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Boyboy BAG, Ichiyanagi K. Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse. Mob DNA 2024; 15:11. [PMID: 38730323 PMCID: PMC11084082 DOI: 10.1186/s13100-024-00321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Gene expression divergence between populations and between individuals can emerge from genetic variations within the genes and/or in the cis regulatory elements. Since epigenetic modifications regulate gene expression, it is conceivable that epigenetic variations in cis regulatory elements can also be a source of gene expression divergence. RESULTS In this study, we compared histone acetylation (namely, H3K9ac) profiles in two mouse strains of different subspecies origin, C57BL/6 J (B6) and MSM/Ms (MSM), as well as their F1 hybrids. This identified 319 regions of strain-specific acetylation, about half of which were observed between the alleles of F1 hybrids. While the allele-specific presence of the interferon regulatory factor 3 (IRF3) binding sequence was associated with allele-specific histone acetylation, we also revealed that B6-specific insertions of a short 3' fragment of LINE-1 (L1) retrotransposon occur within or proximal to MSM-specific acetylated regions. Furthermore, even in hyperacetylated domains, flanking regions of non-polymorphic 3' L1 fragments were hypoacetylated, suggesting a general activity of the 3' L1 fragment to induce hypoacetylation. Indeed, we confirmed the binding of the 3' region of L1 by three Krüppel-associated box domain-containing zinc finger proteins (KZFPs), which interact with histone deacetylases. These results suggest that even a short insertion of L1 would be excluded from gene- and acetylation-rich regions by natural selection. Finally, mRNA-seq analysis for F1 hybrids was carried out, which disclosed a link between allele-specific promoter/enhancer acetylation and gene expression. CONCLUSIONS This study disclosed a number of genetic changes that have changed the histone acetylation levels during the evolution of mouse subspecies, a part of which is associated with gene expression changes. Insertions of even a very short L1 fragment can decrease the acetylation level in their neighboring regions and thereby have been counter-selected in gene-rich regions, which may explain a long-standing mystery of discrete genomic distribution of LINEs and SINEs.
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Affiliation(s)
- Beverly Ann G Boyboy
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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2
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Hansen TJ, Fong SL, Day JK, Capra JA, Hodges E. Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans. Cell Genom 2024; 4:100536. [PMID: 38604126 PMCID: PMC11019363 DOI: 10.1016/j.xgen.2024.100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/03/2024] [Accepted: 03/10/2024] [Indexed: 04/13/2024]
Abstract
Gene regulatory divergence between species can result from cis-acting local changes to regulatory element DNA sequences or global trans-acting changes to the regulatory environment. Understanding how these mechanisms drive regulatory evolution has been limited by challenges in identifying trans-acting changes. We present a comprehensive approach to directly identify cis- and trans-divergent regulatory elements between human and rhesus macaque lymphoblastoid cells using assay for transposase-accessible chromatin coupled to self-transcribing active regulatory region (ATAC-STARR) sequencing. In addition to thousands of cis changes, we discover an unexpected number (∼10,000) of trans changes and show that cis and trans elements exhibit distinct patterns of sequence divergence and function. We further identify differentially expressed transcription factors that underlie ∼37% of trans differences and trace how cis changes can produce cascades of trans changes. Overall, we find that most divergent elements (67%) experienced changes in both cis and trans, revealing a substantial role for trans divergence-alone and together with cis changes-in regulatory differences between species.
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Affiliation(s)
- Tyler J Hansen
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Sarah L Fong
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jessica K Day
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John A Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143, USA.
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Nashville, TN 37232, USA.
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3
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Panten J, Heinen T, Ernst C, Eling N, Wagner RE, Satorius M, Marioni JC, Stegle O, Odom DT. The dynamic genetic determinants of increased transcriptional divergence in spermatids. Nat Commun 2024; 15:1272. [PMID: 38341412 PMCID: PMC10858866 DOI: 10.1038/s41467-024-45133-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation. Collectively, almost half of the genes subject to genetic regulation show evidence for dynamic cis-effects that vary during differentiation. Our system also allows us to robustly identify dynamic trans-effects, which are less pervasive than cis-effects. In aggregate, genetic effects were strongest in round spermatids, which parallels their increased transcriptional divergence we identified between species. Our approach provides a comprehensive quantification of the variability of genetic effects in vivo, and demonstrates a widely applicable strategy to dissect the impact of regulatory variants on gene regulation in dynamic systems.
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Affiliation(s)
- Jasper Panten
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - Tobias Heinen
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Mathematics and Computer Science, Heidelberg University, Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Christina Ernst
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Nils Eling
- University of Zurich, Department of Quantitative Biomedicine, Zurich, 8057, Switzerland
- ETH Zurich, Institute for Molecular Health Sciences, Zurich, 8093, Switzerland
| | - Rebecca E Wagner
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
- Division of Mechanisms Regulating Gene Expression, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Maja Satorius
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Oliver Stegle
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- European Molecular Biology Laboratory, Genome Biology Unit, 69117, Heidelberg, Germany.
| | - Duncan T Odom
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany.
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
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4
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Durkin SM, Ballinger MA, Nachman MW. Tissue-specific and cis-regulatory changes underlie parallel, adaptive gene expression evolution in house mice. PLoS Genet 2024; 20:e1010892. [PMID: 38306396 PMCID: PMC10866503 DOI: 10.1371/journal.pgen.1010892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/14/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Changes in gene regulation have long been appreciated as a driving force of adaptive evolution, however the relative contributions of cis- and trans-acting changes to gene regulation over short evolutionary timescales remain unclear. Instances of recent, parallel phenotypic evolution provide an opportunity to assess whether parallel patterns are seen at the level of gene expression, and to assess the relative contribution of cis- and trans- changes to gene regulation in the early stages of divergence. Here, we studied gene expression in liver and brown adipose tissue in two wild-derived strains of house mice that independently adapted to cold, northern environments, and we compared them to a strain of house mice from a warm, tropical environment. To investigate gene regulatory evolution, we studied expression in parents and allele-specific expression in F1 hybrids of crosses between warm-adapted and cold-adapted strains. First, we found that the different cold-adapted mice showed both unique and shared changes in expression, but that the proportion of shared changes (i.e. parallelism) was greater than expected by chance. Second, we discovered that expression evolution occurred largely at tissue-specific and cis-regulated genes, and that these genes were over-represented in parallel cases of evolution. Finally, we integrated the expression data with scans for selection in natural populations and found substantial parallelism in the two northern populations for genes under selection. Furthermore, selection outliers were associated with cis-regulated genes more than expected by chance; cis-regulated genes under selection influenced phenotypes such as body size, immune functioning, and activity level. These results demonstrate that parallel patterns of gene expression in mice that have independently adapted to cold environments are driven largely by tissue-specific and cis-regulatory changes, providing insight into the mechanisms of adaptive gene regulatory evolution at the earliest stages of divergence.
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Affiliation(s)
- Sylvia M. Durkin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mallory A. Ballinger
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael W. Nachman
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
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5
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Yoo MJ, Koh J, Boatwright JL, Soltis DE, Soltis PS, Barbazuk WB, Chen S. Investigation of regulatory divergence between homoeologs in the recently formed allopolyploids, Tragopogon mirus and T. miscellus (Asteraceae). Plant J 2024; 117:1191-1205. [PMID: 37997015 DOI: 10.1111/tpj.16553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/02/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023]
Abstract
Polyploidy is an important evolutionary process throughout eukaryotes, particularly in flowering plants. Duplicated gene pairs (homoeologs) in allopolyploids provide additional genetic resources for changes in molecular, biochemical, and physiological mechanisms that result in evolutionary novelty. Therefore, understanding how divergent genomes and their regulatory networks reconcile is vital for unraveling the role of polyploidy in plant evolution. Here, we compared the leaf transcriptomes of recently formed natural allotetraploids (Tragopogon mirus and T. miscellus) and their diploid parents (T. porrifolius X T. dubius and T. pratensis X T. dubius, respectively). Analysis of 35 400 expressed loci showed a significantly higher level of transcriptomic additivity compared to old polyploids; only 22% were non-additively expressed in the polyploids, with 5.9% exhibiting transgressive expression (lower or higher expression in the polyploids than in the diploid parents). Among approximately 7400 common orthologous regions (COREs), most loci in both allopolyploids exhibited expression patterns that were vertically inherited from their diploid parents. However, 18% and 20.3% of the loci showed novel expression bias patterns in T. mirus and T. miscellus, respectively. The expression changes of 1500 COREs were explained by cis-regulatory divergence (the condition in which the two parental subgenomes do not interact) between the diploid parents, whereas only about 423 and 461 of the gene expression changes represent trans-effects (the two parental subgenomes interact) in T. mirus and T. miscellus, respectively. The low degree of both non-additivity and trans-effects on gene expression may present the ongoing evolutionary processes of the newly formed Tragopogon polyploids (~80-90 years).
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Affiliation(s)
- Mi-Jeong Yoo
- Department of Biology, Clarkson University, Potsdam, New York, 13699, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, 32610, USA
| | - J Lucas Boatwright
- Plant and Environmental Science Department, Clemson University, Clemson, South Carolina, 29634, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Genetics Institute, University of Florida, Gainesville, Florida, 32610, USA
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, Mississippi, 38677, USA
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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Tsouris A, Brach G, Schacherer J, Hou J. Non-additive genetic components contribute significantly to population-wide gene expression variation. Cell Genom 2024; 4:100459. [PMID: 38190102 PMCID: PMC10794783 DOI: 10.1016/j.xgen.2023.100459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/19/2023] [Accepted: 11/09/2023] [Indexed: 01/09/2024]
Abstract
Gene expression variation, an essential step between genotype and phenotype, is collectively controlled by local (cis) and distant (trans) regulatory changes. Nevertheless, how these regulatory elements differentially influence gene expression variation remains unclear. Here, we bridge this gap by analyzing the transcriptomes of a large diallel panel consisting of 323 unique hybrids originating from genetically divergent Saccharomyces cerevisiae isolates. Our analysis across 5,087 transcript abundance traits showed that non-additive components account for 36% of the gene expression variance on average. By comparing allele-specific read counts in parent-hybrid trios, we found that trans-regulatory changes underlie the majority of gene expression variation in the population. Remarkably, most cis-regulatory variations are also exaggerated or attenuated by additional trans effects. Overall, we showed that the transcriptome is globally buffered at the genetic level mainly due to trans-regulatory variation in the population.
