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Blumenstiel JP. From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements. Semin Cell Dev Biol 2025; 164:1-12. [PMID: 38823219 DOI: 10.1016/j.semcdb.2024.05.001] [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: 10/10/2023] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States.
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2
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Zhang H, Liu Q, Lu J, Wu L, Cheng Z, Qiao G, Huang X. Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality. Mol Ecol Resour 2024; 24:e14019. [PMID: 39262229 DOI: 10.1111/1755-0998.14019] [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: 12/15/2023] [Revised: 08/17/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
The origin of sociality represents one of the most important evolutionary transitions. Insect sociality evolved in some hemipteran aphids, which can produce soldiers and normal nymphs with distinct morphology and behaviour through parthenogenesis. The lack of genomic data resources has hindered the investigations into molecular mechanisms underlying their social evolution. Herein, we generated the first chromosomal-level genome of a social hemipteran (Pseudoregma bambucicola) with highly specialized soldiers and performed comparative genomic and transcriptomic analyses to elucidate the molecular signatures and regulatory mechanisms of caste differentiation. P. bambucicola has a larger known aphid genome of 582.2 Mb with an N50 length of 11.24 Mb, and about 99.6% of the assembly was anchored to six chromosomes with a scaffold N50 of 98.27 Mb. A total of 14,027 protein-coding genes were predicted and 37.33% of the assembly were identified as repeat sequences. The social evolution is accompanied by a variety of changes in genome organization, including expansion of gene families related to transcription factors, transposable elements, as well as species-specific expansions of certain sugar transporters and UGPases involved in carbohydrate metabolism. We also characterized large candidate gene sets linked to caste differentiation and found evidence of expression regulation and positive selection acting on energy metabolism and muscle structure, explaining the soldier-specific traits including morphological and behavioural specialization, developmental arrest and infertility. Overall, this study offers new insights into the molecular basis of social aphids and the evolution of insect sociality and also provides valuable data resources for further comparative and functional studies.
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Affiliation(s)
- Hui Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianjun Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liying Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhentao Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaolei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Insect Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
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Du P, Li J, Hua M, Zhu L, Chen C, Zeng H. Potential Contributions of Human Endogenous Retroviruses in Innate Immune Memory. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1225-1233. [PMID: 39230265 DOI: 10.4049/jimmunol.2300411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/08/2024] [Indexed: 09/05/2024]
Abstract
The phenomenon wherein innate immune cells adopt long-term inflammatory phenotypes following the first stimuli is named trained immunity and can improve host defense against infections. Transcriptional and epigenetic reprogramming are critical mechanisms of trained immunity; however, the regulatory networks are not entirely clear at present. The human endogenous retroviruses (HERVs) provide large amounts of transcriptional regulators in the regulatory pathways. In this study, we analyzed published large omics data to explore the roles of such "dark matter" of the human genome in trained and tolerant macrophages. We collected 80 RNA sequencing data and 62 sequencing data to detect histone modifications and active regulatory regions from nine published studies on trained and tolerant macrophages. By analyzing the characteristics of transcription and epigenetic modification of HERVs, as well as their association with gene expression, we found that 15.3% of HERVs were transcribed nonrandomly from noncoding regions and enriched in specific HERV families and specific chromosomes, such as chromosomes 11, 15, 17, and 19, and they were highly related with the expression of adjacent genes. We found that 295 differentially expressed HERVs are located in 50-kbp flanking regions of 142 differentially expressed genes. We found epigenetic changes of these HERVs and that overlap with predicted enhancers and identified 35 enhancer-like HERVs. The related genes were highly involved in the activation and inflammatory responses, such as the TLR pathway. Other pathways including phosphoinositide signaling and transport of folate and K+ might be also related with trained immunity, which require further study. These results demonstrated that HERVs might play important roles in trained immunity.
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Affiliation(s)
- Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China; and
| | - Jiarui Li
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mingxi Hua
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Liuluan Zhu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China; and
| | - Chen Chen
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Hui Zeng
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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Wang R, Zheng Y, Zhang Z, Song K, Wu E, Zhu X, Wu TP, Ding J. MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell. Nat Commun 2024; 15:8798. [PMID: 39394211 DOI: 10.1038/s41467-024-53114-7] [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: 09/25/2023] [Accepted: 09/24/2024] [Indexed: 10/13/2024] Open
Abstract
Transposable elements (TEs) are crucial for genetic diversity and gene regulation. Current single-cell quantification methods often align multi-mapping reads to either 'best-mapped' or 'random-mapped' locations and categorize them at the subfamily levels, overlooking the biological necessity for accurate, locus-specific TE quantification. Moreover, these existing methods are primarily designed for and focused on transcriptomics data, which restricts their adaptability to single-cell data of other modalities. To address these challenges, here we introduce MATES, a deep-learning approach that accurately allocates multi-mapping reads to specific loci of TEs, utilizing context from adjacent read alignments flanking the TE locus. When applied to diverse single-cell omics datasets, MATES shows improved performance over existing methods, enhancing the accuracy of TE quantification and aiding in the identification of marker TEs for identified cell populations. This development facilitates the exploration of single-cell heterogeneity and gene regulation through the lens of TEs, offering an effective transposon quantification tool for the single-cell genomics community.
