1
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Gopalan SS, Perry BW, Francioli YZ, Schield DR, Guss HD, Bernstein JM, Ballard K, Smith CF, Saviola AJ, Adams RH, Mackessy SP, Castoe TA. Diverse Gene Regulatory Mechanisms Alter Rattlesnake Venom Gene Expression at Fine Evolutionary Scales. Genome Biol Evol 2024; 16:evae110. [PMID: 38753011 PMCID: PMC11243404 DOI: 10.1093/gbe/evae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2024] [Indexed: 07/13/2024] Open
Abstract
Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole-genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation.
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Affiliation(s)
- Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yannick Z Francioli
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Drew R Schield
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Hannah D Guss
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Justin M Bernstein
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Kaas Ballard
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Cara F Smith
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Richard H Adams
- Department of Entomology and Plant Pathology, University of Arkansas Agricultural Experimental Station, University of Arkansas, Fayetteville, AR 72701, USA
| | - Stephen P Mackessy
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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2
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Zhao H, Liu LL, Sun J, Jin L, Xie HB, Li JB, Xu H, Wu DD, Zhuang XL, Peng MS, Guo YJ, Qian WZ, Otecko NO, Sun WJ, Qu LH, He J, Chen ZL, Liu R, Chen CS, Zhang YP. A human-specific insertion promotes cell proliferation and migration by enhancing TBC1D8B expression. SCIENCE CHINA. LIFE SCIENCES 2024; 67:765-777. [PMID: 38110796 DOI: 10.1007/s11427-023-2442-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/28/2023] [Indexed: 12/20/2023]
Abstract
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.
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Affiliation(s)
- Hui Zhao
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
| | - Lin-Lin Liu
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Jian Sun
- The Third Affiliated Hospital, Kunming Medical University, Kunming, 650118, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian Jin
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Hai-Bing Xie
- 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, 650201, China
| | - Jian-Bo Li
- 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, 650201, China
| | - Hui Xu
- The Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Dong-Dong Wu
- 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, 650201, China
| | - Xiao-Lin Zhuang
- 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, 650201, China
| | - Min-Sheng Peng
- 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, 650201, China
| | - Ya-Jun Guo
- National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering and Antibody, Shanghai, 201203, China
| | - Wei-Zhu Qian
- National Engineering Research Center for Antibody Medicine and Shanghai Key Laboratory of Cell Engineering and Antibody, Shanghai, 201203, China
| | - Newton O Otecko
- 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, 650201, China
| | - Wei-Jie Sun
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Liang-Hu Qu
- The Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jie He
- Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhao-Li Chen
- Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Rong Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ce-Shi Chen
- Academy of Biomedical Engineering, Kunming Medical University, Kunming, 650500, China.
- The Third Affiliated Hospital, Kunming Medical University, Kunming, 650118, China.
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resource, School of Life Sciences, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
- 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, 650201, China.
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3
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Zintel TM, Pizzollo J, Claypool CG, Babbitt CC. Astrocytes Drive Divergent Metabolic Gene Expression in Humans and Chimpanzees. Genome Biol Evol 2024; 16:evad239. [PMID: 38159045 PMCID: PMC10829071 DOI: 10.1093/gbe/evad239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 11/13/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024] Open
Abstract
The human brain utilizes ∼20% of all of the body's metabolic resources, while chimpanzee brains use <10%. Although previous work shows significant differences in metabolic gene expression between the brains of primates, we have yet to fully resolve the contribution of distinct brain cell types. To investigate cell type-specific interspecies differences in brain gene expression, we conducted RNA-seq on neural progenitor cells, neurons, and astrocytes generated from induced pluripotent stem cells from humans and chimpanzees. Interspecies differential expression analyses revealed that twice as many genes exhibit differential expression in astrocytes (12.2% of all genes expressed) than neurons (5.8%). Pathway enrichment analyses determined that astrocytes, rather than neurons, diverged in expression of glucose and lactate transmembrane transport, as well as pyruvate processing and oxidative phosphorylation. These findings suggest that astrocytes may have contributed significantly to the evolution of greater brain glucose metabolism with proximity to humans.