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Affiliation(s)
- Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Gauthier Brach
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France; Institut Universitaire de France (IUF), Paris, France.
| | - Jing Hou
- Université de Strasbourg, CNRS, GMGM UMR, 7156 Strasbourg, France.
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8
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Abraham LN, Croll D. Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen. BMC Biol 2023; 21:263. [PMID: 37981685 PMCID: PMC10658818 DOI: 10.1186/s12915-023-01763-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/07/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND In agricultural ecosystems, outbreaks of diseases are frequent and pose a significant threat to food security. A successful pathogen undergoes a complex and well-timed sequence of regulatory changes to avoid detection by the host immune system; hence, well-tuned gene regulation is essential for survival. However, the extent to which the regulatory polymorphisms in a pathogen population provide an adaptive advantage is poorly understood. RESULTS We used Zymoseptoria tritici, one of the most important pathogens of wheat, to generate a genome-wide map of regulatory polymorphism governing gene expression. We investigated genome-wide transcription levels of 146 strains grown under nutrient starvation and performed expression quantitative trait loci (eQTL) mapping. We identified cis-eQTLs for 65.3% of all genes and the majority of all eQTL loci are within 2kb upstream and downstream of the transcription start site (TSS). We also show that polymorphism in different gene elements contributes disproportionally to gene expression variation. Investigating regulatory polymorphism in gene categories, we found an enrichment of regulatory variants for genes predicted to be important for fungal pathogenesis but with comparatively low effect size, suggesting a separate layer of gene regulation involving epigenetics. We also show that previously reported trait-associated SNPs in pathogen populations are frequently cis-regulatory variants of neighboring genes with implications for the trait architecture. CONCLUSIONS Overall, our study provides extensive evidence that single populations segregate large-scale regulatory variation and are likely to fuel rapid adaptation to resistant hosts and environmental change.
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Affiliation(s)
- Leen Nanchira Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
- Present address: Institute of Plant Sciences, University of Cologne, Cologne, Germany
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland.
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9
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Bennett H, Troutman TD, Zhou E, Spann NJ, Link VM, Seidman JS, Nickl CK, Abe Y, Sakai M, Pasillas MP, Marlman JM, Guzman C, Hosseini M, Schnabl B, Glass CK. Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on Kupffer cell epigenomes and transcriptomes. Nat Immunol 2023; 24:1825-1838. [PMID: 37735593 PMCID: PMC10602851 DOI: 10.1038/s41590-023-01631-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
Noncoding genetic variation drives phenotypic diversity, but underlying mechanisms and affected cell types are incompletely understood. Here, investigation of effects of natural genetic variation on the epigenomes and transcriptomes of Kupffer cells derived from inbred mouse strains identified strain-specific environmental factors influencing Kupffer cell phenotypes, including leptin signaling in Kupffer cells from a steatohepatitis-resistant strain. Cell-autonomous and non-cell-autonomous effects of genetic variation were resolved by analysis of F1 hybrid mice and cells engrafted into an immunodeficient host. During homeostasis, non-cell-autonomous trans effects of genetic variation dominated control of Kupffer cells, while strain-specific responses to acute lipopolysaccharide injection were dominated by actions of cis-acting effects modifying response elements for lineage-determining and signal-dependent transcription factors. These findings demonstrate that epigenetic landscapes report on trans effects of genetic variation and serve as a resource for deeper analyses into genetic control of transcription in Kupffer cells and macrophages in vitro.
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Affiliation(s)
- Hunter Bennett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ty D Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Division of Allergy and Immunology, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Enchen Zhou
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Nathanael J Spann
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Jason S Seidman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Christian K Nickl
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yohei Abe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mashito Sakai
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Justin M Marlman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carlos Guzman
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Mojgan Hosseini
- Department of Pathology, University of California, San Diego, San Diego, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
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10
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Ballinger MA, Mack KL, Durkin SM, Riddell EA, Nachman MW. Environmentally robust cis-regulatory changes underlie rapid climatic adaptation. Proc Natl Acad Sci U S A 2023; 120:e2214614120. [PMID: 37725649 PMCID: PMC10523592 DOI: 10.1073/pnas.2214614120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/26/2023] [Indexed: 09/21/2023] Open
Abstract
Changes in gene expression are thought to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene expression differences in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5 to 10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis-regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans-effects, which showed greater sensitivity to temperature. Nonetheless, we found a small subset of temperature-dependent cis-regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis-regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis-regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans, may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis, illustrating the genetic and nongenetic mechanisms underlying the establishment of populations in new environments.
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Affiliation(s)
- Mallory A. Ballinger
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
- Department of Biology, Utah State University, Logan, UT84322
| | - Katya L. Mack
- Department of Biology, Stanford University, Stanford, CA94305
| | - Sylvia M. Durkin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
| | - Eric A. Riddell
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA50011
| | - Michael W. Nachman
- Museum of Vertebrate Zoology, University of California, Berkeley, CA94720
- Department of Integrative Biology, University of California, Berkeley, CA94720
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11
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Tsouris A, Brach G, Schacherer J, Hou J. Non-additive genetic components contribute significantly to population-wide gene expression variation. bioRxiv 2023:2023.07.21.550013. [PMID: 37546809 PMCID: PMC10401925 DOI: 10.1101/2023.07.21.550013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Gene expression variation, an essential step between genomic variation and phenotypic landscape, is collectively controlled by local (cis) and distant (trans) regulatory changes. Nevertheless, how these regulatory elements differentially influence the heritability of expression traits remains unclear. Here, we bridge this gap by analyzing the transcriptomes of a large diallel panel consisting of 323 unique hybrids originated from genetically divergent yeast isolates. We estimated the broad- and narrow-sense heritability across 5,087 transcript abundance traits and showed that non-additive components account for 36% of the phenotypic variance on average. By comparing allelic expression ratios in the hybrid and the corresponding parental pair, we identified regulatory changes in 25% of all cases, with a majority acting in trans. We further showed that trans-regulation could underlie coordinated expression variation across highly connected genes, resulting in significantly higher non-additive variance and most likely in some of the missing heritability of gene expression traits.
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Affiliation(s)
- Andreas Tsouris
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Gauthier Brach
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
| | - Jing Hou
- Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
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12
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Hsu P, Cheng Y, Liao C, Litan RRR, Jhou Y, Opoc FJG, Amine AAA, Leu J. Rapid evolutionary repair by secondary perturbation of a primary disrupted transcriptional network. EMBO Rep 2023; 24:e56019. [PMID: 37009824 PMCID: PMC10240213 DOI: 10.15252/embr.202256019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
The discrete steps of transcriptional rewiring have been proposed to occur neutrally to ensure steady gene expression under stabilizing selection. A conflict-free switch of a regulon between regulators may require an immediate compensatory evolution to minimize deleterious effects. Here, we perform an evolutionary repair experiment on the Lachancea kluyveri yeast sef1Δ mutant using a suppressor development strategy. Complete loss of SEF1 forces cells to initiate a compensatory process for the pleiotropic defects arising from misexpression of TCA cycle genes. Using different selective conditions, we identify two adaptive loss-of-function mutations of IRA1 and AZF1. Subsequent analyses show that Azf1 is a weak transcriptional activator regulated by the Ras1-PKA pathway. Azf1 loss-of-function triggers extensive gene expression changes responsible for compensatory, beneficial, and trade-off phenotypes. The trade-offs can be alleviated by higher cell density. Our results not only indicate that secondary transcriptional perturbation provides rapid and adaptive mechanisms potentially stabilizing the initial stage of transcriptional rewiring but also suggest how genetic polymorphisms of pleiotropic mutations could be maintained in the population.
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Affiliation(s)
- Po‐Chen Hsu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Yu‐Hsuan Cheng
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
- Present address:
Morgridge Institute for ResearchMadisonWIUSA
- Present address:
Howard Hughes Medical InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Chia‐Wei Liao
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | - Yu‐Ting Jhou
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | | | - Jun‐Yi Leu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
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13
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Harry ND, Zakas C. Maternal patterns of inheritance alter transcript expression in eggs. BMC Genomics 2023; 24:191. [PMID: 37038099 PMCID: PMC10084599 DOI: 10.1186/s12864-023-09291-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/01/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Modifications to early development can lead to evolutionary diversification. The early stages of development are under maternal control, as mothers produce eggs loaded with nutrients, proteins and mRNAs that direct early embryogenesis. Maternally provided mRNAs are the only expressed genes in initial stages of development and are tightly regulated. Differences in maternal mRNA provisioning could lead to phenotypic changes in embryogenesis and ultimately evolutionary changes in development. However, the extent that maternal mRNA expression in eggs can vary is unknown for most developmental models. Here, we use a species with dimorphic development- where females make eggs and larvae of different sizes and life-history modes-to investigate the extent of variation in maternal mRNA provisioning to the egg. RESULTS We find that there is significant variation in gene expression across eggs of different development modes, and that there are both qualitative and quantitative differences in mRNA expression. We separate parental effects from allelic effects, and find that both mechanisms contribute to mRNA expression differences. We also find that offspring of intraspecific crosses differentially provision their eggs based on the parental cross direction (a parental effect), which has not been previously demonstrated in reproductive traits like oogenesis. CONCLUSION We find that maternally controlled initiation of development is functionally distinct between eggs of different sizes and maternal genotypes. Both allele-specific effects and parent-of-origin effects contribute to gene expression differences in eggs. The latter indicates an intergenerational effect where a parent's genotype can affect gene expression in an egg made by the next generation.
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Affiliation(s)
- Nathan D Harry
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA
| | - Christina Zakas
- Department of Biological Sciences, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA.
