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A human-specific insertion promotes cell proliferation and migration by enhancing TBC1D8B expression

Science China(Life Sciences) 2024年第4期67卷 765-777页

作者： Hui Zhao Lin-Lin Liu Jian Sun Lian Jin Hai-Bing Xie Jian-Bo Li Hui Xu dong-dong wu Xiao-Lin Zhuang Min-Sheng Peng Ya-Jun Guo Wei-Zhu Qian Newton OOtecko Wei-Jie Sun Liang-Hu Qu Jie He Zhao-Li Chen Rong Liu Ce-Shi Chen Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-resource School of Life SciencesSchool of Ecology and Environmental ScienceYunnan UniversityKunming 650091China School of Forensic Medicine Kunming Medical UniversityKunming 650500China Academy of Biomedical Engineering Kunming Medical UniversityKunming 650500China The Third Affiliated Hospital Kunming Medical UniversityKunming 650118China Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province Kunming Institute of ZoologyChinese Academy of SciencesKunming 650201China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650201China The Key Laboratory of Gene Engineering of the Ministry of Education State Key Laboratory for BiocontrolSun Yat-sen UniversityGuangzhou 510275China National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering and Antibody Shanghai 201203China Department of Thoracic Surgery Cancer Institute and HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China

Human-specific insertions play important roles in human phenotypes and diseases.Here we reported a 446-bp insertion(Insert-446)in intron 11 of the TBC1D8B gene,located on chromosome X,and traced its origin to a portion of intron 6 of the EBF1 gene on chromosome 5.Interestingly,Insert-446 was present in the human Neanderthal and Denisovans genomes,and was fixed in humans after human-chimpanzee divergence.We have demonstrated that Insert-446 acts as an enhancer through binding transcript factors that promotes a higher expression of human TBC1D8B gene as compared with orthologs in macaques.In addition,over-expression TBC1D8B promoted cell proliferation and migration through“a dual finger”catalytic mechanism(Arg538 and Gln573)in the TBC domain in vitro and knockdown of TBC1D8B attenuated tumorigenesis in vivo.Knockout of Insert-446 prevented cell proliferation and migration in cancer and normal cells.Our results reveal that the human-specific Insert-446 promotes cell proliferation and migration by upregulating the expression of TBC1D8B gene.These findings provide a significant insight into the effects of human-specific insertions on evolution.

关键词： human-specific insertion enhancer gene expression cell proliferation and migration

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Hydrogen sulfide-induced post-translational modification as a potential drug target

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Genes & Diseases 2023年第5期10卷 1870-1882页

作者： Hao-Jie Chen Lei Qian Ke Li Yang-Zhe Qin Jing-Jing Zhou Xin-Ying Ji dong-dong wu School of Basic Medical Sciences Henan UniversityKaifengHenan 475004China Henan International Joint Laboratory for Nuclear Protein Regulation Henan UniversityKaifengHenan 475004China Kaifeng Key Laboratory of Infection and Biological Safety School of Basic Medical SciencesHenan UniversityKaifengHenan 475004China School of Stomatology Henan UniversityKaifengHenan 475004China

Hydrogen sulfide (H_(2)S) is one of the three known gas signal transducers, and since its potential physiological role was reported, the literature on H_(2)S has been increasing. H_(2)S is involved in processes such as vasodilation, neurotransmission, angiogenesis, inflammation, and the prevention of ischemia-reperfusion injury, and its mechanism remains to be further studied. At present, the role of post-translational processing of proteins has been considered as a possible mechanism for the involvement of H_(2)S in a variety of physiological processes. Current studies have shown that H_(2)S is involved in S-sulfhydration, phosphorylation, and S-nitrosylation of proteins, etc. This paper focuses on the effects of protein modification involving H_(2)S on physiological and pathological processes, looking forward to providing guidance for subsequent research.

