1
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Wang B, Starr AL, Fraser HB. Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells. eLife 2024; 12:RP89594. [PMID: 38358392 PMCID: PMC10942608 DOI: 10.7554/elife.89594] [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] [Indexed: 02/16/2024] Open
Abstract
Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell-type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell-type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells-the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell-type-specific cis-regulatory changes. We find that cell-type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell-type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.
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Affiliation(s)
- Ban Wang
- Department of Biology, Stanford UniversityStanfordUnited States
| | | | - Hunter B Fraser
- Department of Biology, Stanford UniversityStanfordUnited States
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2
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Kautt AF, Chen J, Lewarch CL, Hu C, Turner K, Lassance JM, Baier F, Bedford NL, Bendesky A, Hoekstra HE. Evolution of gene expression across brain regions in behaviourally divergent deer mice. Mol Ecol 2024:e17270. [PMID: 38263608 DOI: 10.1111/mec.17270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/03/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024]
Abstract
The evolution of innate behaviours is ultimately due to genetic variation likely acting in the nervous system. Gene regulation may be particularly important because it can evolve in a modular brain-region specific fashion through the concerted action of cis- and trans-regulatory changes. Here, to investigate transcriptional variation and its regulatory basis across the brain, we perform RNA sequencing (RNA-Seq) on ten brain subregions in two sister species of deer mice (Peromyscus maniculatus and P. polionotus)-which differ in a range of innate behaviours, including their social system-and their F1 hybrids. We find that most of the variation in gene expression distinguishes subregions, followed by species. Interspecific differential expression (DE) is pervasive (52-59% of expressed genes), whereas the number of DE genes between sexes is modest overall (~3%). Interestingly, the identity of DE genes varies considerably across brain regions. Much of this modularity is due to cis-regulatory divergence, and while 43% of genes were consistently assigned to the same gene regulatory class across subregions (e.g. conserved, cis- or trans-regulatory divergence), a similar number were assigned to two or more different gene regulatory classes. Together, these results highlight the modularity of gene expression differences and divergence in the brain, which may be key to explain how the evolution of brain gene expression can contribute to the astonishing diversity of animal behaviours.
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Affiliation(s)
- Andreas F Kautt
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Jenny Chen
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Caitlin L Lewarch
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Caroline Hu
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Kyle Turner
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Jean-Marc Lassance
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Felix Baier
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Nicole L Bedford
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Andres Bendesky
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology, Department of Molecular & Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts, USA
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3
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Louder MIM, Justen H, Kimmitt AA, Lawley KS, Turner LM, Dickman JD, Delmore KE. Gene regulation and speciation in a migratory divide between songbirds. Nat Commun 2024; 15:98. [PMID: 38167733 PMCID: PMC10761872 DOI: 10.1038/s41467-023-44352-2] [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: 04/16/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Behavioral variation abounds in nature. This variation is important for adaptation and speciation, but its molecular basis remains elusive. Here, we use a hybrid zone between two subspecies of songbirds that differ in migration - an ecologically important and taxonomically widespread behavior---to gain insight into this topic. We measure gene expression in five brain regions. Differential expression between migratory states was dominated by circadian genes in all brain regions. The remaining patterns were largely brain-region specific. For example, expression differences between the subspecies that interact with migratory state likely help maintain reproductive isolation in this system and were documented in only three brain regions. Contrary to existing work on regulatory mechanisms underlying species-specific traits, two lines of evidence suggest that trans- (vs. cis) regulatory changes underlie these patterns - no evidence for allele-specific expression in hybrids and minimal associations between genomic differentiation and expression differences. Additional work with hybrids shows expression levels were often distinct (transgressive) from parental forms. Behavioral contrasts and functional enrichment analyses allowed us to connect these patterns to mitonuclear incompatibilities and compensatory responses to stress that could exacerbate selection on hybrids and contribute to speciation.
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Affiliation(s)
| | - Hannah Justen
- Biology Department, Texas A&M University, College Station, TX, USA
| | | | - Koedi S Lawley
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Leslie M Turner
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Bath, UK
| | - J David Dickman
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Kira E Delmore
- Biology Department, Texas A&M University, College Station, TX, USA.