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14
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Richard Albert J, Kobayashi T, Inoue A, Monteagudo-Sánchez A, Kumamoto S, Takashima T, Miura A, Oikawa M, Miura F, Takada S, Hirabayashi M, Korthauer K, Kurimoto K, Greenberg MVC, Lorincz M, Kobayashi H. Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biol 2023; 24:48. [PMID: 36918927 PMCID: PMC10012579 DOI: 10.1186/s13059-023-02869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/09/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.
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Affiliation(s)
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Azusa Inoue
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Soichiro Kumamoto
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Asuka Miura
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan
| | - Keegan Korthauer
- Department of Statistics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan
| | | | - Matthew Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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15
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Hansen T, Fong S, Capra JA, Hodges E. Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans. bioRxiv 2023:2023.02.14.528376. [PMID: 36824965 PMCID: PMC9949080 DOI: 10.1101/2023.02.14.528376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Gene regulatory divergence between species can result from cis-acting local changes to regulatory element DNA sequences or global trans-acting changes to the regulatory environment. Understanding how these mechanisms drive regulatory evolution has been limited by challenges in identifying trans-acting changes. We present a comprehensive approach to directly identify cis- and trans-divergent regulatory elements between human and rhesus macaque lymphoblastoid cells using ATAC-STARR-seq. In addition to thousands of cis changes, we discover an unexpected number (~10,000) of trans changes and show that cis and trans elements exhibit distinct patterns of sequence divergence and function. We further identify differentially expressed transcription factors that underlie >50% of trans differences and trace how cis changes can produce cascades of trans changes. Overall, we find that most divergent elements (67%) experienced changes in both cis and trans, revealing a substantial role for trans divergence-alone and together with cis changes-to regulatory differences between species.
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Affiliation(s)
- Tyler Hansen
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA
| | - Sarah Fong
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37212, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John A. Capra
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37212, USA
- Lead contact
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16
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Lin Y, Li J, Chen L, Bai J, Zhang J, Wang Y, Liu P, Long K, Ge L, Jin L, Gu Y, Li M. Allele-specific regulatory effects on the pig transcriptome. Gigascience 2022; 12:giad076. [PMID: 37776365 PMCID: PMC10541795 DOI: 10.1093/gigascience/giad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 06/25/2023] [Accepted: 08/30/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Allele-specific expression (ASE) refers to the preferential expression of one allele over the other and contributes to adaptive phenotypic plasticity. Here, we used a reciprocal cross-model between phenotypically divergent European Berkshire and Asian Tibetan pigs to characterize 2 ASE classes: imprinting (i.e., the unequal expression between parental alleles) and sequence dependent (i.e., unequal expression between breed-specific alleles). We examined 3 transcript types, including protein-coding genes (PCGs), long noncoding RNAs, and transcripts of unknown coding potential, across 7 representative somatic tissues from hybrid pigs generated by reciprocal crosses. RESULTS We identified a total of 92 putative imprinted transcripts, 69 (75.00%) of which are described here for the first time. By combining the transcriptome from purebred Berkshire and Tibetan pigs, we found ∼6.59% of PCGs are differentially expressed between breeds that are regulated by trans-elements (e.g., transcriptional factors), while only ∼1.35% are attributable to cis (e.g., promoters). The higher prevalence of trans-PCGs indicates the dominated effects of trans-regulation in driving expression differences and shaping adaptive phenotypic plasticity between breeds, which were supported by functional enrichment analysis. We also found strong evidence that expression changes mediated by cis-effects were associated with accumulated variants in promoters. CONCLUSIONS Our study provides a comprehensive map of expression regulation that constitutes a valuable resource for the agricultural improvement of pig breeds.
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Affiliation(s)
- Yu Lin
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Chen
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Jingyi Bai
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Pengliang Liu
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Keren Long
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Liangpeng Ge
- Pig Industry Sciences Key Laboratory of Ministry of Agriculture and Rural Affairs, Chongqing Academy of Animal Sciences, Chongqing 402460, China
- National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Long Jin
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiren Gu
- College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Mingzhou Li
- Livestock and Poultry Multi-omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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17
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Vendrami DLJ, Hoffman JI, Wilding CS. Heterogeneous Genomic Divergence Landscape in Two Commercially Important European Scallop Species. Genes (Basel) 2022; 14:14. [PMID: 36672754 PMCID: PMC9858869 DOI: 10.3390/genes14010014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Two commercially important scallop species of the genus Pecten are found in Europe: the north Atlantic Pecten maximus and the Mediterranean Pecten jacobaeus whose distributions abut at the Almeria-Orán front. Whilst previous studies have quantified genetic divergence between these species, the pattern of differentiation along the Pecten genome is unknown. Here, we mapped RADseq data from 235 P. maximus and 27 P. jacobaeus to a chromosome-level reference genome, finding a heterogeneous landscape of genomic differentiation. Highly divergent genomic regions were identified across 14 chromosomes, while the remaining five showed little differentiation. Demographic and comparative genomics analyses suggest that this pattern resulted from an initial extended period of isolation, which promoted divergence, followed by differential gene flow across the genome during secondary contact. Single nucleotide polymorphisms present within highly divergent genomic regions were located in areas of low recombination and contrasting patterns of LD decay were found between the two species, hinting at the presence of chromosomal inversions in P. jacobaeus. Functional annotations revealed that highly differentiated regions were enriched for immune-related processes and mRNA modification. While future work is necessary to characterize structural differences, this study provides new insights into the speciation genomics of P. maximus and P. jacobaeus.
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Affiliation(s)
- David L. J. Vendrami
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33615 Bielefeld, Germany
| | - Joseph I. Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33615 Bielefeld, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK
| | - Craig S. Wilding
- School of Biological and Environmental Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
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18
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Ta TM, Malik S, Anderson EM, Jones AD, Perchik J, Freylikh M, Sardo L, Klase ZA, Izumi T. Insights Into Persistent HIV-1 Infection and Functional Cure: Novel Capabilities and Strategies. Front Microbiol 2022; 13:862270. [PMID: 35572626 PMCID: PMC9093714 DOI: 10.3389/fmicb.2022.862270] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/23/2022] Open
Abstract
Although HIV-1 replication can be efficiently suppressed to undetectable levels in peripheral blood by combination antiretroviral therapy (cART), lifelong medication is still required in people living with HIV (PLWH). Life expectancies have been extended by cART, but age-related comorbidities have increased which are associated with heavy physiological and economic burdens on PLWH. The obstacle to a functional HIV cure can be ascribed to the formation of latent reservoir establishment at the time of acute infection that persists during cART. Recent studies suggest that some HIV reservoirs are established in the early acute stages of HIV infection within multiple immune cells that are gradually shaped by various host and viral mechanisms and may undergo clonal expansion. Early cART initiation has been shown to reduce the reservoir size in HIV-infected individuals. Memory CD4+ T cell subsets are regarded as the predominant cellular compartment of the HIV reservoir, but monocytes and derivative macrophages or dendritic cells also play a role in the persistent virus infection. HIV latency is regulated at multiple molecular levels in transcriptional and post-transcriptional processes. Epigenetic regulation of the proviral promoter can profoundly regulate the viral transcription. In addition, transcriptional elongation, RNA splicing, and nuclear export pathways are also involved in maintaining HIV latency. Although most proviruses contain large internal deletions, some defective proviruses may induce immune activation by expressing viral proteins or producing replication-defective viral-like particles. In this review article, we discuss the state of the art on mechanisms of virus persistence in the periphery and tissue and summarize interdisciplinary approaches toward a functional HIV cure, including novel capabilities and strategies to measure and eliminate the infected reservoirs and induce immune control.
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Affiliation(s)
- Tram M. Ta
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Sajjaf Malik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Elizabeth M. Anderson
- Office of the Assistant Secretary for Health, Region 3, U.S. Department of Health and Human Services, Washington, DC, United States
| | - Amber D. Jones
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jocelyn Perchik
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Maryann Freylikh
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States
| | - Luca Sardo
- Department of Infectious Disease and Vaccines, Merck & Co., Inc., Kenilworth, NJ, United States
| | - Zackary A. Klase
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA, United States,Center for Neuroimmunology and CNS Therapeutics, Institute of Molecular Medicine and Infectious Diseases, Drexel University of Medicine, Philadelphia, PA, United States
| | - Taisuke Izumi
- Department of Biological Sciences, Misher College of Arts and Sciences, University of the Sciences in Philadelphia, Philadelphia, PA, United States,*Correspondence: Taisuke Izumi,
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19
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Hu CK, York RA, Metz HC, Bedford NL, Fraser HB, Hoekstra HE. cis-Regulatory changes in locomotor genes are associated with the evolution of burrowing behavior. Cell Rep 2022; 38:110360. [PMID: 35172153 DOI: 10.1016/j.celrep.2022.110360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 12/13/2022] Open
Abstract
How evolution modifies complex, innate behaviors is largely unknown. Divergence in many morphological traits, and some behaviors, is linked to cis-regulatory changes in gene expression. Given this, we compare brain gene expression of two interfertile sister species of Peromyscus mice that show large and heritable differences in burrowing behavior. Species-level differential expression and allele-specific expression in F1 hybrids indicate a preponderance of cis-regulatory divergence, including many genes whose cis-regulation is affected by burrowing behavior. Genes related to locomotor coordination show the strongest signals of lineage-specific selection on burrowing-induced cis-regulatory changes. Furthermore, genetic markers closest to these candidate genes associate with variation in burrow shape in a genetic cross, suggesting an enrichment for loci affecting burrowing behavior near these candidate locomotor genes. Our results provide insight into how cis-regulated gene expression can depend on behavioral context and how this dynamic regulatory divergence between species may contribute to behavioral evolution.
