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Wu J, Duan C, Lan L, Chen W, Mao X. Sex Differences in Cochlear Transcriptomes in Horseshoe Bats. Animals (Basel) 2024; 14:1177. [PMID: 38672325 PMCID: PMC11047584 DOI: 10.3390/ani14081177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Sexual dimorphism of calls is common in animals, whereas studies on the molecular basis underlying this phenotypic variation are still scarce. In this study, we used comparative transcriptomics of cochlea to investigate the sex-related difference in gene expression and alternative splicing in four Rhinolophus taxa. Based on 31 cochlear transcriptomes, we performed differential gene expression (DGE) and alternative splicing (AS) analyses between the sexes in each taxon. Consistent with the degree of difference in the echolocation pulse frequency between the sexes across the four taxa, we identified the largest number of differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) in R. sinicus. However, we also detected multiple DEGs and ASGs in taxa without sexual differences in echolocation pulse frequency, suggesting that these genes might be related to other parameters of echolocation pulse rather than the frequency component. Some DEGs and ASGs are related to hearing loss or deafness genes in human or mice and they can be considered to be candidates associated with the sexual differences of echolocation pulse in bats. We also detected more than the expected overlap of DEGs and ASGs in two taxa. Overall, our current study supports the important roles of both DGE and AS in generating or maintaining sexual differences in animals.
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Affiliation(s)
| | | | | | | | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; (J.W.); (C.D.); (L.L.); (W.C.)
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2
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Liu D, Yu H, Xue N, Bao H, Gao Q, Tian Y. Alternative splicing patterns of hnrnp genes in gill tissues of rainbow trout (Oncorhynchus mykiss) during salinity changes. Comp Biochem Physiol B Biochem Mol Biol 2024; 271:110948. [PMID: 38281704 DOI: 10.1016/j.cbpb.2024.110948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 01/30/2024]
Abstract
Alternative splicing (AS) plays an important role in various physiological processes in eukaryotes, such as the stress response. However, patterns of AS events remain largely unexplored during salinity acclimation in fishes. In this study, we conducted AS analysis using RNA-seq datasets to explore splicing patterns in the gill tissues of rainbow trout exposed to altered salinity environments, ranging from 0 ‰ (T0) to 30 ‰ (T30). The results revealed 1441, 351, 483, 1051 and 1049 differentially alternatively spliced (DAS) events in 5 pairwise comparisons, including T6 vs. T0, T12 vs. T0, T18 vs. T0, T24 vs. T0, and T30 vs. T0, respectively. These DAS events were derived from 1290, 328, 444, 963 and 948 genes. Enrichment analysis indicated that these DAS genes were related to RNA splicing and processing. Among these, 14 DAS genes were identified as members of the large heterogeneous nuclear RNP (hnRNP) gene family. Alternative 3' splice site (A3SS), exon skipping (SE) and intron retention (RI) events resulted in the fragmentation or even loss of the functional RNA recognition motif (RRM) domains in hnrnpa0, hnrnp1a, hnrnp1b and hnrnpc genes. The incomplete RRM domains would hinder the interactions between hnRNP genes and pre-mRNAs. It would in turn influence the splicing patterns and mRNA stability of downstream target genes in response to salinity changes. The study provides insights into salinity acclimation in gill tissues of rainbow trout and serves as a significant reference on the osmoregulation mechanisms at post-transcription regulation levels in fish.
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Affiliation(s)
- Dazhi Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Han Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Na Xue
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Hancheng Bao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China
| | - Qinfeng Gao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
| | - Yuan Tian
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, Shandong Province, China.
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3
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Krueger CJ, Dai Z, Zhu C, Zhang B. Heritable CRISPR Mutagenesis of Essential Maternal Effect Genes as a Simple Tool for Sustained Population Suppression of Invasive Species in a Zebrafish Model. Zebrafish 2024. [PMID: 38512221 DOI: 10.1089/zeb.2023.0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
Invasive species control is important for ecological and agricultural management. Genetic methods can provide species specificity for population control. We developed heritable maternal effect embryo lethality (HMEL), a novel strategy allowing negative population pressure from HMEL individuals to be transmitted within a population across generations. We demonstrate the HMEL technique in zebrafish through genome-integrated CRISPR/Cas targeted mutagenic disruption of nucleoplasmin 2b (npm2b), a female-specific essential maternal effect gene, causing heritable sex-limited disruption of reproduction. HMEL-induced high-efficiency mutation of npm2b in females suppresses population, while males transmit the HMEL allele across generations. HMEL could be easily modified to target other genes causing sex-specific sterility, or generalized to control invasive fish or other vertebrate species for environmental conservation or agricultural protection.