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Affiliation(s)
- Ruohan Wang
- School of Computer Science, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Yumin Zheng
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Zijian Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kailu Song
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Erxi Wu
- Department of Neurosurgery, Baylor College of Medicine, Temple, TX, USA
- College of Medicine and Irma Lerma Rangel College of Pharmacy, Texas A&M University, College Station, TX, USA
- LIVESTRONG Cancer Institutes and Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX, USA
| | | | - Tao P Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Jun Ding
- School of Computer Science, McGill University, Montreal, Quebec, Canada.
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
- Department of Medicine, McGill University, Montreal, Quebec, Canada.
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, Quebec, Canada.
- Mila-Quebec AI Institue, Montreal, Quebec, Canada.
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Azad MF, Tong T, Lau NC. Transposable Element (TE) insertion predictions from RNAseq inputs and TE impact on RNA splicing and gene expression in Drosophila brain transcriptomes. Mob DNA 2024; 15:20. [PMID: 39385293 PMCID: PMC11462757 DOI: 10.1186/s13100-024-00330-z] [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: 06/07/2024] [Accepted: 09/23/2024] [Indexed: 10/12/2024] Open
Abstract
Recent studies have suggested that Transposable Elements (TEs) residing in introns frequently splice into and alter primary gene-coding transcripts. To re-examine the exonization frequency of TEs into protein-coding gene transcripts, we re-analyzed a Drosophila neuron circadian rhythm RNAseq dataset and a deep long RNA fly midbrain RNAseq dataset using our Transposon Insertion and Depletion Analyzer (TIDAL) program. Our TIDAL results were able to predict several TE insertions from RNAseq data that were consistent with previous published studies. However, we also uncovered many discrepancies in TE-exonization calls, such as reads that mainly support intron retention of the TE and little support for chimeric mRNA spliced to the TE. We then deployed rigorous genomic DNA-PCR (gDNA-PCR) and RT-PCR procedures on TE-mRNA fusion candidates to see how many of bioinformatics predictions could be validated. By testing a w1118 strain from which the deeper long RNAseq data was derived and comparing to an OreR strain, only 9 of 23 TIDAL candidates (< 40%) could be validated as a novel TE insertion by gDNA-PCR, indicating that deeper study is needed when using RNAseq data as inputs into current TE-insertion prediction programs. Of these validated calls, our RT-PCR results only supported TE-intron retention. Lastly, in the Dscam2 and Bx genes of the w1118 strain that contained intronic TEs, gene expression was 23 times higher than the OreR genes lacking the TEs. This study's validation approach indicates that chimeric TE-mRNAs are infrequent and cautions that more optimization is required in bioinformatics programs to call TE insertions using RNAseq datasets.
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Affiliation(s)
- Md Fakhrul Azad
- Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Tong Tong
- Graduate Program in Bioinformatics, Boston University, Boston, MA, 02118, USA
| | - Nelson C Lau
- Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA.
- Graduate Program in Bioinformatics, Boston University, Boston, MA, 02118, USA.
- Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA.
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Kosuge M, Ito J, Hamada M. Landscape of evolutionary arms races between transposable elements and KRAB-ZFP family. Sci Rep 2024; 14:23358. [PMID: 39375372 PMCID: PMC11458898 DOI: 10.1038/s41598-024-73752-7] [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: 07/24/2024] [Accepted: 09/20/2024] [Indexed: 10/09/2024] Open
Abstract
Transposable elements (TEs) are mobile parasitic sequences that have expanded within the host genome. It has been hypothesized that host organisms have expanded the Krüppel-associated box-containing zinc finger proteins (KRAB-ZFPs), which epigenetically suppress TEs, to counteract disorderly TE transpositions. This process is referred to as the evolutionary arms race. However, the extent to which this evolutionary arms race occurred across various TE families remains unclear. In the present study, we systematically explored the evolutionary arms race between TE families and human KRAB-ZFPs using public ChIP-seq data. We discovered and characterized new instances of evolutionary arms races with KRAB-ZFPs in endogenous retroviruses. Furthermore, we found that the regulatory landscape shaped by this arms race contributed to the gene regulatory networks. In summary, our results provide insight into the impact of the evolutionary arms race on TE families, the KRAB-ZFP family, and host gene regulatory networks.