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20
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Abstract
Genes involved in spermatogenesis tend to evolve rapidly, but we lack a clear understanding of how protein sequences and patterns of gene expression evolve across this complex developmental process. We used fluorescence-activated cell sorting (FACS) to generate expression data for early (meiotic) and late (postmeiotic) cell types across 13 inbred strains of mice (Mus) spanning ∼7 My of evolution. We used these comparative developmental data to investigate the evolution of lineage-specific expression, protein-coding sequences, and expression levels. We found increased lineage specificity and more rapid protein-coding and expression divergence during late spermatogenesis, suggesting that signatures of rapid testis molecular evolution are punctuated across sperm development. Despite strong overall developmental parallels in these components of molecular evolution, protein and expression divergences were only weakly correlated across genes. We detected more rapid protein evolution on the X chromosome relative to the autosomes, whereas X-linked gene expression tended to be relatively more conserved likely reflecting chromosome-specific regulatory constraints. Using allele-specific FACS expression data from crosses between four strains, we found that the relative contributions of different regulatory mechanisms also differed between cell types. Genes showing cis-regulatory changes were more common late in spermatogenesis, and tended to be associated with larger differences in expression levels and greater expression divergence between species. In contrast, genes with trans-acting changes were more common early and tended to be more conserved across species. Our findings advance understanding of gene evolution across spermatogenesis and underscore the fundamental importance of developmental context in molecular evolutionary studies.
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Affiliation(s)
- Emily E K Kopania
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Erica L Larson
- Department of Biological Sciences, University of Denver, Denver, CO, 80208, USA
| | - Colin Callahan
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Sara Keeble
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
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21
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Matthews BJ, Melia T, Waxman DJ. Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model. PLoS Genet 2021; 17:e1009588. [PMID: 34752452 PMCID: PMC8664386 DOI: 10.1371/journal.pgen.1009588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/10/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Sex differences in gene expression are widespread in the liver, where many autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57BL/6J and CAST/EiJ, representing two subspecies separated by 0.5-1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24, Tox, and Zfp809, lose their sex-biased expression in CAST/EiJ mouse liver. To elucidate the observed strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of the sex differences in expression between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-dependent gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs apparently lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations.
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Affiliation(s)
- Bryan J. Matthews
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Tisha Melia
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - David J. Waxman
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
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22
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Liang W, Zou X, Li G, Zhou S, Tian C, Schaefke B. Systematic Analysis of Monoallelic Gene Expression and Chromatin Accessibility Across Multiple Tissues in Hybrid Mice. Front Cell Dev Biol 2021; 9:717555. [PMID: 34631706 PMCID: PMC8495204 DOI: 10.3389/fcell.2021.717555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
In diploid eukaryotic organisms, both alleles of each autosomal gene are usually assumed to be simultaneously expressed at similar levels. However, some genes can be expressed preferentially or strictly from a single allele, a process known as monoallelic expression. Classic monoallelic expression of X-chromosome-linked genes, olfactory receptor genes and developmentally imprinted genes is the result of epigenetic modifications. Genetic-origin-dependent monoallelic expression, however, is caused by cis-regulatory differences between the alleles. There is a paucity of systematic study to investigate these phenomena across multiple tissues, and the mechanisms underlying such monoallelic expression are not yet fully understood. Here we provide a detailed portrait of monoallelic gene expression across multiple tissues/cell lines in a hybrid mouse cross between the Mus musculus strain C57BL/6J and the Mus spretus strain SPRET/EiJ. We observed pervasive tissue-dependent allele-specific gene expression: in total, 1,839 genes exhibited monoallelic expression in at least one tissue, and 410 genes in at least two tissues. Among these 88 are monoallelic genes with different active alleles between tissues, probably representing genetic-origin-dependent monoallelic expression. We also identified six autosomal monoallelic genes with the active allele being identical in all eight tissues, which are likely novel candidates of imprinted genes. To depict the underlying regulatory mechanisms at the chromatin layer, we performed ATAC-seq in two different cell lines derived from the F1 mouse. Consistent with the global expression pattern, cell-type dependent monoallelic peaks were found, and a higher proportion of C57BL/6J-active peaks were observed in both cell types, implying possible species-specific regulation. Finally, only a small part of monoallelic gene expression could be explained by allelic differences in chromatin organization in promoter regions, suggesting that other distal elements may play important roles in shaping the patterns of allelic gene expression across tissues.
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Affiliation(s)
- Weizheng Liang
- Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Shaojie Zhou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Chi Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Bernhard Schaefke
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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Ramirez-Corona BA, Fruth S, Ofoegbu O, Wunderlich Z. The mode of expression divergence in Drosophila fat body is infection-specific. Genome Res 2021; 31:1024-1034. [PMID: 33858842 PMCID: PMC8168590 DOI: 10.1101/gr.269597.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 04/07/2021] [Indexed: 12/13/2022]
Abstract
Transcription is controlled by interactions of cis-acting DNA elements with diffusible trans-acting factors. Changes in cis or trans factors can drive expression divergence within and between species, and their relative prevalence can reveal the evolutionary history and pressures that drive expression variation. Previous work delineating the mode of expression divergence in animals has largely used whole-body expression measurements in one condition. Because cis-acting elements often drive expression in a subset of cell types or conditions, these measurements may not capture the complete contribution of cis-acting changes. Here, we quantify the mode of expression divergence in the Drosophila fat body, the primary immune organ, in several conditions, using two geographically distinct lines of D. melanogaster and their F1 hybrids. We measured expression in the absence of infection and in infections with Gram-negative S. marcescens or Gram-positive E. faecalis bacteria, which trigger the two primary signaling pathways in the Drosophila innate immune response. The mode of expression divergence strongly depends on the condition, with trans-acting effects dominating in response to Gram-negative infection and cis-acting effects dominating in Gram-positive and preinfection conditions. Expression divergence in several receptor proteins may underlie the infection-specific trans effects. Before infection, when the fat body has a metabolic role, there are many compensatory effects, changes in cis and trans that counteract each other to maintain expression levels. This work shows that within a single tissue, the mode of expression divergence varies between conditions and suggests that these differences reflect the diverse evolutionary histories of host–pathogen interactions.
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Affiliation(s)
- Bryan A Ramirez-Corona
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA
| | - Stephanie Fruth
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA
| | - Oluchi Ofoegbu
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA
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24
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Kerwin RE, Sweigart AL. Rampant Misexpression in a Mimulus (Monkeyflower) Introgression Line Caused by Hybrid Sterility, Not Regulatory Divergence. Mol Biol Evol 2021; 37:2084-2098. [PMID: 32196085 PMCID: PMC7306685 DOI: 10.1093/molbev/msaa071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Divergence in gene expression regulation is common between closely related species and may give rise to incompatibilities in their hybrid progeny. In this study, we investigated the relationship between regulatory evolution within species and reproductive isolation between species. We focused on a well-studied case of hybrid sterility between two closely related yellow monkeyflower species, Mimulus guttatus and Mimulus nasutus, that is caused by two epistatic loci, hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2). We compared genome-wide transcript abundance across male and female reproductive tissues (i.e., stamens and carpels) from four genotypes: M. guttatus, M. nasutus, and sterile and fertile progeny from an advanced M. nasutus–M. guttatus introgression line carrying the hms1–hms2 incompatibility. We observed substantial variation in transcript abundance between M. guttatus and M. nasutus, including distinct but overlapping patterns of tissue-biased expression, providing evidence for regulatory divergence between these species. We also found rampant genome-wide misexpression, but only in the affected tissues (i.e., stamens) of sterile introgression hybrids carrying incompatible alleles at hms1 and hms2. Examining patterns of allele-specific expression in sterile and fertile introgression hybrids, we found evidence for interspecific divergence in cis- and trans-regulation, including compensatory cis–trans mutations likely to be driven by stabilizing selection. Nevertheless, species divergence in gene regulatory networks cannot explain the vast majority of the gene misexpression we observe in Mimulus introgression hybrids, which instead likely manifests as a downstream consequence of sterility itself.
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Affiliation(s)
- Rachel E Kerwin
- Department of Genetics, University of Georgia, Athens, GA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
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25
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Abstract
Background Large-scale biological data sets are often contaminated by noise, which can impede accurate inferences about underlying processes. Such measurement noise can arise from endogenous biological factors like cell cycle and life history variation, and from exogenous technical factors like sample preparation and instrument variation. Results We describe a general method for automatically reducing noise in large-scale biological data sets. This method uses an interaction network to identify groups of correlated or anti-correlated measurements that can be combined or “filtered” to better recover an underlying biological signal. Similar to the process of denoising an image, a single network filter may be applied to an entire system, or the system may be first decomposed into distinct modules and a different filter applied to each. Applied to synthetic data with known network structure and signal, network filters accurately reduce noise across a wide range of noise levels and structures. Applied to a machine learning task of predicting changes in human protein expression in healthy and cancerous tissues, network filtering prior to training increases accuracy up to 43% compared to using unfiltered data. Conclusions Network filters are a general way to denoise biological data and can account for both correlation and anti-correlation between different measurements. Furthermore, we find that partitioning a network prior to filtering can significantly reduce errors in networks with heterogenous data and correlation patterns, and this approach outperforms existing diffusion based methods. Our results on proteomics data indicate the broad potential utility of network filters to applications in systems biology. Supplementary Information The online version supplementary material available at 10.1186/s12859-021-04075-x.
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Affiliation(s)
- Andrew J Kavran
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Aaron Clauset
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA. .,Department of Computer Science, University of Colorado, Boulder, CO, USA. .,Santa Fe Institute, Santa Fe, NM, USA.
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26
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Hayashi M, Inaba A, Hakukawa M, Iwatsuki K, Imai H, Masuda K. Expression of TAS2R14 in the intestinal endocrine cells of non-human primates. Genes Genomics 2021; 43:259-267. [PMID: 33609226 DOI: 10.1007/s13258-021-01054-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Recent studies have demonstrated that genes related to bitter taste receptors (TAS2Rs) on various chromosomes are expressed in extra-oral organs of various animals. The bitter taste receptor TAS2R14 is conserved among primate species and shows broad ligand sensitivity. Mice have a number of orthologues to primate TAS2R14 located in tandem on chromosome 16; however, their expression patterns are not unique. OBJECTIVE We characterized the expression of TAS2R14 in various cell types in the intestines of the rhesus macaque and evaluated its role in hormone production in the gut. METHODS TAS2R14 expression was examined in the intestines of rhesus macaques, a common non-human primate model, by RT-qPCR and immunohistochemical staining. RESULTS Mean expression levels of TAS2R14 in the duodenum, ileum, and colon were similar to each other and were lower than those in circumvallate papillae. An immunohistochemical analysis revealed TAS2R14 immunoreactivity in enteroendocrine cells positive for cholecystokinin, serotonin, and the G protein GNAT3. CONCLUSION These results suggest that primate TAS2R14 is broadly expressed in the intestine, mainly in enteroendocrine cells, and promotes gut hormone secretion in response to bitter stimuli.