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Affiliation(s)
- Christopher J Krueger
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Zhifei Dai
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Cheng Zhu
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
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4
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Jones EF, Haldar A, Oza VH, Lasseigne BN. Quantifying transcriptome diversity: a review. Brief Funct Genomics 2024; 23:83-94. [PMID: 37225889 DOI: 10.1093/bfgp/elad019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/14/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Following the central dogma of molecular biology, gene expression heterogeneity can aid in predicting and explaining the wide variety of protein products, functions and, ultimately, heterogeneity in phenotypes. There is currently overlapping terminology used to describe the types of diversity in gene expression profiles, and overlooking these nuances can misrepresent important biological information. Here, we describe transcriptome diversity as a measure of the heterogeneity in (1) the expression of all genes within a sample or a single gene across samples in a population (gene-level diversity) or (2) the isoform-specific expression of a given gene (isoform-level diversity). We first overview modulators and quantification of transcriptome diversity at the gene level. Then, we discuss the role alternative splicing plays in driving transcript isoform-level diversity and how it can be quantified. Additionally, we overview computational resources for calculating gene-level and isoform-level diversity for high-throughput sequencing data. Finally, we discuss future applications of transcriptome diversity. This review provides a comprehensive overview of how gene expression diversity arises, and how measuring it determines a more complete picture of heterogeneity across proteins, cells, tissues, organisms and species.
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Affiliation(s)
- Emma F Jones
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anisha Haldar
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vishal H Oza
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brittany N Lasseigne
- The Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
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5
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Grieshop K, Ho EKH, Kasimatis KR. Dominance reversals: the resolution of genetic conflict and maintenance of genetic variation. Proc Biol Sci 2024; 291:20232816. [PMID: 38471544 DOI: 10.1098/rspb.2023.2816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/05/2024] [Indexed: 03/14/2024] Open
Abstract
Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait or sex) being dominant in that context but recessive where deleterious. This context dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here, we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods that could facilitate the identification of antagonistic genetic variation (dominance ordination, allele-specific expression and allele-specific ATAC-Seq (assay for transposase-accessible chromatin with sequencing)). There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.
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Affiliation(s)
- Karl Grieshop
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada M5S 1A1
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Eddie K H Ho
- Department of Biology, Reed College, 3203 SE Woodstock Blvd, Portland, OR 97202, USA
| | - Katja R Kasimatis
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada M5S 1A1
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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6
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Shaw DE, Naftaly AS, White MA. Positive Selection Drives cis-regulatory Evolution Across the Threespine Stickleback Y Chromosome. Mol Biol Evol 2024; 41:msae020. [PMID: 38306314 PMCID: PMC10899008 DOI: 10.1093/molbev/msae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 02/04/2024] Open
Abstract
Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive selection can also favor the down-regulation of coding regions on the Y chromosome that contain deleterious mutations. Identifying the relative rates of cis-regulatory sequence evolution across Y chromosomes has been challenging due to the limited number of reference assemblies. The threespine stickleback (Gasterosteus aculeatus) Y chromosome is an excellent model to identify how regulatory mutations accumulate on Y chromosomes due to its intermediate state of divergence from the X chromosome. A large number of Y-linked gametologs still exist across 3 differently aged evolutionary strata to test these hypotheses. We found that putative enhancer regions on the Y chromosome exhibited elevated substitution rates and decreased polymorphism when compared to nonfunctional sites, like intergenic regions and synonymous sites. This suggests that many cis-regulatory regions are under positive selection on the Y chromosome. This divergence was correlated with X-biased gametolog expression, indicating the loss of expression from the Y chromosome may be favored by selection. Our findings provide evidence that Y-linked cis-regulatory regions exhibit signs of positive selection quickly after the suppression of recombination and allow comparisons with recent theoretical models that suggest the rapid divergence of regulatory regions may be favored to mask deleterious mutations on the Y chromosome.