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Affiliation(s)
- Masato Kosuge
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
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Feng Y, Yang X, Hou Y, Zhou Y, Leverenz JB, Eng C, Pieper AA, Goate A, Shen Y, Cheng F. Widespread transposable element dysregulation in human aging brains with Alzheimer's disease. Alzheimers Dement 2024. [PMID: 39356058 DOI: 10.1002/alz.14164] [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: 01/16/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 10/03/2024]
Abstract
INTRODUCTION Transposable element (TE) dysregulation is associated with neuroinflammation in Alzheimer's disease (AD) brains. Yet, TE quantitative trait loci (teQTL) have not been well characterized in human aged brains with AD. METHODS We leveraged large-scale bulk and single-cell RNA sequencing, whole-genome sequencing (WGS), and xQTL from three human AD brain biobanks to characterize TE expression dysregulation and experimentally validate AD-associated TEs using CRISPR interference (CRISPRi) assays in human induced pluripotent stem cell (iPSC)-derived neurons. RESULTS We identified 26,188 genome-wide significant TE expression QTLs (teQTLs) in human aged brains. Subsequent colocalization analysis of teQTLs with AD genetic loci identified AD-associated teQTLs and linked locus TEs. Using CRISPRi assays, we pinpointed a neuron-specific suppressive role of the activated short interspersed nuclear element (SINE; chr11:47608036-47608220) on expression of C1QTNF4 via reducing neuroinflammation in human iPSC-derived neurons. DISCUSSION We identified widespread TE dysregulation in human AD brains and teQTLs offer a complementary analytic approach to identify likely AD risk genes. HIGHLIGHTS Widespread transposable element (TE) dysregulations are observed in human aging brains with degrees of neuropathology, apolipoprotein E (APOE) genotypes, and neuroinflammation in Alzheimer's disease (AD). A catalog of TE quantitative trait loci (teQTLs) in human aging brains was created using matched RNA sequencing and whole-genome sequencing data. CRISPR interference assays reveal that an upregulated intergenic TE from the MIR family (chr11: 47608036-47608220) suppresses expression of its nearest anti-inflammatory gene C1QTNF4 in human induced pluripotent stem cell-derived neurons.
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Affiliation(s)
- Yayan Feng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Xiaoyu Yang
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
| | - Yuan Hou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Yadi Zhou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - James B Leverenz
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Andrew A Pieper
- Department of Psychiatry, Case Western Reserve University, Cleveland, Ohio, USA
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
- Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
- Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, Ohio, USA
| | - Alison Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, USA
| | - Feixiong Cheng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Karttunen K, Patel D, Sahu B. Transposable elements as drivers of dedifferentiation: Connections between enhancers in embryonic stem cells, placenta, and cancer. Bioessays 2024; 46:e2400059. [PMID: 39073128 DOI: 10.1002/bies.202400059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
Transposable elements (TEs) have emerged as important factors in establishing the cell type-specific gene regulatory networks and evolutionary novelty of embryonic and placental development. Recently, studies on the role of TEs and their dysregulation in cancers have shed light on the transcriptional, transpositional, and regulatory activity of TEs, revealing that the activation of developmental transcriptional programs by TEs may have a role in the dedifferentiation of cancer cells to the progenitor-like cell states. This essay reviews the recent evidence of the cis-regulatory TEs (henceforth crTE) in normal development and malignancy as well as the key transcription factors and regulatory pathways that are implicated in both cell states, and presents existing gaps remaining to be studied, limitations of current technologies, and therapeutic possibilities.
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Affiliation(s)
- Konsta Karttunen
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Divyesh Patel
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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Lebedin M, de la Rosa K. Diversification of Antibodies: From V(D)J Recombination to Somatic Exon Shuffling. Annu Rev Cell Dev Biol 2024; 40:265-281. [PMID: 39356809 DOI: 10.1146/annurev-cellbio-112122-030835] [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] [Indexed: 10/04/2024]
Abstract
Antibodies that gain specificity by a large insert encoding for an extra domain were described for the first time in 2016. In malaria-exposed individuals, an exon deriving from the leukocyte-associated immunoglobulin-like 1 (LAIR1) gene integrated via a copy-and-paste insertion into the immunoglobulin heavy chain encoding region. A few years later, a second example was identified, namely a dual exon integration from the leukocyte immunoglobulin-like receptor B1 (LILRB1) gene that is located in close proximity to LAIR1. A dedicated high-throughput characterization of chimeric immunoglobulin heavy chain transcripts unraveled, that insertions from distant genomic regions (including mitochondrial DNA) can contribute to human antibody diversity. This review describes the modalities of insert-containing antibodies. The role of known DNA mobility aspects, such as genomic translocation, gene conversion, and DNA fragility, is discussed in the context of insert-antibody generation. Finally, the review covers why insert antibodies were omitted from the past repertoire analyses and how insert antibodies can contribute to protective immunity or an autoreactive response.