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Affiliation(s)
- Misa Hayashi
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi, 484-8506, Japan
| | - Akihiko Inaba
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi, 484-8506, Japan
| | - Miho Hakukawa
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi, 484-8506, Japan
| | - Ken Iwatsuki
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, Tokyo, 1568502, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi, 484-8506, Japan.
| | - Katsuyoshi Masuda
- Structural Bioscience for Taste Molecular Recognition, Graduate School of Medicine, Kyoto University, Kyoto, 6068507, Japan.
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27
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Floc'hlay S, Wong ES, Zhao B, Viales RR, Thomas-Chollier M, Thieffry D, Garfield DA, Furlong EEM. Cis-acting variation is common across regulatory layers but is often buffered during embryonic development. Genome Res 2021; 31:211-224. [PMID: 33310749 PMCID: PMC7849415 DOI: 10.1101/gr.266338.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Precise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequences, and chromatin. How DNA mutations affecting any one of these regulatory "layers" are buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eight Drosophila crosses at three embryonic stages, yielding a comprehensive data set of 240 samples spanning multiple regulatory layers. Genetic variation (allelic imbalance) impacts gene expression more frequently than chromatin features, with metabolic and environmental response genes being most often affected. Allelic imbalance in cis-regulatory elements (enhancers) is common and highly heritable, yet its functional impact does not generally propagate to gene expression. When it does, genetic variation impacts RNA levels through two alternative mechanisms involving either H3K4me3 or chromatin accessibility and H3K27ac. Changes in RNA are more predictive of variation in H3K4me3 than vice versa, suggesting a role for H3K4me3 downstream from transcription. The impact of a substantial proportion of genetic variation is consistent across embryonic stages, with 50% of allelic imbalanced features at one stage being also imbalanced at subsequent developmental stages. Crucially, buffering, as well as the magnitude and evolutionary impact of genetic variants, is influenced by regulatory complexity (i.e., number of enhancers regulating a gene), with transcription factors being most robust to cis-acting, but most influenced by trans-acting, variation.
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Affiliation(s)
- Swann Floc'hlay
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Emily S Wong
- Molecular, Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, New South Wales 2052, Australia
| | - Bingqing Zhao
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Morgane Thomas-Chollier
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Denis Thieffry
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - David A Garfield
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117 Heidelberg, Germany
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28
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McGirr JA, Martin CH. Few Fixed Variants between Trophic Specialist Pupfish Species Reveal Candidate Cis-Regulatory Alleles Underlying Rapid Craniofacial Divergence. Mol Biol Evol 2021; 38:405-423. [PMID: 32877534 PMCID: PMC7826174 DOI: 10.1093/molbev/msaa218] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Investigating closely related species that rapidly evolved divergent feeding morphology is a powerful approach to identify genetic variation underlying variation in complex traits. This can also lead to the discovery of novel candidate genes influencing natural and clinical variation in human craniofacial phenotypes. We combined whole-genome resequencing of 258 individuals with 50 transcriptomes to identify candidate cis-acting genetic variation underlying rapidly evolving craniofacial phenotypes within an adaptive radiation of Cyprinodon pupfishes. This radiation consists of a dietary generalist species and two derived trophic niche specialists-a molluscivore and a scale-eating species. Despite extensive morphological divergence, these species only diverged 10 kya and produce fertile hybrids in the laboratory. Out of 9.3 million genome-wide SNPs and 80,012 structural variants, we found very few alleles fixed between species-only 157 SNPs and 87 deletions. Comparing gene expression across 38 purebred F1 offspring sampled at three early developmental stages, we identified 17 fixed variants within 10 kb of 12 genes that were highly differentially expressed between species. By measuring allele-specific expression in F1 hybrids from multiple crosses, we found that the majority of expression divergence between species was explained by trans-regulatory mechanisms. We also found strong evidence for two cis-regulatory alleles affecting expression divergence of two genes with putative effects on skeletal development (dync2li1 and pycr3). These results suggest that SNPs and structural variants contribute to the evolution of novel traits and highlight the utility of the San Salvador Island pupfish system as an evolutionary model for craniofacial development.
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Affiliation(s)
- Joseph A McGirr
- Environmental Toxicology Department, University of California, Davis, CA
| | - Christopher H Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA
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29
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Cooper RD, Shaffer HB. Allele-specific expression and gene regulation help explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense). Mol Ecol 2021; 30:987-1004. [PMID: 33338297 DOI: 10.1111/mec.15779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 01/26/2023]
Abstract
Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their potential to outperform native species. Effective management of hybrid populations requires an understanding of both physiological performance and the underlying mechanisms that drive transgressive hybrid traits. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and F1 hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 33% (4/12) able to tolerate temperatures greater than either parent. We then quantified the genomic response, measured at the RNA transcript level, of each salamander, to explore the mechanisms underlying thermal tolerance strategies. We found that CTS and BTS have strikingly different values and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. F1 hybrids display abundant and variable degrees of allele-specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms between CTS and BTS. We found evidence that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting a link between ASE and expanded thermal tolerance that may contribute to the success of hybrid salamanders in California. Future climate change may further complicate management of CTS if hybrid salamanders are better equipped to deal with rising temperatures.
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Affiliation(s)
- Robert D Cooper
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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30
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Zhao N, Ding X, Lian T, Wang M, Tong Y, Liang D, An Q, Sun S, Jackson SA, Liu B, Xu C. The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean. Front Genet 2020; 11:601003. [PMID: 33363574 PMCID: PMC7753205 DOI: 10.3389/fgene.2020.601003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/04/2020] [Indexed: 12/22/2022] Open
Abstract
Regulatory changes include divergence in both cis-elements and trans-factors, which play roles in organismal evolution. Whole genome duplications (WGD) followed by diploidization are a recurrent feature in the evolutionary history of angiosperms. Prior studies have shown that duplicated genes have different evolutionary fates due to variable selection constraints and results in genomic compositions with hallmarks of paleopolyploidy. The recent sequential WGDs and post-WGD evolution in the common ancestor of cultivated soybean (Glycine max) and wild soybean (Glycine soja), together with other models of gene duplication, have resulted in a highly duplicated genome. In this study, we investigated the transcriptional changes in G. soja and G. max. We identified a sizable proportion of interspecific differentially expressed genes (DEGs) and found parental expression level dominance of G. max in their F1 hybrids. By classifying genes into different regulatory divergence types, we found the trans-regulatory changes played a predominant role in transcriptional divergence between wild and cultivated soybean. The same gene ontology (GO) and protein family (Pfam) terms were found to be over-represented in DEGs and genes of cis-only between JY47 and GS, suggesting the substantial contribution of cis-regulatory divergences to the evolution of wild and cultivated soybeans. By further dissecting genes into five different duplication modes, we found genes in different duplication modes tend to accumulate different types of regulatory differences. A relatively higher proportion of cis-only regulatory divergences was detected in singleton, dispersed, proximal, and tandem duplicates than WGD duplicates and genome-wide level, which is in line with the prediction of gene balance hypothesis for the differential fates of duplicated genes post-WGD. The numbers of cis-only and trans-only regulated genes were similar for singletons, whereas there were more genes of trans-only than cis-only in the rest duplication types, especially in WGD in which there were two times more trans-only genes than that in cis-only type. Tandem duplicates showed the highest proportion of trans-only genes probably due to some special features of this class. In summary, our results demonstrate that genes in different duplication modes have different fates in transcriptional evolution underpinned by cis- or trans-regulatory divergences in soybean and likely in other paleopolyploid higher organisms.
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Affiliation(s)
- Na Zhao
- Department of Agronomy, Jilin Agricultural University, Changchun, China.,Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Xiaoyang Ding
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Taotao Lian
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Meng Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yan Tong
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Di Liang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Qi An
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Siwen Sun
- Department of Agronomy, Jilin Agricultural University, Changchun, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
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31
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Hill MS, Vande Zande P, Wittkopp PJ. Molecular and evolutionary processes generating variation in gene expression. Nat Rev Genet 2021; 22:203-15. [PMID: 33268840 DOI: 10.1038/s41576-020-00304-w] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/18/2022]
Abstract
Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection. High-throughput methods for introducing mutations and characterizing their cis- and trans-regulatory effects on gene expression (particularly, transcription) are revealing how different molecular mechanisms generate regulatory variation, and studies comparing these mutational effects with variation seen in the wild are teasing apart the role of neutral and non-neutral evolutionary processes. This integration of molecular and evolutionary biology allows us to understand how the variation in gene expression we see today came to be and to predict how it is most likely to evolve in the future.
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32
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Mugal CF, Wang M, Backström N, Wheatcroft D, Ålund M, Sémon M, McFarlane SE, Dutoit L, Qvarnström A, Ellegren H. Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F 1 hybrids. Genome Res 2020; 30:1727-1739. [PMID: 33144405 PMCID: PMC7706733 DOI: 10.1101/gr.254508.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
Changes in interacting cis- and trans-regulatory elements are important candidates for Dobzhansky-Muller hybrid incompatibilities and may contribute to hybrid dysfunction by giving rise to misexpression in hybrids. To gain insight into the molecular mechanisms and determinants of gene expression evolution in natural populations, we analyzed the transcriptome from multiple tissues of two recently diverged Ficedula flycatcher species and their naturally occurring F1 hybrids. Differential gene expression analysis revealed that the extent of differentiation between species and the set of differentially expressed genes varied across tissues. Common to all tissues, a higher proportion of Z-linked genes than autosomal genes showed differential expression, providing evidence for a fast-Z effect. We further found clear signatures of hybrid misexpression in brain, heart, kidney, and liver. However, while testis showed the highest divergence of gene expression among tissues, it showed no clear signature of misexpression in F1 hybrids, even though these hybrids were found to be sterile. It is therefore unlikely that incompatibilities between cis-trans regulatory changes explain the observed sterility. Instead, we found evidence that cis-regulatory changes play a significant role in the evolution of gene expression in testis, which illustrates the tissue-specific nature of cis-regulatory evolution bypassing constraints associated with pleiotropic effects of genes.