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Affiliation(s)
- Trisha M Zintel
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Jason Pizzollo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christopher G Claypool
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
| | - Courtney C Babbitt
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA, USA
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4
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Devens HR, Davidson PL, Byrne M, Wray GA. Hybrid Epigenomes Reveal Extensive Local Genetic Changes to Chromatin Accessibility Contribute to Divergence in Embryonic Gene Expression Between Species. Mol Biol Evol 2023; 40:msad222. [PMID: 37823438 PMCID: PMC10638671 DOI: 10.1093/molbev/msad222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/14/2023] [Accepted: 07/27/2023] [Indexed: 10/13/2023] Open
Abstract
Chromatin accessibility plays an important role in shaping gene expression, yet little is known about the genetic and molecular mechanisms that influence the evolution of chromatin configuration. Both local (cis) and distant (trans) genetic influences can in principle influence chromatin accessibility and are based on distinct molecular mechanisms. We, therefore, sought to characterize the role that each of these plays in altering chromatin accessibility in 2 closely related sea urchin species. Using hybrids of Heliocidaris erythrogramma and Heliocidaris tuberculata, and adapting a statistical framework previously developed for the analysis of cis and trans influences on the transcriptome, we examined how these mechanisms shape the regulatory landscape at 3 important developmental stages, and compared our results to similar analyses of the transcriptome. We found extensive cis- and trans-based influences on evolutionary changes in chromatin, with cis effects generally larger in effect. Evolutionary changes in accessibility and gene expression are correlated, especially when expression has a local genetic basis. Maternal influences appear to have more of an effect on chromatin accessibility than on gene expression, persisting well past the maternal-to-zygotic transition. Chromatin accessibility near gene regulatory network genes appears to be distinctly regulated, with trans factors appearing to play an outsized role in the configuration of chromatin near these genes. Together, our results represent the first attempt to quantify cis and trans influences on evolutionary divergence in chromatin configuration in an outbred natural study system and suggest that chromatin regulation is more genetically complex than was previously appreciated.
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Affiliation(s)
| | | | - Maria Byrne
- School of Medical Science, The University of Sydney, Sydney, New South Wales, Australia
- School of Life and Environmental Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Gregory A Wray
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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5
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Barr KA, Rhodes KL, Gilad Y. The relationship between regulatory changes in cis and trans and the evolution of gene expression in humans and chimpanzees. Genome Biol 2023; 24:207. [PMID: 37697401 PMCID: PMC10496171 DOI: 10.1186/s13059-023-03019-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 07/21/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Comparative gene expression studies in apes are fundamentally limited by the challenges associated with sampling across different tissues. Here, we used single-cell RNA sequencing of embryoid bodies to collect transcriptomic data from over 70 cell types in three humans and three chimpanzees. RESULTS We find hundreds of genes whose regulation is conserved across cell types, as well as genes whose regulation likely evolves under directional selection in one or a handful of cell types. Using embryoid bodies from a human-chimpanzee fused cell line, we also infer the proportion of inter-species regulatory differences due to changes in cis and trans elements between the species. Using the cis/trans inference and an analysis of transcription factor binding sites, we identify dozens of transcription factors whose inter-species differences in expression are affecting expression differences between humans and chimpanzees in hundreds of target genes. CONCLUSIONS Here, we present the most comprehensive dataset of comparative gene expression from humans and chimpanzees to date, including a catalog of regulatory mechanisms associated with inter-species differences.
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Affiliation(s)
- Kenneth A Barr
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | | | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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6
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Fair T, Pollen AA. Genetic architecture of human brain evolution. Curr Opin Neurobiol 2023; 80:102710. [PMID: 37003107 DOI: 10.1016/j.conb.2023.102710] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/20/2023] [Accepted: 02/26/2023] [Indexed: 04/03/2023]
Abstract
Comparative studies of hominids have long sought to identify mutational events that shaped the evolution of the human nervous system. However, functional genetic differences are outnumbered by millions of nearly neutral mutations, and the developmental mechanisms underlying human nervous system specializations are difficult to model and incompletely understood. Candidate-gene studies have attempted to map select human-specific genetic differences to neurodevelopmental functions, but it remains unclear how to contextualize the relative effects of genes that are investigated independently. Considering these limitations, we discuss scalable approaches for probing the functional contributions of human-specific genetic differences. We propose that a systems-level view will enable a more quantitative and integrative understanding of the genetic, molecular and cellular underpinnings of human nervous system evolution.