关键词： Hydrogen sulfide Modification Phosphorylation S-nitrosylation S-sulfhydration

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Harvesting the fruits of the first stage of the Primate Genome Project

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Zoological Research 2023年第4期44卷 725-728页

作者： Yuan-Ting Guo Yong Shao Xupeng Bi Bao-Lin Zhang Hong wu Yang Zhou Ming-Li Li Li Yu Guojie Zhang dong-dong wu Xiao-Guang Qi College of Life Sciences Northwest UniversityXi’anShaanxi 710069China State Key Laboratory of Genetic Resources and Evolution Kunming Natural History Museum of ZoologyKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650201China Centre for Evolutionary&Organismal Biology and Women’s HospitalZhejiang University School of MedicineHangzhouZhejiang 310058China State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan School of Life SciencesYunnan UniversityKunmingYunnan 650091China BGI-Shenzhen ShenzhenGuangdong 518083China Department of Neurology First Affiliated Hospital of Zhengzhou UniversityZhengzhou UniversityZhengzhouHenan 450052China Liangzhu Laboratory Zhejiang University Medical CenterHangzhouZhejiang 311121China Villum Centre for Biodiversity Genomics Section for Ecology and EvolutionDepartment of BiologyUniversity of CopenhagenCopenhagen DK-2100Denmark Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650201China National Resource Center for Non-Human Primates Kunming Primate Research Centerand National Research Facility for Phenotypic&Genetic Analysis of Model Animals(Primate Facility)Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650107China KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650204China

Primates are highly successful mammals with significant morphological,behavioral,and physiological diversity.Studying the genomes of non-human primates,as the closest relative of humans,can provide insights into human evolution,genetic structure,and potential drug targets relevant to human health,thus making important contributions to medical research.Additionally,primate genome research can support ecological balance and resource conservation and promote sustainable development and human well-being.Despite the existence of more than 500 primate species belonging to 80 genera and 16 families worldwide,with new species still being discovered in recent years(Fan et al.,2017;Khanal et al.,2021;Roos et al.,2020),genome sequencing efforts have been limited to a relatively small number of species from only 22 genera(Ensembl v103).Notably,approximately 72%of primate genera remain unsequenced,leading to significant knowledge gaps in our understanding of their evolutionary history.This situation presents considerable challenges for the development,utilization,and protection of primate genetic resources.It is for these compelling reasons that we initiated the Primate Genome Project(PGP)(wu et al.,2022).

关键词： initiated spite genera

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Unveiling the functional and evolutionary landscape of RNA editing in chicken using genomics and transcriptomics

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Zoological Research 2022年第6期43卷 1011-1022页

作者： Yun-Mei Wang Ling-Qun Ye Ming-Shan Wang Jin-Jin Zhang Saber Khederzadeh David M Irwin Xiao-Die Ren Ya-Ping Zhang dong-dong wu State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan650223China Kunming College of Life Science University of the Chinese Academy of SciencesKunmingYunnan650223China KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650201China Department of Ecology and Evolutionary Biology Howard Hughes Medical InstituteUniversity of California Santa CruzSanta CruzCA 95064USA Department of Laboratory Medicine and Pathobiology University of TorontoTorontoOntario M5S 1A8Canada Kunming Natural History Museum of Zoology Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China

The evolutionary and functional features of RNA editing are well studied in mammals,cephalopods,and insects,but not in birds.Here,we integrated transcriptomic and whole-genomic analyses to exhaustively characterize the expansive repertoire of adenosine-to-inosine(A-to-I)RNA editing sites(RESs)in the chicken.In addition,we investigated the evolutionary status of the chicken editome as a potential mechanism of domestication.We detected the lowest editing level in the liver of chickens,compared to muscles in humans,and found higher editing activity and specificity in the brain than in non-neural tissues,consistent with the brain’s functional complexity.To a certain extent,specific editing activity may account for the specific functions of tissues.Our results also revealed that sequences critical to RES secondary structures remained conserved within avian evolution.Furthermore,the RNA editome was shaped by purifying selection during chicken domestication and most RESs may have served as a selection pool for a few functional RESs involved in chicken domestication,including evolution of nervous and immune systems.Regulation of RNA editing in chickens by adenosine deaminase acting on RNA(ADAR)enzymes may be affected by non-ADAR factors whose expression levels changed widely after ADAR knockdown.Collectively,we provide comprehensive lists of candidate RESs and non-ADAR-editing regulators in the chicken,thus contributing to our current understanding of the functions and evolution of RNA editing in animals.