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Affiliation(s)
- Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - Mi Wang
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - Niclas Backström
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - David Wheatcroft
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Murielle Ålund
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Marie Sémon
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,ENS de Lyon, Laboratory of Biology and Modelling of the Cell, Lyon University, 69364 Lyon Cedex 07, France
| | - S Eryn McFarlane
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Ludovic Dutoit
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden.,Department of Zoology, University of Otago, Dunedin 9016, New Zealand
| | - Anna Qvarnström
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden
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33
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Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka SHM, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M. PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/β-Catenin Response to Suppress Apc Min-Triggered Intestinal Tumor Formation. Cancer Res 2020; 81:38-49. [PMID: 33154092 DOI: 10.1158/0008-5472.can-20-1480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/26/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Genetic predisposition affects the penetrance of tumor-initiating mutations, such as APC mutations that stabilize β-catenin and cause intestinal tumors in mice and humans. However, the mechanisms involved in genetically predisposed penetrance are not well understood. Here, we analyzed tumor multiplicity and gene expression in tumor-prone Apc Min/+ mice on highly variant C57BL/6J (B6) and PWD/Ph (PWD) genetic backgrounds. (B6 × PWD) F1 APC Min offspring mice were largely free of intestinal adenoma, and several chromosome substitution (consomic) strains carrying single PWD chromosomes on the B6 genetic background displayed reduced adenoma numbers. Multiple dosage-dependent modifier loci on PWD chromosome 5 each contributed to tumor suppression. Activation of β-catenin-driven and stem cell-specific gene expression in the presence of Apc Min or following APC loss remained moderate in intestines carrying PWD chromosome 5, suggesting that PWD variants restrict adenoma initiation by controlling stem cell homeostasis. Gene expression of modifier candidates and DNA methylation on chromosome 5 were predominantly cis controlled and largely reflected parental patterns, providing a genetic basis for inheritance of tumor susceptibility. Human SNP variants of several modifier candidates were depleted in colorectal cancer genomes, suggesting that similar mechanisms may also affect the penetrance of cancer driver mutations in humans. Overall, our analysis highlights the strong impact that multiple genetic variants acting in networks can exert on tumor development. SIGNIFICANCE: These findings in mice show that, in addition to accidental mutations, cancer risk is determined by networks of individual gene variants.
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Affiliation(s)
- Alexandra L Farrall
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | | | - Christina Grimm
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecophysiology and Aquaculture, Berlin, Germany
| | | | - Marta Caparros
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jiri Forejt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Prague, Czech Republic
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.
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34
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Li Y, Schwalie PC, Bast-Habersbrunner A, Mocek S, Russeil J, Fromme T, Deplancke B, Klingenspor M. Systems-Genetics-Based Inference of a Core Regulatory Network Underlying White Fat Browning. Cell Rep 2020; 29:4099-4113.e5. [PMID: 31851936 DOI: 10.1016/j.celrep.2019.11.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/02/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Recruitment of brite/beige cells, known as browning of white adipose tissue (WAT), is an efficient way to turn an energy-storing organ into an energy-dissipating one and may therefore be of therapeutic value in combating obesity. However, a comprehensive understanding of the regulatory mechanisms mediating WAT browning is still lacking. Here, we exploit the large natural variation in WAT browning propensity between inbred mouse strains to gain an inclusive view of the core regulatory network coordinating this cellular process. Combining comparative transcriptomics, perturbation-based validations, and gene network analyses, we present a comprehensive gene regulatory network of inguinal WAT browning, revealing up to four distinct regulatory modules with key roles for uncovered transcriptional factors, while also providing deep insights into the genetic architecture of brite adipogenesis. The presented findings therefore greatly increase our understanding of the molecular drivers mediating the intriguing cellular heterogeneity and plasticity of adipose tissue.
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Affiliation(s)
- Yongguo Li
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Petra C Schwalie
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrea Bast-Habersbrunner
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Sabine Mocek
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Julie Russeil
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tobias Fromme
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Bart Deplancke
- Institute of Bio-engineering, School of Life Sciences, EPFL and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Martin Klingenspor
- Chair for Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany; EKFZ-Else Kröner-Fresenius Center for Nutritional Medicine, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany.
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35
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Abstract
Background The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion, particularly in the murine lineage. The exact mechanism and functional impact of evolutionarily novel CTCF binding sites are not yet fully understood. We investigated the impact of novel subspecies-specific CTCF binding sites in two Mus genus subspecies, Mus musculus domesticus and Mus musculus castaneus, that diverged 0.5 million years ago. Results CTCF binding site evolution is influenced by the action of the B2-B4 family of transposable elements independently in both lineages, leading to the proliferation of novel CTCF binding sites. A subset of evolutionarily young sites may harbour transcriptional functionality as evidenced by the stability of their binding across multiple tissues in M. musculus domesticus (BL6), while overall the distance of subspecies-specific CTCF binding to the nearest transcription start sites and/or topologically associated domains (TADs) is largely similar to musculus-common CTCF sites. Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome 4, thus forming a novel BL6 specific immune locus in which CTCF may play a regulatory role. Conclusions Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome.
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Affiliation(s)
- Dhoyazan Azazi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.,German Cancer Research Center (DKFZ), Division Regulatory Genomics and Cancer Evolution, 69120, Heidelberg, Germany
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. .,University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK. .,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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36
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Abstract
New species arise as the genomes of populations diverge. The developmental 'alarm clock' of speciation sounds off when sufficient divergence in genetic control of development leads hybrid individuals to infertility or inviability, the world awoken to the dawn of new species with intrinsic post-zygotic reproductive isolation. Some developmental stages will be more prone to hybrid dysfunction due to how molecular evolution interacts with the ontogenetic timing of gene expression. Considering the ontogeny of hybrid incompatibilities provides a profitable connection between 'evo-devo' and speciation genetics to better link macroevolutionary pattern, microevolutionary process, and molecular mechanisms. Here, we explore speciation alongside development, emphasizing their mutual dependence on genetic network features, fitness landscapes, and developmental system drift. We assess models for how ontogenetic timing of reproductive isolation can be predictable. Experiments and theory within this synthetic perspective can help identify new rules of speciation as well as rules in the molecular evolution of development.
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Affiliation(s)
- Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of TorontoTorontoCanada
| | - Joanna D Bundus
- Department of Integrative Biology, University of Wisconsin – MadisonMadisonUnited States
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Mattioli K, Oliveros W, Gerhardinger C, Andergassen D, Maass PG, Rinn JL, Melé M. Cis and trans effects differentially contribute to the evolution of promoters and enhancers. Genome Biol 2020; 21:210. [PMID: 32819422 PMCID: PMC7439725 DOI: 10.1186/s13059-020-02110-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Gene expression differences between species are driven by both cis and trans effects. Whereas cis effects are caused by genetic variants located on the same DNA molecule as the target gene, trans effects are due to genetic variants that affect diffusible elements. Previous studies have mostly assessed the impact of cis and trans effects at the gene level. However, how cis and trans effects differentially impact regulatory elements such as enhancers and promoters remains poorly understood. Here, we use massively parallel reporter assays to directly measure the transcriptional outputs of thousands of individual regulatory elements in embryonic stem cells and measure cis and trans effects between human and mouse. RESULTS Our approach reveals that cis effects are widespread across transcribed regulatory elements, and the strongest cis effects are associated with the disruption of motifs recognized by strong transcriptional activators. Conversely, we find that trans effects are rare but stronger in enhancers than promoters and are associated with a subset of transcription factors that are differentially expressed between human and mouse. While we find that cis-trans compensation is common within promoters, we do not see evidence of widespread cis-trans compensation at enhancers. Cis-trans compensation is inversely correlated with enhancer redundancy, suggesting that such compensation may often occur across multiple enhancers. CONCLUSIONS Our results highlight differences in the mode of evolution between promoters and enhancers in complex mammalian genomes and indicate that studying the evolution of individual regulatory elements is pivotal to understand the tempo and mode of gene expression evolution.
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Affiliation(s)
- Kaia Mattioli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA
| | - Winona Oliveros
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Daniel Andergassen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Philipp G Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - John L Rinn
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, CO, 80301, USA
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, 08034, Barcelona, Catalonia, Spain.
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38
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Han Z, Cui K, Placek K, Hong N, Lin C, Chen W, Zhao K, Jin W. Diploid genome architecture revealed by multi-omic data of hybrid mice. Genome Res 2020; 30:1097-1106. [PMID: 32759226 PMCID: PMC7462080 DOI: 10.1101/gr.257568.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 07/23/2020] [Indexed: 12/24/2022]
Abstract
Although mammalian genomes are diploid, previous studies extensively investigated the average chromatin architectures without considering the differences between homologous chromosomes. We generated Hi-C, ChIP-seq, and RNA-seq data sets from CD4 T cells of B6, Cast, and hybrid mice, to investigate the diploid chromatin organization and epigenetic regulation. Our data indicate that inter-chromosomal interaction patterns between homologous chromosomes are similar, and the similarity is highly correlated with their allelic coexpression levels. Reconstruction of the 3D nucleus revealed that distances of the homologous chromosomes to the center of nucleus are almost the same. The inter-chromosomal interactions at centromere ends are significantly weaker than those at telomere ends, suggesting that they are located in different regions within the chromosome territories. The majority of A|B compartments or topologically associated domains (TADs) are consistent between B6 and Cast. We found 58% of the haploids in hybrids maintain their parental compartment status at B6/Cast divergent compartments owing to cis effect. About 95% of the trans-effected B6/Cast divergent compartments converge to the same compartment status potentially because of a shared cellular environment. We showed the differentially expressed genes between the two haploids in hybrid were associated with either genetic or epigenetic effects. In summary, our multi-omics data from the hybrid mice provided haploid-specific information on the 3D nuclear architecture and a rich resource for further understanding the epigenetic regulation of haploid-specific gene expression.