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Affiliation(s)
- Mikhail Lebedin
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany;
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Kathrin de la Rosa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany;
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
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10
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Valdebenito-Maturana B. The spatial and cellular portrait of transposable element expression during gastric cancer. Sci Rep 2024; 14:22727. [PMID: 39349689 PMCID: PMC11442604 DOI: 10.1038/s41598-024-73744-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024] Open
Abstract
Gastric Cancer (GC) is a lethal malignancy, with urgent need for the discovery of novel biomarkers for its early detection. I previously showed that Transposable Elements (TEs) become activated in early GC (EGC), suggesting a role in gene expression. Here, I follow-up on that evidence using single-cell data from gastritis to EGC, and show that TEs are expressed and follow the disease progression, with 2,430 of them being cell populations markers. Pseudotemporal trajectory modeling revealed 111 TEs associated with the origination of cancer cells. Analysis of spatial data from GC also confirms TE expression, with 204 TEs being spatially enriched in the tumor regions and the tumor microenvironment, hinting at a role of TEs in tumorigenesis. Finally, a network of TE-mediated gene regulation was modeled, indicating that ~ 2,000 genes could be modulated by TEs, with ~ 500 of them already implicated in cancer. These results suggest that TEs might play a functional role in GC progression, and highlights them as potential biomarker for its early detection.
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Baniulyte G, Hicks SM, Sammons MA. p53motifDB: integration of genomic information and tumor suppressor p53 binding motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614594. [PMID: 39386591 PMCID: PMC11463528 DOI: 10.1101/2024.09.24.614594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
The tumor suppressor gene TP53 encodes the DNA binding transcription factor p53 and is one of the most commonly mutated genes in human cancer. Tumor suppressor activity requires binding of p53 to its DNA response elements and subsequent transcriptional activation of a diverse set of target genes. Despite decades of close study, the logic underlying p53 interactions with its numerous potential genomic binding sites and target genes is not yet fully understood. Here, we present a database of DNA and chromatin-based information focused on putative p53 binding sites in the human genome to allow users to generate and test new hypotheses related to p53 activity in the genome. Users can query genomic locations based on experimentally observed p53 binding, regulatory element activity, genetic variation, evolutionary conservation, chromatin modification state, and chromatin structure. We present multiple use cases demonstrating the utility of this database for generating novel biological hypotheses, such as chromatin-based determinants of p53 binding and potential cell type-specific p53 activity. All database information is also available as a precompiled sqlite database for use in local analysis or as a Shiny web application.
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Zhang G, Félix MA, Andersen EC. Transposon-mediated genic rearrangements underlie variation in small RNA pathways. SCIENCE ADVANCES 2024; 10:eado9461. [PMID: 39303031 DOI: 10.1126/sciadv.ado9461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 08/13/2024] [Indexed: 09/22/2024]
Abstract
Transposable elements (TEs) can alter host gene structure and expression, whereas host organisms develop mechanisms to repress TE activities. In the nematode Caenorhabditis elegans, a small interfering RNA pathway dependent on the helicase ERI-6/7 primarily silences retrotransposons and recent genes of likely viral origin. By studying gene expression variation among wild C. elegans strains, we found that structural variants and transposon remnants likely underlie expression variation in eri-6/7 and the pathway targets. We further found that multiple insertions of the DNA transposons, Polintons, reshuffled the eri-6/7 locus and induced inversion of eri-6 in some wild strains. In the inverted configuration, gene function was previously shown to be repaired by unusual trans-splicing mediated by direct repeats. We identified that these direct repeats originated from terminal inverted repeats of Polintons. Our findings highlight the role of host-transposon interactions in driving rapid host genome diversification among natural populations and shed light on evolutionary novelty in genes and splicing mechanisms.
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Affiliation(s)
- Gaotian Zhang
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Erik C Andersen
- Biology Department, Johns Hopkins University, Baltimore, MD, USA
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Polimeni B, Marasca F, Ranzani V, Bodega B. IRescue: uncertainty-aware quantification of transposable elements expression at single cell level. Nucleic Acids Res 2024:gkae793. [PMID: 39271103 DOI: 10.1093/nar/gkae793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 08/22/2024] [Accepted: 09/02/2024] [Indexed: 09/15/2024] Open
Abstract
Transposable elements (TEs) are mobile DNA repeats known to shape the evolution of eukaryotic genomes. In complex organisms, they exhibit tissue-specific transcription. However, understanding their role in cellular diversity across most tissues remains a challenge, when employing single-cell RNA sequencing (scRNA-seq), due to their widespread presence and genetic similarity. To address this, we present IRescue (Interspersed Repeats single-cell quantifier), a software capable of estimating the expression of TE subfamilies at the single-cell level. IRescue incorporates a unique UMI deduplication algorithm to rectify sequencing errors and employs an Expectation-Maximization procedure to effectively redistribute the counts of multi-mapping reads. Our study showcases the precision of IRescue through analysis of both simulated and real single cell and nuclei RNA-seq data from human colorectal cancer, brain, skin aging, and PBMCs during SARS-CoV-2 infection and recovery. By linking the expression patterns of TE signatures to specific conditions and biological contexts, we unveil insights into their potential roles in cellular heterogeneity and disease progression.