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Affiliation(s)
- Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA. https://twitter.com/@TylerFair_
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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7
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Devens HR, Davidson PL, Byrne M, Wray GA. Hybrid epigenomes reveal extensive local genetic changes to chromatin accessibility contribute to divergence in embryonic gene expression between species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522781. [PMID: 36711588 PMCID: PMC9881966 DOI: 10.1101/2023.01.04.522781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chromatin accessibility plays an important role in shaping gene expression patterns across development and evolution; however, little is known about the genetic and molecular mechanisms that influence chromatin configuration itself. Because cis and trans influences can both theoretically influence the accessibility of the epigenome, we sought to better characterize the role that both of these mechanisms play in altering chromatin accessibility in two closely related sea urchin species. Using hybrids of the two species, and adapting a statistical framework previously developed for the analysis of cis and trans influences on the transcriptome, we examined how these mechanisms shape the regulatory landscape at three important developmental stages, and compared our results to similar patterns in the transcriptome. We found extensive cis- and trans-based influences on evolutionary changes in chromatin, with cis effects slightly more numerous and larger in effect. Genetic mechanisms influencing gene expression and chromatin configuration are correlated, but differ in several important ways. Maternal influences also appear to have more of an effect on chromatin accessibility than on gene expression, persisting well past the maternal-to-zygotic transition. Furthermore, chromatin accessibility near GRN genes appears to be regulated differently than the rest of the epigenome, and indicates that trans factors may play an outsized role in the configuration of chromatin near these genes. Together, our results represent the first attempt to quantify cis and trans influences on evolutionary divergence in chromatin configuration in an outbred natural study system, and suggest that the regulation of chromatin is more genetically complex than was previously appreciated.
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Affiliation(s)
| | | | - Maria Byrne
- School of Medical Science, The University of Sydney, NSW 2006, Australia
- School of Life and Environmental Science, The University of Sydney, NSW 2006, Australia
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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8
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Fraser HB. Existing methods are effective at measuring natural selection on gene expression. Nat Ecol Evol 2022; 6:1836-1837. [PMID: 36344679 DOI: 10.1038/s41559-022-01889-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
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9
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Davidson PL, Byrne M, Wray GA. Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins. Mol Biol Evol 2022; 39:6659243. [PMID: 35946348 PMCID: PMC9435058 DOI: 10.1093/molbev/msac172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin configuration to the evolution of gene expression and organismal traits. Genome-wide assays of chromatin configuration, coupled with whole-genome alignments, can help address this gap in knowledge in several ways. In this study we present a comparative analysis of regulatory element sequences and accessibility throughout embryogenesis in three sea urchin species with divergent life histories: a lecithotroph Heliocidaris erythrogramma, a closely related planktotroph H. tuberculata, and a distantly related planktotroph Lytechinus variegatus. We identified distinct epigenetic and mutational signatures of evolutionary modifications to the function of putative cis-regulatory elements in H. erythrogramma that have accumulated nonuniformly throughout the genome, suggesting selection, rather than drift, underlies many modifications associated with the derived life history. Specifically, regulatory elements composing the sea urchin developmental gene regulatory network are enriched for signatures of positive selection and accessibility changes which may function to alter binding affinity and access of developmental transcription factors to these sites. Furthermore, regulatory element changes often correlate with divergent expression patterns of genes involved in cell type specification, morphogenesis, and development of other derived traits, suggesting these evolutionary modifications have been consequential for phenotypic evolution in H. erythrogramma. Collectively, our results demonstrate that selective pressures imposed by changes in developmental life history rapidly reshape the cis-regulatory landscape of core developmental genes to generate novel traits and embryonic programs.