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Affiliation(s)
- Daniel E Shaw
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | - Michael A White
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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7
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Chen G, Chen J, Qi L, Yin Y, Lin Z, Wen H, Zhang S, Xiao C, Bello SF, Zhang X, Nie Q, Luo W. Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation. Cell Prolif 2024; 57:e13545. [PMID: 37705195 PMCID: PMC10849790 DOI: 10.1111/cpr.13545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/08/2023] [Accepted: 08/28/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative splicing (AS) disruption has been linked to disorders of muscle development, as well as muscular atrophy. However, the precise changes in AS patterns that occur during myogenesis are not well understood. Here, we employed isoform long-reads RNA-seq (Iso-seq) and single-cell RNA-seq (scRNA-seq) to investigate the AS landscape during myogenesis. Our Iso-seq data identified 61,146 full-length isoforms representing 11,682 expressed genes, of which over 52% were novel. We identified 38,022 AS events, with most of these events altering coding sequences and exhibiting stage-specific splicing patterns. We identified AS dynamics in different types of muscle cells through scRNA-seq analysis, revealing genes essential for the contractile muscle system and cytoskeleton that undergo differential splicing across cell types. Gene-splicing analysis demonstrated that AS acts as a regulator, independent of changes in overall gene expression. Two isoforms of splicing factor TRA2B play distinct roles in myogenic differentiation by triggering AS of TGFBR2 to regulate canonical TGF-β signalling cascades differently. Our study provides a valuable transcriptome resource for myogenesis and reveals the complexity of AS and its regulation during myogenesis.
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Affiliation(s)
- Genghua Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Jiahui Chen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Lin Qi
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Yunqian Yin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Zetong Lin
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Huaqiang Wen
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Shuai Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Chuanyun Xiao
- Human and Animal PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Semiu Folaniyi Bello
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Xiquan Zhang
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Qinghua Nie
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
| | - Wen Luo
- College of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina
- Guangdong Provincial Key Lab of Agro‐Animal Genomics and Molecular Breeding, Lingnan Guangdong Laboratory of Modern Agriculture & State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of AgricultureGuangzhouGuangdongChina
- State Key Laboratory of Livestock and Poultry Breeding, and Lingnan Guangdong Laboratory of AgricultureSouth China Agricultural UniversityGuangzhouChina
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8
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Chen W, Zhou W, Li Q, Mao X. Sex differences in gene expression and alternative splicing in the Chinese horseshoe bat. PeerJ 2023; 11:e15231. [PMID: 37123006 PMCID: PMC10135408 DOI: 10.7717/peerj.15231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Sexually dimorphic traits are common in sexually reproducing organisms and can be encoded by differential gene regulation between males and females. Although alternative splicing is common mechanism in generating transcriptional diversity, its role in generating sex differences relative to differential gene expression is less clear. Here, we investigate the relative roles of differential gene expression and alternative splicing between male and female the horseshoe bat species, Rhinolophus sinicus. Horseshoe bats are an excellent model to study acoustic differences between sexes. Using RNA-seq analyses of two somatic tissues (brain and liver) from males and females of the same population, we identified 3,471 and 2,208 differentially expressed genes between the sexes (DEGs) in the brain and liver, respectively. DEGs were enriched with functional categories associated with physiological difference of the sexes (e.g.,gamete generation and energy production for reproduction in females). In addition, we also detected many differentially spliced genes between the sexes (DSGs, 2,231 and 1,027 in the brain and liver, respectively) which were mainly involved in regulation of RNA splicing and mRNA metabolic process. Interestingly, we found a significant enrichment of DEGs on the X chromosome, but not for DSGs. As for the extent of overlap between the two sets of genes, more than expected overlap of DEGs and DSGs was observed in the brain but not in the liver. This suggests that more complex tissues, such as the brain, may require the intricate and simultaneous interplay of both differential gene expression and splicing of genes to govern sex-specific functions. Overall, our results support that variation in gene expression and alternative splicing are important and complementary mechanisms governing sex differences.
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Affiliation(s)
- Wenli Chen
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Qianqian Li
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
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9
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Nath S, Welch LA, Flanagan MK, White MA. Meiotic pairing and double-strand break formation along the heteromorphic threespine stickleback sex chromosomes. Chromosome Res 2022; 30:429-442. [PMID: 35635635 DOI: 10.1007/s10577-022-09699-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 01/25/2023]
Abstract
Double-strand break repair during meiosis is normally achieved using the homologous chromosome as a repair template. Heteromorphic sex chromosomes share little sequence homology, presenting unique challenges to the repair of double-strand breaks. Our understanding of how heteromorphic sex chromosomes behave during meiosis has been focused on ancient sex chromosomes, where the X and Y differ markedly in overall structure and gene content. It remains unclear how more recently evolved sex chromosomes that share considerably more sequence homology with one another pair and form double-strand breaks. One possibility is barriers to pairing evolve rapidly. Alternatively, recently evolved sex chromosomes may exhibit pairing and double-strand break repair that more closely resembles that of their autosomal ancestors. Here, we use the recently evolved X and Y chromosomes of the threespine stickleback fish (Gasterosteus aculeatus) to study patterns of pairing and double-stranded break formation using molecular cytogenetics. We found that the sex chromosomes of threespine stickleback fish did not pair exclusively in the pseudoautosomal region. Instead, the chromosomes fully paired in a non-homologous fashion. To achieve this, the X chromosome underwent synaptic adjustment during pachytene to match the axis length of the Y chromosome. Double-strand break formation and repair rate also matched that of the autosomes. Our results highlight that recently evolved sex chromosomes exhibit meiotic behavior that is reminiscent of autosomes and argues for further work to identify the homologous templates that are used to repair double-strand breaks on the X and Y chromosomes.