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Affiliation(s)
- Benedetto Polimeni
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Federica Marasca
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Valeria Ranzani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Beatrice Bodega
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
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14
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Alizada A, Martins A, Mouniée N, Rodriguez Suarez JV, Bertin B, Gueguen N, Mirouse V, Maupetit-Mehouas S, Rivera AJ, Lau NC, Hannon GJ, Nicholson BC, Brasset E. The transcription factor Traffic jam orchestrates the somatic piRNA pathway in Drosophila ovaries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.612307. [PMID: 39314383 PMCID: PMC11419008 DOI: 10.1101/2024.09.10.612307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Transposable elements (TEs) pose a threat to genome integrity, and the piRNA pathway in animal gonads plays a crucial role in silencing TE activity. While the transcriptional regulation of the piRNA pathway components in germ cells has been documented in mice and flies, the mechanisms orchestrating the transcriptional program of the somatic piRNA pathway in Drosophila ovaries remains unresolved. Here, we demonstrate that Traffic jam (Tj), an orthologue of a large Maf transcription factor in mammals, is a master regulator of the piRNA pathway in ovarian somatic cells, playing a crucial role in maintaining TE silencing and genomic integrity in somatic tissues. We show that Tj directly binds to the promoters of somatic-enriched piRNA factors such as fs(1)Yb , nxf2 , panx , and armi , as well as the flamenco piRNA cluster, a major locus for TE silencing in somatic cells. Depletion of Tj in somatic follicle cells results in a significant downregulation of these piRNA factors, a complete loss of flam expression and de-repression of gypsy -family TEs, which have gained the ability to activate in ovarian somatic cells allowing them to infect germ cells and be transmitted to future generations. We have identified an enhancer carrying Tj binding motifs located downstream of the flam promoter that is essential for robust and tissue-specific flam expression in somatic follicle cells of the adult ovary. This work uncovers a previously unappreciated layer of transcriptional regulation of the piRNA pathway, and we propose that the arms race between the host and TEs has driven the evolution of promoters in piRNA genes and clusters to respond to a unique transcription factor thereby ensuring efficient silencing of gypsy -family TEs. Highlights Traffic jam (Tj) acts as a master regulator of the somatic piRNA pathway in Drosophila . Tj directly controls the expression of the flamenco piRNA cluster, crucial for transposon silencing. Tj regulates a network of piRNA pathway genes, mirroring the gene-regulatory mechanism of A-MYB in the mouse testis.Cis-regulatory elements with Tj motifs are arranged in a palindromic sequence.
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15
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Kulkarni S, Morrissey A, Sebastian A, Keller CA, Giardine B, Smith C, Akinniyi OT, Arnaoutov A, Albert I, Mahony S, Reese JC. Human CCR4-NOT is a global regulator of gene expression and is a novel silencer of retrotransposon activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.612038. [PMID: 39314347 PMCID: PMC11419117 DOI: 10.1101/2024.09.10.612038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation, and translation. It has been well studied in budding yeast; however, relatively less is known about its regulation and functions in mammals. To characterize the functions of the human CCR4-NOT complex, we developed a rapid auxin-induced degron system to deplete CNOT1 (the scaffold of the complex) and CNOT4 (E3 ubiquitin ligase) in cell culture. Transcriptome-wide measurements of gene-expression revealed that depleting CNOT1 changed several thousand transcripts, wherein most mRNAs were increased and resulted in a global decrease in mRNA decay rates. In contrast to what was observed in CNOT1-depleted cells, CNOT4 depletion only modestly changed RNA steady-state levels and, surprisingly, led to a global acceleration in mRNA decay. To further investigate the role of CCR4-NOT in transcription, we used transient transcriptome sequencing (TT-seq) to measure ongoing RNA synthesis. Depletion of either subunit resulted in increased RNA synthesis of several thousand genes. In contrast to most of the genome, a rapid reduction in the synthesis of KRAB-Zinc-Finger-proteins (KZNFs) genes, especially those clustered on chromosome 19, was observed. KZNFs are transcriptional repressors of retro-transposable elements (rTEs), and consistent with the decreased KZNFs expression, we observed a significant and rapid activation of rTEs, mainly Long interspersed Nuclear Elements (LINEs). Our data reveal that CCR4-NOT regulates gene expression and silences retrotransposons across the genome by maintaining KZNF expression. These data establish CCR4-NOT as a global regulator of gene expression, and we have identified a novel mammalian-specific function of the complex, the suppression of rTEs.