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Affiliation(s)
| | - Maria Byrne
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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10
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Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. Nat Genet 2021; 53:467-476. [PMID: 33731941 PMCID: PMC8038968 DOI: 10.1038/s41588-021-00804-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023]
Abstract
Gene regulatory divergence is thought to play a central role in determining human-specific traits. However, our ability to link divergent regulation to divergent phenotypes is limited. Here, we utilized human-chimpanzee hybrid induced pluripotent stem cells to study gene expression separating these species. The tetraploid hybrid cells allowed us to separate cis- from trans-regulatory effects, and to control for non-genetic confounding factors. We differentiated these cells into cranial neural crest cells (CNCCs), the primary cell type giving rise to the face. We discovered evidence of lineage-specific selection on the hedgehog signaling pathway, including a human-specific 6-fold down-regulation of EVC2 (LIMBIN), a key hedgehog gene. Inducing a similar down-regulation of EVC2 substantially reduced hedgehog signaling output. Mice and humans lacking functional EVC2 show striking phenotypic parallels to human-chimpanzee craniofacial differences, suggesting that the regulatory divergence of hedgehog signaling may have contributed to the unique craniofacial morphology of humans.
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11
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Doncheva NT, Palasca O, Yarani R, Litman T, Anthon C, Groenen MAM, Stadler PF, Pociot F, Jensen LJ, Gorodkin J. Human pathways in animal models: possibilities and limitations. Nucleic Acids Res 2021; 49:1859-1871. [PMID: 33524155 PMCID: PMC7913694 DOI: 10.1093/nar/gkab012] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/08/2020] [Accepted: 01/07/2021] [Indexed: 12/20/2022] Open
Abstract
Animal models are crucial for advancing our knowledge about the molecular pathways involved in human diseases. However, it remains unclear to what extent tissue expression of pathways in healthy individuals is conserved between species. In addition, organism-specific information on pathways in animal models is often lacking. Within these limitations, we explore the possibilities that arise from publicly available data for the animal models mouse, rat, and pig. We approximate the animal pathways activity by integrating the human counterparts of curated pathways with tissue expression data from the models. Specifically, we compare whether the animal orthologs of the human genes are expressed in the same tissue. This is complicated by the lower coverage and worse quality of data in rat and pig as compared to mouse. Despite that, from 203 human KEGG pathways and the seven tissues with best experimental coverage, we identify 95 distinct pathways, for which the tissue expression in one animal model agrees better with human than the others. Our systematic pathway-tissue comparison between human and three animal modes points to specific similarities with human and to distinct differences among the animal models, thereby suggesting the most suitable organism for modeling a human pathway or tissue.
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Affiliation(s)
- Nadezhda T Doncheva
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 1871 Frederiksberg, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Oana Palasca
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 1871 Frederiksberg, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Reza Yarani
- Translational Type 1 Diabetes Research, Steno Diabetes Center Copenhagen, 2820 Gentofte, Denmark
| | - Thomas Litman
- Department of Immunology and Microbiology, University of Copenhagen, 2200 Copenhagen, Denmark.,Exploratory Biology, LEO Pharma A/S, 2750 Ballerup, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 1871 Frederiksberg, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, 6700 Wageningen, The Netherlands
| | - Peter F Stadler
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 1871 Frederiksberg, Denmark.,Bioinformatics Group, Department of Computer Science; Interdisciplinary Center for Bioinformatics; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Competence Center for Scalable Data Services and Solutions Dresden-Leipzig; Leipzig Research Center for Civilization Diseases; and Centre for Biotechnology and Biomedicine, University of Leipzig, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany.,Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá D.C., Colombia.,The Santa Fe Institute, 87501 Santa Fe, NM, USA
| | - Flemming Pociot
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 1871 Frederiksberg, Denmark.,Translational Type 1 Diabetes Research, Steno Diabetes Center Copenhagen, 2820 Gentofte, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lars J Jensen
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 1871 Frederiksberg, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, University of Copenhagen, 1871 Frederiksberg, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
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12