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Affiliation(s)
- Zhijun Han
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.,Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Katarzyna Placek
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ni Hong
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chengqi Lin
- Institute of Life Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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39
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McGirr JA, Martin CH. Ecological divergence in sympatry causes gene misexpression in hybrids. Mol Ecol 2020; 29:2707-2721. [PMID: 32557903 DOI: 10.1111/mec.15512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 12/17/2022]
Abstract
Ecological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. Selection favouring gene regulatory divergence between species could result in transgressive levels of gene expression in F1 hybrids that may lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to identify patterns of hybrid gene misexpression that may be driven by adaptive regulatory divergence within a young radiation of Cyprinodon pupfishes, which consists of a dietary generalist and two trophic specialists-a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1,000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misexpressed in F1 hybrids. A subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length-the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can contribute to hybrid gene misexpression which may act as a reproductive barrier between nascent species.
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Affiliation(s)
- Joseph A McGirr
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Christopher H Martin
- Department of Biology, University of North Carolina, Chapel Hill, NC.,Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA
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40
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Krieger G, Lupo O, Levy AA, Barkai N. Independent evolution of transcript abundance and gene regulatory dynamics. Genome Res 2020; 30:1000-1011. [PMID: 32699020 PMCID: PMC7397873 DOI: 10.1101/gr.261537.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels, but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels. The majority of genes whose expression varied between the species maintained a conserved dynamic pattern. Cases of diverged dynamic pattern correspond to genes that were induced under distinct subsets of conditions in the two species. Profiling the interspecific hybrid allowed us to distinguish between genes with predominantly cis- or trans-regulatory variation. We find that trans-varying alleles are dominantly inherited, and that cis-variations are often complemented by variations in trans Based on these results, we suggest that gene expression diverges primarily through changes in expression levels, but does not alter the pattern by which these levels are dynamically regulated.
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Affiliation(s)
- Gat Krieger
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Offir Lupo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Avraham A Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Haas M, Himmelbach A, Mascher M. The contribution of cis- and trans-acting variants to gene regulation in wild and domesticated barley under cold stress and control conditions. J Exp Bot 2020; 71:2573-2584. [PMID: 31989179 PMCID: PMC7210754 DOI: 10.1093/jxb/eraa036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 01/27/2020] [Indexed: 05/16/2023]
Abstract
Barley, like other crops, has experienced a series of genetic changes that have impacted its architecture and growth habit to suit the needs of humans, termed the domestication syndrome. Domestication also resulted in a concomitant bottleneck that reduced sequence diversity in genes and regulatory regions. Little is known about regulatory changes resulting from domestication in barley. We used RNA sequencing to examine allele-specific expression in hybrids between wild and domesticated barley. Our results show that most genes have conserved regulation. In contrast to studies of allele-specific expression in interspecific hybrids, we find almost a complete absence of trans effects. We also find that cis regulation is largely stable in response to short-term cold stress. Our study has practical implications for crop improvement using wild relatives. Genes regulated in cis are more likely to be expressed in a new genetic background at the same level as in their native background.
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Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
- Correspondence: or Present address: University of Minnesota, Department of Agronomy and Plant Genetics, Saint Paul, MN 55108, USA
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany
- Correspondence: or Present address: University of Minnesota, Department of Agronomy and Plant Genetics, Saint Paul, MN 55108, USA
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42
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Zhong Y, Li L, He Y, He B, Li Z, Zhang Z, Zhang H, Yuan X, Li J. Activation of Steroidogenesis, Anti-Apoptotic Activity, and Proliferation in Porcine Granulosa Cells by RUNX1 Is Negatively Regulated by H3K27me3 Transcriptional Repression. Genes (Basel) 2020; 11:genes11050495. [PMID: 32365901 PMCID: PMC7290568 DOI: 10.3390/genes11050495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/20/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
H3K27me3 is an epigenetic modification that results in the repression of gene transcription. The transcription factor RUNX1 (the runt-related transcription factor 1) influences granulosa cells' growth and ovulation. This research uses ELISA, flow cytometry, EDU, ChIP-PCR, WB and qPCR to investigate steroidogenesis, cell apoptosis, and the proliferation effect of RUNX1 in porcine granulosa cells (pGCs) as regulated by H3K27me3. Decreased H3K27me3 stimulates the expression of steroidogenesis-related genes, including CYP11A1, PTGS2, and STAR, as well as prostaglandin. H3K27me3 transcriptionally represses RUNX1 here, whereas RUNX1 acts as an activator of FSHR, CYP11A1, and CYP19A1, promoting the production of androgen, estrogen, and prostaglandin, as well as increasing anti-apoptotic and cell proliferation activity, but decreasing progesterone. Both the complementary recovery of the H3K27me3 antagonist with the siRUNX1 signal, and the H3K27me3 agonist with the RUNX1 signal to maintain RUNX1 lead to the activation of CYP19A1, ER1, HSD17β4, and STAR here. Androgen and prostaglandin are significantly repressed but progesterone is markedly increased with the antagonist and siRUNX1. Prostaglandin is significantly promoted with the agonist and RUNX1. Furthermore, H3K27me3-RUNX1 affects the anti-apoptotic activity and stimulation of proliferation in pGCs. The present work verifies the transcriptional suppression of RUNX1 by H3K27me3 during antral follicular development and maturation, which determines the levels of hormone synthesis and cell apoptosis and proliferation in the pGC microenvironment.
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Affiliation(s)
- Yuyi Zhong
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
| | - Liying Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
| | - Yingting He
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
| | - Bo He
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
| | - Zhonghui Li
- Institute of Animal Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang 830000, China;
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
| | - Hao Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
| | - Xiaolong Yuan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
- Correspondence: (X.Y.); (J.L.); Tel.: +86-8528-2019 (X.Y.); +86-8528-5159 (J.L.)
| | - Jiaqi Li
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Centre for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Y.Z.); (L.L.); (Y.H.); (B.H.); (Z.Z.); (H.Z.)
- Correspondence: (X.Y.); (J.L.); Tel.: +86-8528-2019 (X.Y.); +86-8528-5159 (J.L.)
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43
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Yang J, Ruan H, Zou Y, Su Z, Gu X. Ancestral transcriptome inference based on RNA-Seq and ChIP-seq data. Methods 2020; 176:99-105. [DOI: 10.1016/j.ymeth.2018.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 11/24/2022] Open
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44
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Bartoš O, Röslein J, Kotusz J, Paces J, Pekárik L, Petrtýl M, Halačka K, Štefková Kašparová E, Mendel J, Boroń A, Juchno D, Leska A, Jablonska O, Benes V, Šídová M, Janko K. The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids. Mol Biol Evol 2020; 36:1902-1920. [PMID: 31077330 PMCID: PMC6735777 DOI: 10.1093/molbev/msz114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hybridization and polyploidization are important evolutionary processes whose impacts range from the alteration of gene expression and phenotypic variation to the triggering of asexual reproduction. We investigated fishes of the Cobitis taenia-elongatoides hybrid complex, which allowed us to disentangle the direct effects of both processes, due to the co-occurrence of parental species with their diploid and triploid hybrids. Employing morphological, ecological, and RNAseq approaches, we investigated the molecular determinants of hybrid and polyploid forms. In contrast with other studies, hybridization and polyploidy induced relatively very little transgressivity. Instead, Cobitis hybrids appeared intermediate with a clear effect of genomic dosing when triploids expressed higher similarity to the parent contributing two genome sets. This dosage effect was symmetric in the germline (oocyte gene expression), interestingly though, we observed an overall bias toward C. taenia in somatic tissues and traits. At the level of individual genes, expression-level dominance vastly prevailed over additivity or transgressivity. Also, trans-regulation of gene expression was less efficient in diploid hybrids than in triploids, where the expression modulation of homoeologs derived from the "haploid" parent was stronger than those derived from the "diploid" parent. Our findings suggest that the apparent intermediacy of hybrid phenotypes results from the combination of individual genes with dominant expression rather than from simple additivity. The efficiency of cross-talk between trans-regulatory elements further appears dosage dependent. Important effects of polyploidization may thus stem from changes in relative concentrations of trans-regulatory elements and their binding sites between hybridizing genomes. Links between gene regulation and asexuality are discussed.
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Affiliation(s)
- Oldřich Bartoš
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Röslein
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Paces
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Institute of Molecular Genetics, Laboratory of Genomics and Bioinformatics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Ladislav Pekárik
- Plant Science and Biodiversity Center, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia.,Faculty of Education, Trnava University, Trnava, Slovakia
| | - Miloslav Petrtýl
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karel Halačka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Štefková Kašparová
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Jan Mendel
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alicja Boroń
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Leska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Olga Jablonska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Monika Šídová
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Vestec, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biol 2020; 21:5. [PMID: 31910870 PMCID: PMC6945661 DOI: 10.1186/s13059-019-1894-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. CONCLUSIONS Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.
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Affiliation(s)
- Elissavet Kentepozidou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD UK
| | - Sarah J. Aitken
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Histopathology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ UK
| | - Christine Feig
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Klara Stefflova
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Duncan T. Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Division Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Maša Roller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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Wang Q, Jia Y, Wang Y, Jiang Z, Zhou X, Zhang Z, Nie C, Li J, Yang N, Qu L. Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old. BMC Genomics 2019; 20:933. [PMID: 31805870 PMCID: PMC6896592 DOI: 10.1186/s12864-019-6342-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background Gene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens. Results We provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements. Conclusions We present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.