关键词： RNA editing Transcriptomics Population genomics Domestication Evolution Chicken

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Finding unknown species in the genomes of extant species

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Journal of Genetics and Genomics 2021年第10期48卷 867-871页

作者： Yan Li dong-dong wu State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Life Science&School of Ecology and Environmental Science Yunnan UniversityKunming 650091China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Although many species have gone extinct,their genetic components might exist in extant species because of ancient hybridization.Via advances in genome sequencing and development of modern population genetics,one can find the legacy of unknown or extinct species in the context of available genomes from extant species.Such discovery can be used as a strategy to search for hidden species or fossils in conservation biology and archeology,gain novel insight into complex evolutionary history,and provide the new sources of genetic variation for breeding and trait improvement in agriculture.

关键词： Unknown species Introgression Extant species Extinct species Genetic legacy

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First reference genome assembly of the Indochinese silvered langur(Trachypithecus germaini)

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Zoological Research 2022年第4期43卷 604-607页

作者： Jin-Wei wu Ru Zhang Ya-Lin Qin Li Wang Ming-Bo Han Zi-Fan Zhao Pei Jing Hai-Lu Sun Song Wang Ning Huang Bao-Guo Li dong-dong wu Chi Zhang Xiao-Guang Qi College of Life Sciences Northwest UniversityXi’anShaanxi 710069China BGI-Shenzhen ShenzhenGuangdong 518083China Nanning Zoo NanningGuangxi 450107China Kunming Institute of Zoology Chinese Academy of SciencesKunmingYunnan 650223China Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghai 810008China

DEAR EDITOR,Of the seven genera recognized in Asian colobines,Trachypithecus is the only genus that contains species groups.Compared with the species groups characterized by calcium tolerance(T.francoisi species group),multi-male,multi-female society(T.obscurus species group),and impressive hybridization(T.pileatus species group),the T.cristatus species group is distinguished by its southernmost distribution and silvery appearance.Hence,Trachypithecus is an excellent model for investigating evolutionary radiation and behavioral adaptation in Asian primates.However,comprehensive comparison of species groups remains difficult due to the lack of a reference genome for the T.cristatus species group.

关键词： Trachypithecus silver evolutionary

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Initiation of the Primate Genome Project

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Zoological Research 2022年第2期43卷 147-149页

作者： dong-dong wu Xiao-Guang Qi Li Yu Ming Li Zhi-Jin Liu Anne DYoder Christian Roos Takashi Hayakawa Jeffrey Rogers Tomas Marques-Bonet Bing Su Yong-Gang Yao Ya-Ping Zhang Guojie Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China National Resource Center for Non-Human Primates Kunming Primate Research Centerand National Research Facility for Phenotypic&Genetic Analysis of Model Animals(Primate Facility)Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650107China Kunming Natural History Museum of Zoology Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingYunnan 650223China Shaanxi Key Laboratory for Animal Conservation College of Life SciencesNorthwest UniversityXi’anShaanxi 710069China State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan Yunnan UniversityKunmingYunnan 650091China CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Department of Biology Duke UniversityDurhamNC 27708USA Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchGöttingen 37077Germany Faculty of Environmental Earth Science Hokkaido UniversitySapporoHokkaido 060-0810Japan Japan Monkey Centre InuyamaAichi 484-0081Japan Human Genome Sequencing Center Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX 77030USA Institute of Evolutionary Biology(UPF-CSIC) PRBBDr.Aiguader 88Barcelona 08003Spain Catalan Institution of Research and Advanced Studies(ICREA) Passeig de Lluis Companys23Barcelona 08010Spain CNAG-CRG Centre for Genomic Regulation(CRG)Barcelona Institute of Science and Technology(BIST)Baldiri i Reixac 4Barcelona 08028Spain Institut Catalade Paleontologia Miquel Crusafont Universitat Autonoma de BarcelonaEdifici ICTA-ICPc/Columnes s/nCerdanyola del VallèsBarcelona 08193Spain Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese

A crucial step for understanding human evolution is to identify the genomic changes that occurred during primate evolution,thus allowing investigators to reconstruct the ancestral states preceding the human condition.In the past several decades,the primate clade has been a research focus in genome sequencing due to its unique phylogenetic position and key importance.