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16
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Garcia P, Jarassier W, Brun C, Giordani L, Agostini F, Kung WH, Peccate C, Ravent J, Fall S, Petit V, Cheung TH, Ait-Si-Ali S, Le Grand F. Setdb1 protects genome integrity in murine muscle stem cells to allow for regenerative myogenesis and inflammation. Dev Cell 2024; 59:2375-2392.e8. [PMID: 38848717 DOI: 10.1016/j.devcel.2024.05.012] [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: 06/01/2023] [Revised: 01/02/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
The histone H3 lysine 9 methyltransferase SETDB1 controls transcriptional repression to direct stem cell fate. Here, we show that Setdb1 expression by adult muscle stem cells (MuSCs) is required for skeletal muscle regeneration. We find that SETDB1 represses the expression of endogenous retroviruses (ERVs) in MuSCs. ERV de-repression in Setdb1-null MuSCs prevents their amplification following exit from quiescence and promotes cell death. Multi-omics profiling shows that chromatin decompaction at ERV loci activates the DNA-sensing cGAS-STING pathway, entailing cytokine expression by Setdb1-null MuSCs. This is followed by aberrant infiltration of inflammatory cells, including pathological macrophages. The ensuing histiocytosis is accompanied by myofiber necrosis, which, in addition to progressive MuSCs depletion, completely abolishes tissue repair. In contrast, loss of Setdb1 in fibro-adipogenic progenitors (FAPs) does not impact immune cells. In conclusion, genome maintenance by SETDB1 in an adult somatic stem cell is necessary for both its regenerative potential and adequate reparative inflammation.
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Affiliation(s)
- Pauline Garcia
- Université Claude Bernard-Lyon 1, CNRS UMR 5261, Inserm U1315, Institut NeuroMyoGène, Pathophysiology and Genetics of Neuron and Muscle Unit, 69008 Lyon, France
| | - William Jarassier
- Université Claude Bernard-Lyon 1, CNRS UMR 5261, Inserm U1315, Institut NeuroMyoGène, Pathophysiology and Genetics of Neuron and Muscle Unit, 69008 Lyon, France
| | - Caroline Brun
- Université Claude Bernard-Lyon 1, CNRS UMR 5261, Inserm U1315, Institut NeuroMyoGène, Pathophysiology and Genetics of Neuron and Muscle Unit, 69008 Lyon, France
| | - Lorenzo Giordani
- Sorbonne Université, Inserm UMRS 974, Institut de Myologie, Myology Research Center Unit, 75013 Paris, France
| | - Fany Agostini
- Université Claude Bernard-Lyon 1, CNRS UMR 5261, Inserm U1315, Institut NeuroMyoGène, Pathophysiology and Genetics of Neuron and Muscle Unit, 69008 Lyon, France
| | - Wai Hing Kung
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Cécile Peccate
- Sorbonne Université, Inserm UMRS 974, Institut de Myologie, Myology Research Center Unit, 75013 Paris, France
| | - Jade Ravent
- Université Claude Bernard-Lyon 1, CNRS UMR 5261, Inserm U1315, Institut NeuroMyoGène, Pathophysiology and Genetics of Neuron and Muscle Unit, 69008 Lyon, France
| | - Sidy Fall
- Université Claude Bernard-Lyon 1, CNRS UMR 5261, Inserm U1315, Institut NeuroMyoGène, Pathophysiology and Genetics of Neuron and Muscle Unit, 69008 Lyon, France
| | - Valentin Petit
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR 7216, 75013 Paris, France
| | - Tom H Cheung
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Slimane Ait-Si-Ali
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR 7216, 75013 Paris, France
| | - Fabien Le Grand
- Université Claude Bernard-Lyon 1, CNRS UMR 5261, Inserm U1315, Institut NeuroMyoGène, Pathophysiology and Genetics of Neuron and Muscle Unit, 69008 Lyon, France.
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17
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Wang Y, Xu H, He Q, Wu Z, Han GZ. Natural Transposable Element Insertions Contribute to Host Fitness in Model Yeasts. Genome Biol Evol 2024; 16:evae193. [PMID: 39228319 PMCID: PMC11403283 DOI: 10.1093/gbe/evae193] [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: 05/13/2024] [Revised: 08/30/2024] [Accepted: 08/31/2024] [Indexed: 09/05/2024] Open
Abstract
Transposable elements (TEs) are ubiquitous in the eukaryote genomes, but their evolutionary and functional significance remains largely obscure and contentious. Here, we explore the evolution and functional impact of TEs in two model unicellular eukaryotes, the fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae, which diverged around 330 to 420 million years ago. We analyze the distribution of LTR retrotransposons (LTR-RTs, the only TE order identified in both species) and their solo-LTR derivatives in 35 strains of S. pombe and 128 strains of S. cerevisiae. We find that natural LTR-RT and solo-LTR insertions exhibit high presence-absence polymorphism among individuals in both species. Population genetics analyses show that solo-LTR insertions experienced functional constraints similar to synonymous sites of host genes in both species, indicating a majority of solo-LTR insertions might have evolved in a neutral manner. When knocking out nine representative solo-LTR insertions separately in the S. pombe strain 972h- and 12 representative solo-LTR insertions separately in the S. cerevisiae strain S288C, we find that one solo-LTR insertion in S. pombe has a significant effect on the fitness and transcriptome of its host. Together, our findings indicate that a fraction of natural TE insertions likely shape their host transcriptomes and thereby contribute to their host fitness, with implications for understanding the functional significance of TEs in eukaryotes.