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Affiliation(s)
- Shivangi Nath
- Department of Genetics, University of Georgia, 120 Green St, Athens, GA, 30602, USA
| | - Lucille A Welch
- Department of Genetics, University of Georgia, 120 Green St, Athens, GA, 30602, USA
| | - Mary K Flanagan
- Department of Genetics, University of Georgia, 120 Green St, Athens, GA, 30602, USA
| | - Michael A White
- Department of Genetics, University of Georgia, 120 Green St, Athens, GA, 30602, USA.
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10
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Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes. Int J Mol Sci 2022; 23:ijms231911135. [PMID: 36232445 PMCID: PMC9570262 DOI: 10.3390/ijms231911135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.
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11
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Detecting signatures of selection on gene expression. Nat Ecol Evol 2022; 6:1035-1045. [PMID: 35551249 DOI: 10.1038/s41559-022-01761-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major unanswered questions in disentangling how selection acts on the transcriptome.
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12
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Healey HM, Bassham S, Cresko WA. Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis. Genetics 2022; 220:iyac017. [PMID: 35143654 PMCID: PMC8893252 DOI: 10.1093/genetics/iyac017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/24/2022] [Indexed: 12/02/2022] Open
Abstract
Single-cell RNA sequencing is a powerful technique that continues to expand across various biological applications. However, incomplete 3'-UTR annotations can impede single-cell analysis resulting in genes that are partially or completely uncounted. Performing single-cell RNA sequencing with incomplete 3'-UTR annotations can hinder the identification of cell identities and gene expression patterns and lead to erroneous biological inferences. We demonstrate that performing single-cell isoform sequencing in tandem with single-cell RNA sequencing can rapidly improve 3'-UTR annotations. Using threespine stickleback fish (Gasterosteus aculeatus), we show that gene models resulting from a minimal embryonic single-cell isoform sequencing dataset retained 26.1% greater single-cell RNA sequencing reads than gene models from Ensembl alone. Furthermore, pooling our single-cell sequencing isoforms with a previously published adult bulk Iso-Seq dataset from stickleback, and merging the annotation with the Ensembl gene models, resulted in a marginal improvement (+0.8%) over the single-cell isoform sequencing only dataset. In addition, isoforms identified by single-cell isoform sequencing included thousands of new splicing variants. The improved gene models obtained using single-cell isoform sequencing led to successful identification of cell types and increased the reads identified of many genes in our single-cell RNA sequencing stickleback dataset. Our work illuminates single-cell isoform sequencing as a cost-effective and efficient mechanism to rapidly annotate genomes for single-cell RNA sequencing.
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Affiliation(s)
- Hope M Healey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, OR 97403, USA
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Verta JP, Jacobs A. The role of alternative splicing in adaptation and evolution. Trends Ecol Evol 2021; 37:299-308. [PMID: 34920907 DOI: 10.1016/j.tree.2021.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/26/2021] [Accepted: 11/19/2021] [Indexed: 01/02/2023]
Abstract
Regulation of gene expression plays a central role in adaptive divergence and evolution. Although the role of gene regulation in microevolutionary processes is gaining wide acceptance, most studies have only investigated the evolution of transcript levels, ignoring the potentially significant role of transcript structures. We argue that variation in alternative splicing plays an important and widely unexplored role in adaptation (e.g., by increasing transcriptome and/or proteome diversity, or buffering potentially deleterious genetic variation). New studies increasingly highlight the potential for independent evolution in alternative splicing and transcript level, providing alternative paths for selection to act upon. We propose that alternative splicing and transcript levels can provide contrasting, nonredundant mechanisms of equal importance for adaptive diversification of gene function and regulation.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK.
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