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4
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Herbert AL, Allard CAH, McCoy MJ, Wucherpfennig JI, Krueger SP, Chen HI, Gourlay AN, Jackson KD, Abbo LA, Bennett SH, Sears JD, Rhyne AL, Bellono NW, Kingsley DM. The genetic basis of novel trait gain in walking fish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.562356. [PMID: 37873105 PMCID: PMC10592820 DOI: 10.1101/2023.10.14.562356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A major goal in biology is to understand how organisms evolve novel traits. Multiple studies have identified genes contributing to regressive evolution, the loss of structures that existed in a recent ancestor. However, fewer examples exist for genes underlying constructive evolution, the gain of novel structures and capabilities in lineages that previously lacked them. Sea robins are fish that have evolved enlarged pectoral fins, six mobile locomotory fin rays (legs) and six novel macroscopic lobes in the central nervous system (CNS) that innervate the corresponding legs. Here, we establish successful husbandry and use a combination of transcriptomics, CRISPR-Cas9 editing, and behavioral assays to identify key transcription factors that are required for leg formation and function in sea robins. We also generate hybrids between two sea robin species with distinct leg morphologies and use allele-specific expression analysis and gene editing to explore the genetic basis of species-specific trait diversity, including a novel sensory gain of function. Collectively, our study establishes sea robins as a new model for studying the genetic basis of novel organ formation, and demonstrates a crucial role for the conserved limb gene tbx3a in the evolution of chemosensory legs in walking fish.
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Affiliation(s)
- Amy L Herbert
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Corey AH Allard
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Matthew J McCoy
- Department of Pathology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Julia I Wucherpfennig
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Stephanie P Krueger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | | | - Kohle D Jackson
- Department of Developmental Biology, Stanford University School of Medicine, Stanford CA 94305 USA
| | - Lisa A Abbo
- Marine Biological Laboratory, Woods Hole, MA, 02543 USA
| | | | | | | | - Nicholas W Bellono
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138 USA
| | - David M Kingsley
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford CA 94305 USA
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5
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Mack KL, Talbott HE, Griffin MF, Parker JBL, Guardino NJ, Spielman AF, Davitt MF, Mascharak S, Downer M, Morgan A, Valencia C, Akras D, Berger MJ, Wan DC, Fraser HB, Longaker MT. Allele-specific expression reveals genetic drivers of tissue regeneration in mice. Cell Stem Cell 2023; 30:1368-1381.e6. [PMID: 37714154 PMCID: PMC10592051 DOI: 10.1016/j.stem.2023.08.010] [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: 08/05/2022] [Revised: 06/16/2023] [Accepted: 08/22/2023] [Indexed: 09/17/2023]
Abstract
In adult mammals, skin wounds typically heal by scarring rather than through regeneration. In contrast, "super-healer" Murphy Roths Large (MRL) mice have the unusual ability to regenerate ear punch wounds; however, the molecular basis for this regeneration remains elusive. Here, in hybrid crosses between MRL and non-regenerating mice, we used allele-specific gene expression to identify cis-regulatory variation associated with ear regeneration. Analyzing three major cell populations (immune, fibroblast, and endothelial), we found that genes with cis-regulatory differences specifically in fibroblasts were associated with wound-healing pathways and also co-localized with quantitative trait loci for ear wound-healing. Ectopic treatment with one of these proteins, complement factor H (CFH), accelerated wound repair and induced regeneration in typically fibrotic wounds. Through single-cell RNA sequencing (RNA-seq), we observed that CFH treatment dramatically reduced immune cell recruitment to wounds, suggesting a potential mechanism for CFH's effect. Overall, our results provide insights into the molecular drivers of regeneration with potential clinical implications.
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Affiliation(s)
- Katya L Mack
- Stanford University, Department of Biology, Stanford, CA, USA
| | - Heather E Talbott
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Michelle F Griffin
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Jennifer B L Parker
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Nicholas J Guardino
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Amanda F Spielman
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Michael F Davitt
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Shamik Mascharak
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA
| | - Mauricio Downer
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Annah Morgan
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Caleb Valencia
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Deena Akras
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Mark J Berger
- Stanford University, Department of Computer Science, Stanford, CA 94305, USA
| | - Derrick C Wan
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA
| | - Hunter B Fraser
- Stanford University, Department of Biology, Stanford, CA, USA.
| | - Michael T Longaker
- Stanford School of Medicine, Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford, CA, USA; Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, USA.