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Affiliation(s)
- Yan Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Hao Xu
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Qinliu He
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Zhiwei Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
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18
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Wu Y, Wang F, Lyu K, Liu R. Comparative Analysis of Transposable Elements in the Genomes of Citrus and Citrus-Related Genera. PLANTS (BASEL, SWITZERLAND) 2024; 13:2462. [PMID: 39273946 PMCID: PMC11397423 DOI: 10.3390/plants13172462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/28/2024] [Accepted: 09/01/2024] [Indexed: 09/15/2024]
Abstract
Transposable elements (TEs) significantly contribute to the evolution and diversity of plant genomes. In this study, we explored the roles of TEs in the genomes of Citrus and Citrus-related genera by constructing a pan-genome TE library from 20 published genomes of Citrus and Citrus-related accessions. Our results revealed an increase in TE content and the number of TE types compared to the original annotations, as well as a decrease in the content of unclassified TEs. The average length of TEs per assembly was approximately 194.23 Mb, representing 41.76% (Murraya paniculata) to 64.76% (Citrus gilletiana) of the genomes, with a mean value of 56.95%. A significant positive correlation was found between genome size and both the number of TE types and TE content. Consistent with the difference in mean whole-genome size (39.83 Mb) between Citrus and Citrus-related genera, Citrus genomes contained an average of 34.36 Mb more TE sequences than Citrus-related genomes. Analysis of the estimated insertion time and half-life of long terminal repeat retrotransposons (LTR-RTs) suggested that TE removal was not the primary factor contributing to the differences among genomes. These findings collectively indicate that TEs are the primary determinants of genome size and play a major role in shaping genome structures. Principal coordinate analysis (PCoA) of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) identifiers revealed that the fragmented TEs were predominantly derived from ancestral genomes, while intact TEs were crucial in the recent evolutionary diversification of Citrus. Moreover, the presence or absence of intact TEs near the AdhE superfamily was closely associated with the bitterness trait in the Citrus species. Overall, this study enhances TE annotation in Citrus and Citrus-related genomes and provides valuable data for future genetic breeding and agronomic trait research in Citrus.
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Affiliation(s)
- Yilei Wu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fusheng Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China
| | - Keliang Lyu
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Renyi Liu
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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19
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Wang J, Tao W, Kocher TD, Wang D. Sex chromosome turnover and biodiversity in fishes. J Genet Genomics 2024:S1673-8527(24)00222-4. [PMID: 39233051 DOI: 10.1016/j.jgg.2024.08.008] [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: 06/12/2024] [Revised: 08/22/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024]
Abstract
The impact of sex chromosomes and their turnover in speciation remains a subject of ongoing debate in the field of evolutionary biology. Fishes are the largest group of vertebrates, and they exhibit unparalleled sexual plasticity, as well as diverse sex-determining (SD) genes, sex chromosomes, and sex determination mechanisms. This diversity is hypothesized to be associated with the frequent turnover of sex chromosomes in fishes. Although it is evident that amh and amhr2 are repeatedly and independently recruited as SD genes, their relationship with the rapid turnover of sex chromosomes and the biodiversity of fishes remains unknown. We summarize the canonical models of sex chromosome turnover and highlight the vital roles of gene mutation and hybridization with empirical evidence. We revisit Haldane's rule and the large X-effect and propose the hypothesis that sex chromosomes accelerate speciation by multiplying genotypes via hybridization. By integrating recent findings on the turnover of SD genes, sex chromosomes, and sex determination systems in fish species, this review provides insights into the relationship between sex chromosome evolution and biodiversity in fishes.
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Affiliation(s)
- Jingrong Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Wenjing Tao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Deshou Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
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20
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Nie Y, Liu X, Zhao L, Huang Y. Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea). Genomics 2024; 116:110896. [PMID: 39025318 DOI: 10.1016/j.ygeno.2024.110896] [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: 03/25/2024] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Pamphagidae is a family of Acridoidea that inhabits the desert steppes of Eurasia and Africa. This study employed flow cytometry to estimate the genome size of eight species in the Pamphagidae. The results indicate that the genome size of the eight species ranged from 13.88 pg to 14.66 pg, with an average of 14.26 pg. This is the largest average genome size recorded for the Orthoptera families, as well as for the entire Insecta. Furthermore, the study explored the role of repetitive sequences in the genome, including their evolutionary dynamics and activity, using low-coverage next-generation sequencing data. The genome is composed of 14 different types of repetitive sequences, which collectively make up between 59.9% and 68.17% of the total genome. The Pamphagidae family displays high levels of transposable element (TE) activity, with the number of TEs increasing and accumulating since the family's emergence. The study found that the types of repetitive sequences contributing to the TE outburst events are similar across species. Additionally, the study identified unique repetitive elements for each species. The differences in repetitive sequences among the eight Pamphagidae species correspond to their phylogenetic relationships. The study sheds new light on genome gigantism in the Pamphagidae and provides insight into the correlation between genome size and repetitive sequences within the family.
