J, He BZ, Shen QS, Lu F, He A, Zhang YE, Tan BCM, Chen JY, Li CY. Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates. Genome Biol 2019; 20:24. [PMID: 30712515 PMCID: PMC6360793 DOI: 10.1186/s13059-019-1638-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/22/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed. RESULTS Here, we perform a comparative editome study in human and rhesus macaque and uncover a substantial proportion of macaque A-to-I editing sites that are genomically polymorphic in some animals or encoded as non-editable nucleotides in human. The occurrence of these recent gain and loss of RNA editing through DNA point mutation is significantly more prevalent than that expected for the nearby regions. Ancestral state analyses further demonstrate that an increase in recent gain of editing events contribute to the over-representation, with G-to-A mutation site as a favorable location for the origination of robust A-to-I editing events. Population genetics analyses of the focal editing sites further reveal that a portion of these young editing events are evolutionarily significant, indicating general functional relevance for at least a fraction of these sites. CONCLUSIONS Overall, we report a list of A-to-I editing events that recently originated through G-to-A mutations in primates, representing a valuable resource to investigate the features and evolutionary significance of A-to-I editing events at the population and species levels. The unique subset of primate editome also illuminates the general functions of RNA editing by connecting it to particular gene regulatory processes, based on the characterized outcome of a gene regulatory level in different individuals or primate species with or without these editing events.
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Affiliation(s)
- Ni A An
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Wanqiu Ding
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Xin-Zhuang Yang
- Department of Central Research Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jiguang Peng
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Bin Z He
- Biology Department, University of Iowa, Iowa City, IA, USA
| | - Qing Sunny Shen
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Fujian Lu
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Aibin He
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China
| | - Yong E Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bertrand Chin-Ming Tan
- Department of Biomedical Sciences and Graduate Institute of Biomedical Sciences College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Jia-Yu Chen
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093-0651, USA.
| | - Chuan-Yun Li
- Laboratory of Bioinformatics and Genomic Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, 100871, China.
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