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Xie W, Du Z, Chen Y, Liu N, Zhong Z, Shen Y, Tang L. Identification of Metastasis-Associated Genes in Triple-Negative Breast Cancer Using Weighted Gene Co-expression Network Analysis. Evol Bioinform Online 2020; 16:1176934320954868. [PMID: 32952395 PMCID: PMC7476344 DOI: 10.1177/1176934320954868] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/10/2020] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive and fatal sub-type of breast cancer. This study aimed to identify metastasis-associated genes that could serve as biomarkers for TNBC diagnosis and prognosis. RNA-seq data and clinical information on TNBC from the Cancer Genome Atlas were used to conduct analyses. Expression data were used to establish co-expression modules using average linkage hierarchical clustering. We used weighted gene co-expression network analysis to explore the associations between gene sets and clinical features and to identify metastasis-associated candidate biomarkers. The K-M plotter website was used to explore the association between the expression of candidate biomarkers and patient survival. In addition, receiver operating characteristic curve analysis was used to illustrate the diagnostic performance of candidate genes. The pale turquoise module was significantly associated with the occurrence of metastasis. In this module, 64 genes were identified, and its functional enrichment analysis revealed that they were mainly associated with transcriptional misregulation in cancer, microRNAs in cancer, and negative regulation of angiogenesis. Further, 4 genes, IGSF10, RUNX1T1, XIST, and TSHZ2, which were negatively associated with relapse-free survival and have seldom been reported before in TNBC, were selected. In addition, the mRNA expression levels of the 4 candidate genes were significantly lower in TNBC tumor tissues compared with healthy tissues. Based on the K-M plotter, these 4 genes were correlated with poor prognosis of TNBC. The area under the curve of IGSF10, RUNX1T1, TSHZ2, and XIST was 0.918, 0.957, 0.977, and 0.749. These findings provide new insight into TNBC metastasis. IGSF10, RUNX1T1, TSHZ2, and XIST could be used as candidate biomarkers for the diagnosis and prognosis of TNBC metastasis.
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Affiliation(s)
- Wenting Xie
- Department of Ultrasound, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fujian Province, China
| | - Zhongshi Du
- Department of Ultrasound, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fujian Province, China
| | - Yijie Chen
- Department of Ultrasound, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fujian Province, China
| | - Naxiang Liu
- Department of Ultrasound, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fujian Province, China
| | - Zhaoming Zhong
- Department of Ultrasound, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fujian Province, China
| | - Youhong Shen
- Department of Ultrasound, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fujian Province, China
| | - Lina Tang
- Department of Ultrasound, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fujian Province, China
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13
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Qu Y, Chen Y, Zhang L, Tian L. Construction of prognostic predictor by comprehensive analyzing alternative splicing events for colon adenocarcinoma. World J Surg Oncol 2020; 18:236. [PMID: 32883335 PMCID: PMC7650263 DOI: 10.1186/s12957-020-02010-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/24/2020] [Indexed: 02/08/2023] Open
Abstract
Background Colon adenocarcinoma (COAD) is one of the most common malignant tumors, with high incidence and mortality rates worldwide. Reliable prognostic biomarkers are needed to guide clinical practice. Methods Comprehensive gene expression with alternative splicing (AS) profiles for each patient was downloaded using the SpliceSeq database from The Cancer Genome Atlas. Cox regression analysis was conducted to screen for prognostic AS events. The R package limma was used to screen differentially expressed genes (DEGs) between normal and tumor samples in the COAD cohort. A Venn plot analysis was performed between DEGs and prognostic AS events, and the DEGs that co-occurred with prognostic AS events (DEGAS) were identified. The top 30 most-connected DEGAS in protein–protein interaction analysis were identified through Cox proportional hazards regression to establish prognostic models. Results In total, 350 patients were included in the study. A total of 22,451 AS events were detected, of which 2004 from 1439 genes were significantly associated with survival time. By overlapping these 1439 genes with 6455 DEGs, 211 DEGs with AS events were identified. After the construction of the protein–protein interaction network, the top 30 hub genes were included in a multivariate analysis. Finally, a risk score based on 12 genes associated with overall survival was established (P < 0.05). The area under the curve was 0.782. The risk score was an independent predictor (P < 0.001). Conclusions By exploring survival-associated AS events, a powerful prognostic predictor consisting of 12 DEGAS was built. This study aims to propose a novel method to provide treatment targets for COAD and guide clinical practice in the future.
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Affiliation(s)
- Yaqi Qu
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - Yujia Chen
- School of Basic Medical Sciences, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Le Zhang
- Department of Function, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Lifei Tian
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China.