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6
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Wang B, Starr AL, Fraser HB. Cell type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541747. [PMID: 37292820 PMCID: PMC10245923 DOI: 10.1101/2023.05.22.541747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although gene expression divergence has long been postulated to be the primary driver of human evolution, identifying the genes and genetic variants underlying uniquely human traits has proven to be quite challenging. Theory suggests that cell type-specific cis-regulatory variants may fuel evolutionary adaptation due to the specificity of their effects. These variants can precisely tune the expression of a single gene in a single cell type, avoiding the potentially deleterious consequences of trans-acting changes and non-cell type-specific changes that can impact many genes and cell types, respectively. It has recently become possible to quantify human-specific cis-acting regulatory divergence by measuring allele-specific expression in human-chimpanzee hybrid cells-the product of fusing induced pluripotent stem (iPS) cells of each species in vitro. However, these cis-regulatory changes have only been explored in a limited number of cell types. Here, we quantify human-chimpanzee cis-regulatory divergence in gene expression and chromatin accessibility across six cell types, enabling the identification of highly cell type-specific cis-regulatory changes. We find that cell type-specific genes and regulatory elements evolve faster than those shared across cell types, suggesting an important role for genes with cell type-specific expression in human evolution. Furthermore, we identify several instances of lineage-specific natural selection that may have played key roles in specific cell types, such as coordinated changes in the cis-regulation of dozens of genes involved in neuronal firing in motor neurons. Finally, using novel metrics and a machine learning model, we identify genetic variants that likely alter chromatin accessibility and transcription factor binding, leading to neuron-specific changes in the expression of the neurodevelopmentally important genes FABP7 and GAD1. Overall, our results demonstrate that integrative analysis of cis-regulatory divergence in chromatin accessibility and gene expression across cell types is a promising approach to identify the specific genes and genetic variants that make us human.
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Affiliation(s)
- Ban Wang
- Department of Biology, Stanford University, Stanford, CA, USA
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7
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Starr AL, Gokhman D, Fraser HB. Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits. Genome Biol 2023; 24:11. [PMID: 36658652 PMCID: PMC9850818 DOI: 10.1186/s13059-023-02846-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
Measuring allele-specific expression in interspecies hybrids is a powerful way to detect cis-regulatory changes underlying adaptation. However, it remains difficult to identify genes most likely to explain species-specific traits. Here, we outline a simple strategy that leverages population-scale allele-specific RNA-seq data to identify genes that show constrained cis-regulation within species yet show divergence between species. Applying this strategy to data from human-chimpanzee hybrid cortical organoids, we identify signatures of lineage-specific selection on genes related to saccharide metabolism, neurodegeneration, and primary cilia. We also highlight cis-regulatory divergence in CUX1 and EDNRB that may shape the trajectory of human brain development.
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Affiliation(s)
| | - David Gokhman
- Department of Biology, Stanford University, Stanford, CA, USA
- Present Address: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hunter B Fraser
- Department of Biology, Stanford University, Stanford, CA, USA.
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8
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Abstract
The question of the heritability of behavior has been of long fascination to scientists and the broader public. It is now widely accepted that most behavioral variation has a genetic component, although the degree of genetic influence differs widely across behaviors. Starting with Mendel's remarkable discovery of "inheritance factors," it has become increasingly clear that specific genetic variants that influence behavior can be identified. This goal is not without its challenges: Unlike pea morphology, most natural behavioral variation has a complex genetic architecture. However, we can now apply powerful genome-wide approaches to connect variation in DNA to variation in behavior as well as analyses of behaviorally related variation in brain gene expression, which together have provided insights into both the genetic mechanisms underlying behavior and the dynamic relationship between genes and behavior, respectively, in a wide range of species and for a diversity of behaviors. Here, we focus on two systems to illustrate both of these approaches: the genetic basis of burrowing in deer mice and transcriptomic analyses of division of labor in honey bees. Finally, we discuss the troubled relationship between the field of behavioral genetics and eugenics, which reminds us that we must be cautious about how we discuss and contextualize the connections between genes and behavior, especially in humans.
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Affiliation(s)
- Hopi E. Hoekstra
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
- HHMI, Harvard University, Cambridge, MA 02138
| | - Gene E. Robinson
- Department of Entomology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Neuroscience Program, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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9
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Burrowing deeper to uncover the genetic architecture of behavioral evolution. Cell Rep 2022; 38:110378. [PMID: 35172144 DOI: 10.1016/j.celrep.2022.110378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Allele-specific expression analysis of hybrid mice provides new insights into the genetic substrates of behavioral evolution. As a complement to QTL mapping, this approach, described by Hu et al. in this issue of Cell Reports, holds promise for identifying causative regulatory loci that influence species-specific behavior.
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