关键词： Genome evolution condition.

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Conserved sequences identify the closest living relatives of primates

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Zoological Research 2019年第6期40卷 532-540页

作者： Mei-Ling Zhang Ming-Li Li Adeola Oluwakemi Ayoola Robert W. Murphy dong-dong wu Yong Shao Department of Acute Infectious Diseases Control and Prevention Yunnan Provincial Centre for Disease Control and PreventionKunming Yunnan 650022China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Centre for Biodiversity and Conservation Biology Royal Ontario MuseumToronto M5S 2C6Canada Kunming College of Life Science University of the Chinese Academy of SciencesKunming Yunnan 650223China

Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.

关键词： Phylogeny Colugos Primates Conserved non-coding elements Divergence time

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Origin of new genes after zygotic genome activation in vertebrate

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Journal of Molecular Cell Biology 2018年第2期10卷 139-146页

作者： Hai-Bo Xu Yong-Xin Li Yan Li Newton O. Otecko Ya-Ping Zhang Bingyu Mao dong-dong wu State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China College of Life Science Anhui University Hefei China Kunming College of Life Science University of Chinese Academy of Sciences Kunming China State Key Laboratory for Conservation and Utilization of Bio-resource Yunnan University Kunming China

New genes are drivers of evolutionary innovation and phenotypic evolution. Expression of new genes in early development raises the possibility that new genes could originate and be recruited for functions in embryonic development, but this remains undocumented. Here, based on temporal gene expression at different developmental stages inXenopus tropicalis, we found that young protein-coding genes were significantly enriched for expression in developmental stages occurring after the midblastula transition (MBT), and displayed a decreasing trend in abundance in the subsequent stages after MBT. To complement the finding, we demonstrate essential functional attributes of a young orphan gene, named asFog2, in morphological development. Our data indicate that new genes could originate after MBT and be recruited for functions in embryonic development, and thus provide insights for better understanding of the origin, evolution, and function of new genes.

关键词：新基因脊椎动物起源染色体激活数据显示编码蛋白质 MBT

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Accelerated evolution of constraint elements for hematophagic adaptation in mosquitoes

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Zoological Research 2015年第6期36卷 320-327页

作者： Ming-Shan WANG Adeniyi C. ADEOLA Yan LI Ya-Ping ZHANG dong-dong wu State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China University of Chinese Academy of Sciences Beijing 100049 China Laboratory for Conservation and Utilization of Bio-resources Yunnan University Kunming 650091 China

Comparative genomics is a powerful approach that comprehensively interprets the genome. Herein, we performed whole genome comparative analysis of 16 Diptera genomes, including four mosquitoes and 12 Drosophilae. We found more than 540 000 constraint elements （CEs） in the Diptera genome, with the majority found in the intergenic, coding and intronic regions. Accelerated elements （AEs） identified in mosquitoes were mostly in the proteincoding regions （〉93%）, which differs from vertebrates in genomic distribution. Some genes functionally enriched in blood digestion, body temperature regulation and insecticide resistance showed rapid evolution not only in the lineage of the recent common ancestor of mosquitoes （RCAM）, but also in some mosquito lineages. This may be associated with lineage-specific traits and/or adaptations in comparison with other insects. Our findings revealed that although universally fast evolution acted on biological systems in RCAM, such as hematophagy, same adaptations also appear to have occurred through distinct degrees of evolution in different mosquito species, enabling them to be successful blood feeders in different environments.

关键词： Mosquitoes Constraint elements Accelerated elements Hematophagy

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