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Affiliation(s)
- Qiong Wang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture and Rural, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yaxiong Jia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Department of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Zhihua Jiang
- Department of Animal Sciences, Center for Reproductive Biology, Veterinary and Biomedical Research Building, Washington State University, Pullman, USA
| | - Xiang Zhou
- College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zebin Zhang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Changsheng Nie
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junying Li
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- State Key Laboratory of Animal Nutrition, Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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47
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Wang H, Sawai A, Toji N, Sugioka R, Shibata Y, Suzuki Y, Ji Y, Hayase S, Akama S, Sese J, Wada K. Transcriptional regulatory divergence underpinning species-specific learned vocalization in songbirds. PLoS Biol 2019; 17:e3000476. [PMID: 31721761 PMCID: PMC6853299 DOI: 10.1371/journal.pbio.3000476] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 09/18/2019] [Indexed: 11/19/2022] Open
Abstract
Learning of most motor skills is constrained in a species-specific manner. However, the proximate mechanisms underlying species-specific learned behaviors remain poorly understood. Songbirds acquire species-specific songs through learning, which is hypothesized to depend on species-specific patterns of gene expression in functionally specialized brain regions for vocal learning and production, called song nuclei. Here, we leveraged two closely related songbird species, zebra finch, owl finch, and their interspecific first-generation (F1) hybrids, to relate transcriptional regulatory divergence between species with the production of species-specific songs. We quantified genome-wide gene expression in both species and compared this with allele-specific expression in F1 hybrids to identify genes whose expression in song nuclei is regulated by species divergence in either cis- or trans-regulation. We found that divergence in transcriptional regulation altered the expression of approximately 10% of total transcribed genes and was linked to differential gene expression between the two species. Furthermore, trans-regulatory changes were more prevalent than cis-regulatory and were associated with synaptic formation and transmission in song nucleus RA, the avian analog of the mammalian laryngeal motor cortex. We identified brain-derived neurotrophic factor (BDNF) as an upstream mediator of trans-regulated genes in RA, with a significant correlation between individual variation in BDNF expression level and species-specific song phenotypes in F1 hybrids. This was supported by the fact that the pharmacological overactivation of BDNF receptors altered the expression of its trans-regulated genes in the RA, thus disrupting the learned song structures of adult zebra finch songs at the acoustic and sequence levels. These results demonstrate functional neurogenetic associations between divergence in region-specific transcriptional regulation and species-specific learned behaviors.
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Affiliation(s)
- Hongdi Wang
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Azusa Sawai
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Noriyuki Toji
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Rintaro Sugioka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yukino Shibata
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yuika Suzuki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yu Ji
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shin Hayase
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Satoru Akama
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Humanome Lab Inc., Tokyo, Japan
| | - Kazuhiro Wada
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Faculty of Science, Hokkaido University, Sapporo, Japan
- Department of Biological Sciences, Hokkaido University, Sapporo, Japan
- * E-mail:
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Zhong H, Zhang X, Xu Q, Yan J, Han Z, Zheng H, Xiao J, Tang Z, Wang F, Luo Y, Zhou Y. Nonadditive and Asymmetric Allelic Expression of Growth Hormone in Hybrid Tilapia. Front Genet 2019; 10:961. [PMID: 31681414 PMCID: PMC6803431 DOI: 10.3389/fgene.2019.00961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 09/09/2019] [Indexed: 12/04/2022] Open
Abstract
Hybridization is a common breeding technique that can improve germplasm through heterosis in aquaculture. However, the regulation of key gene expression, including the details of transcriptional level changes at the beginning of hybridization events, remains largely undefined, especially in teleosts. In this study, by interspecies crossing between two pure lines of Nile tilapia and blue tilapia, we obtained a hybrid tilapia population as a model to elucidate heterosis, and we traced the molecular outcomes of growth hormone (GH) expression and allele-specific expression (ASE) in hybrids. The hybrids display growth vigor compared to their parents in the 120-day growth trial. GH mRNA expression was uniquely expressed in the pituitary. Higher GH expression was found in the hybrid than the midparent value, in both males and females, showing a nonadditive pattern. We identified four single-nucleotide polymorphism sites between Nile tilapia and blue tilapia. Subsequently, by pyrosequencing, we found asymmetric allelic expression in hybrids with higher maternal allelic transcript ratios in both males and females. Fasting significantly increased GH expression in hybrids, but asymmetric allelic expression was not affected by feeding or fasting conditions. Finally, we identified cis and trans effects via overall expression and ASE values in the hybrid, which showed that the cis and trans effects promoted the expression of maternal subgenome in the hybrid, contributing to the expression superiority of GH in hybrid tilapia. Taken together, the results of our study first illustrated the concept of GH expression superiority and its formation mechanism in hybrid fish with growth vigor.
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Affiliation(s)
- Huan Zhong
- Tilapia Genetics and Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiaojin Zhang
- Tilapia Genetics and Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Qian Xu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Jinpeng Yan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Zhuojun Han
- Tilapia Genetics and Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China.,College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Huifang Zheng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jun Xiao
- Tilapia Genetics and Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Zhanyang Tang
- Tilapia Genetics and Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Fenghua Wang
- Sports Biochemistry Laboratory, Institute of Physical Education, Xinjiang Normal University, Urumqi, China
| | - Yongju Luo
- Tilapia Genetics and Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China.,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yi Zhou
- Tilapia Genetics and Breeding Center, Guangxi Academy of Fishery Sciences, Nanning, China
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Baker RL, Leong WF, Brock MT, Rubin MJ, Markelz RJC, Welch S, Maloof JN, Weinig C. Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development. PLoS Genet 2019; 15:e1008367. [PMID: 31513571 DOI: 10.1371/journal.pgen.1008367] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 09/24/2019] [Accepted: 08/13/2019] [Indexed: 12/01/2022] Open
Abstract
Plant developmental dynamics can be heritable, genetically correlated with fitness and yield, and undergo selection. Therefore, characterizing the mechanistic connections between the genetic architecture governing plant development and the resulting ontogenetic dynamics of plants in field settings is critically important for agricultural production and evolutionary ecology. We use hierarchical Bayesian Function-Valued Trait (FVT) models to estimate Brassica rapa growth curves throughout ontogeny, across two treatments, and in two growing seasons. We find genetic variation for plasticity of growth rates and final sizes, but not the inflection point (transition from accelerating to decelerating growth) of growth curves. There are trade-offs between growth rate and duration, indicating that selection for maximum yields at early harvest dates may come at the expense of late harvest yields and vice versa. We generate eigengene modules and determine which are co-expressed with FVT traits using a Weighted Gene Co-expression Analysis. Independently, we seed a Mutual Rank co-expression network model with FVT traits to identify specific genes and gene networks related to FVT. GO-analyses of eigengene modules indicate roles for actin/cytoskeletal genes, herbivore resistance/wounding responses, and cell division, while MR networks demonstrate a close association between metabolic regulation and plant growth. We determine that combining FVT Quantitative Trait Loci (QTL) and MR genes/WGCNA eigengene expression profiles better characterizes phenotypic variation than any single data type (i.e. QTL, gene, or eigengene alone). Our network analysis allows us to employ a targeted eQTL analysis, which we use to identify regulatory hotspots for FVT. We examine cis vs. trans eQTL that mechanistically link FVT QTL with structural trait variation. Colocalization of FVT, gene, and eigengene eQTL provide strong evidence for candidate genes influencing plant height. The study is the first to explore eQTL for FVT, and specifically do so in agroecologically relevant field settings. We estimate the developmental dynamics of plant growth using mathematical functions to fit continuous functions to discrete plant height data collected throughout growth, and we use the parameters defining these mathematical functions as data. We identify genomic regions controlling plant growth and filter a novel transcriptomic data set using network reconstruction models to identify the genes and eigengenes associated with plant height. We combine these genomic and transcriptomic data to predict variation in plant height, and we use quantitative genetics to mechanistically connect plant genetics, transcriptomics, and development. Our approach demonstrates two powerful methods for the type of data reduction (FVT modeling and gene expression network reconstruction for targeted eQTL analyses) and data integration that will be necessary for driving forward the field of genetics in the post-genomic era. To the best of our knowledge, we are the first to apply these techniques to continuous models of plant development, and the first to do so in agroecologically relevant field settings.
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50
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Kondo S, Kato H, Suzuki Y, Takada T, Eitoku M, Shiroishi T, Suganuma N, Sugano S, Kiyosawa H. Monoallelic, antisense and total RNA transcription in an in vitro neural differentiation system based on F1 hybrid mice. J Cell Sci 2019; 132:jcs.228973. [PMID: 31409693 DOI: 10.1242/jcs.228973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/04/2019] [Indexed: 11/20/2022] Open
Abstract
We developed an in vitro system to differentiate embryonic stem cells (ESCs) derived from reciprocally crossed F1 hybrid mice into neurons, and used it to investigate poly(A)+ and total RNA transcription at different stages of cell differentiation. By comparing expression profiles of transcripts assembled from 20 RNA sequencing datasets [2 alleles×(2 cell lines×4 time-points+2 mouse brains)], the relative influence of strain, cell and parent specificities to overall expression could be assessed. Divergent expression profiles of ESCs converged tightly at neural progenitor stage. Patterns of temporal variation of monoallelically expressed transcripts and antisense transcripts were quantified. Comparison of sense and antisense transcript pairs within the poly(A)+ sample, within the total RNA sample, and across poly(A)+ and total RNA samples revealed distinct rates of pairs showing anti-correlated expression variation. Unique patterns of sharing of poly(A)+ and poly(A)- transcription were identified in distinct RNA species. Regulation and functionality of monoallelic expression, antisense transcripts and poly(A)- transcription remain elusive. We demonstrated the effectiveness of our approach to capture these transcriptional activities, and provided new resources to elucidate the mammalian developmental transcriptome.
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Affiliation(s)
- Shinji Kondo
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan
| | - Hidemasa Kato
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Toyoyuki Takada
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan.,Mammalian Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Masamitsu Eitoku
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Toshihiko Shiroishi
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan.,Mammalian Genetics Laboratory, National Institute of Genetics, Shizuoka 411-8540, Japan
| | - Narufumi Suganuma
- Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Hidenori Kiyosawa
- Transdisciplinary Research Integration Center, Research Organization of Information and Systems, Tokyo 105-0001, Japan .,Department of Environmental Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
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