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Housman G, Gilad Y. Prime time for primate functional genomics. Curr Opin Genet Dev 2020; 62:1-7. [PMID: 32544775 DOI: 10.1016/j.gde.2020.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Functional genomics research is continually improving our understanding of genotype-phenotype relationships in humans, and comparative genomics perspectives can provide additional insight into the evolutionary histories of such relationships. To specifically identify conservation or species-specific divergence in humans, we must look to our closest extant evolutionary relatives. Primate functional genomics research has been steadily advancing and expanding, in spite of several limitations and challenges that this field faces. New technologies and cheaper sequencing provide a unique opportunity to enhance and expand primate comparative studies, and we outline possible paths going forward. The potential human-specific insights that can be gained from primate functional genomics research are substantial, and we propose that now is a prime time to expand such endeavors.
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Affiliation(s)
- Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA.
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA; Department of Human Genetics, University of Chicago, Cummings Life Science Center, 928 E. 58th St., Chicago, IL 60637 USA
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15
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Edsall LE, Berrio A, Majoros WH, Swain-Lenz D, Morrow S, Shibata Y, Safi A, Wray GA, Crawford GE, Allen AS. Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach. Genome Biol Evol 2019; 11:3035-3053. [PMID: 31599933 PMCID: PMC6821351 DOI: 10.1093/gbe/evz218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
Changes in transcriptional regulation are thought to be a major contributor to the evolution of phenotypic traits, but the contribution of changes in chromatin accessibility to the evolution of gene expression remains almost entirely unknown. To address this important gap in knowledge, we developed a new method to identify DNase I Hypersensitive (DHS) sites with differential chromatin accessibility between species using a joint modeling approach. Our method overcomes several limitations inherent to conventional threshold-based pairwise comparisons that become increasingly apparent as the number of species analyzed rises. Our approach employs a single quantitative test which is more sensitive than existing pairwise methods. To illustrate, we applied our joint approach to DHS sites in fibroblast cells from five primates (human, chimpanzee, gorilla, orangutan, and rhesus macaque). We identified 89,744 DHS sites, of which 41% are identified as differential between species using the joint model compared with 33% using the conventional pairwise approach. The joint model provides a principled approach to distinguishing single from multiple chromatin accessibility changes among species. We found that nondifferential DHS sites are enriched for nucleotide conservation. Differential DHS sites with decreased chromatin accessibility relative to rhesus macaque occur more commonly near transcription start sites (TSS), while those with increased chromatin accessibility occur more commonly distal to TSS. Further, differential DHS sites near TSS are less cell type-specific than more distal regulatory elements. Taken together, these results point to distinct classes of DHS sites, each with distinct characteristics of selection, genomic location, and cell type specificity.
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Affiliation(s)
- Lee E Edsall
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
- University Program in Genetics and Genomics, Duke University
| | | | | | | | | | - Yoichiro Shibata
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Alexias Safi
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Gregory A Wray
- Center for Genomic and Computational Biology, Duke University
- Department of Biology, Duke University
| | - Gregory E Crawford
- Center for Genomic and Computational Biology, Duke University
- Division of Medical Genetics, Department of Pediatrics, Duke University
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University
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16
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Ward MC, Gilad Y. A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees. eLife 2019; 8:42374. [PMID: 30958265 PMCID: PMC6538380 DOI: 10.7554/elife.42374] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/07/2019] [Indexed: 12/23/2022] Open
Abstract
Despite anatomical similarities, there are differences in susceptibility to cardiovascular disease (CVD) between primates; humans are prone to myocardial ischemia, while chimpanzees are prone to myocardial fibrosis. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) allow for direct inter-species comparisons of the gene regulatory response to CVD-relevant perturbations such as oxygen deprivation, a consequence of ischemia. To gain insight into the evolution of disease susceptibility, we characterized gene expression levels in iPSC-CMs in humans and chimpanzees, before and after hypoxia and re-oxygenation. The transcriptional response to hypoxia is generally conserved across species, yet we were able to identify hundreds of species-specific regulatory responses including in genes previously associated with CVD. The 1,920 genes that respond to hypoxia in both species are enriched for loss-of-function intolerant genes; but are depleted for expression quantitative trait loci and cardiovascular-related genes. Our results indicate that response to hypoxic stress is highly conserved in humans and chimpanzees.
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Affiliation(s)
- Michelle C Ward
- Department of Medicine, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
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