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Affiliation(s)
- Yimeng Nie
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xuanzeng Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lina Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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21
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Du AY, Chobirko JD, Zhuo X, Feschotte C, Wang T. Regulatory transposable elements in the encyclopedia of DNA elements. Nat Commun 2024; 15:7594. [PMID: 39217141 PMCID: PMC11366022 DOI: 10.1038/s41467-024-51921-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Transposable elements (TEs) comprise ~50% of our genome, but knowledge of how TEs affect genome evolution remains incomplete. Leveraging ENCODE4 data, we provide the most comprehensive study to date of TE contributions to the regulatory genome. We find 236,181 (~25%) human candidate cis-regulatory elements (cCREs) are TE-derived, with over 90% lineage-specific since the human-mouse split, accounting for 8-36% of lineage-specific cCREs. Except for SINEs, cCRE-associated transcription factor (TF) motifs in TEs are derived from ancestral TE sequence more than expected by chance. We show that TEs may adopt similar regulatory activities of elements near their integration site. Since human-mouse divergence, TEs have contributed 3-56% of TF binding site turnover events across 30 examined TFs. Finally, TE-derived cCREs are similar to non-TE cCREs in terms of MPRA activity and GWAS variant enrichment. Overall, our results substantiate the notion that TEs have played an important role in shaping the human regulatory genome.
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Affiliation(s)
- Alan Y Du
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason D Chobirko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Xiaoyu Zhuo
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
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22
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Pandiloski N, Horváth V, Karlsson O, Koutounidou S, Dorazehi F, Christoforidou G, Matas-Fuentes J, Gerdes P, Garza R, Jönsson ME, Adami A, Atacho DAM, Johansson JG, Englund E, Kokaia Z, Jakobsson J, Douse CH. DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor. Nat Commun 2024; 15:7534. [PMID: 39214989 PMCID: PMC11364546 DOI: 10.1038/s41467-024-50765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/18/2024] [Indexed: 09/04/2024] Open
Abstract
The human silencing hub (HUSH) complex binds to transcripts of LINE-1 retrotransposons (L1s) and other genomic repeats, recruiting MORC2 and other effectors to remodel chromatin. How HUSH and MORC2 operate alongside DNA methylation, a central epigenetic regulator of repeat transcription, remains largely unknown. Here we interrogate this relationship in human neural progenitor cells (hNPCs), a somatic model of brain development that tolerates removal of DNA methyltransferase DNMT1. Upon loss of MORC2 or HUSH subunit TASOR in hNPCs, L1s remain silenced by robust promoter methylation. However, genome demethylation and activation of evolutionarily-young L1s attracts MORC2 binding, and simultaneous depletion of DNMT1 and MORC2 causes massive accumulation of L1 transcripts. We identify the same mechanistic hierarchy at pericentromeric α-satellites and clustered protocadherin genes, repetitive elements important for chromosome structure and neurodevelopment respectively. Our data delineate the epigenetic control of repeats in somatic cells, with implications for understanding the vital functions of HUSH-MORC2 in hypomethylated contexts throughout human development.
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Affiliation(s)
- Ninoslav Pandiloski
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Vivien Horváth
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Ofelia Karlsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Symela Koutounidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Fereshteh Dorazehi
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Georgia Christoforidou
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jon Matas-Fuentes
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden
| | - Patricia Gerdes
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Diahann A M Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jenny G Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
| | - Elisabet Englund
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Zaal Kokaia
- Lund Stem Cell Center, Lund University, Lund, Sweden
- Laboratory of Stem Cells and Restorative Neurology, Department of Clinical Sciences, BMC B10, Lund University, Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC A11, Lund University, Lund, Sweden
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Christopher H Douse
- Laboratory of Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center, BMC B11, Lund University, Lund, Sweden.
- Lund Stem Cell Center, Lund University, Lund, Sweden.
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23
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Jarosz AS, Halo JV. Transcription of Endogenous Retroviruses: Broad and Precise Mechanisms of Control. Viruses 2024; 16:1312. [PMID: 39205286 PMCID: PMC11359688 DOI: 10.3390/v16081312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous retroviruses (ERVs) are the remnants of retroviral germline infections and are highly abundant in the genomes of vertebrates. At one time considered to be nothing more than inert 'junk' within genomes, ERVs have been tolerated within host genomes over vast timescales, and their study continues to reveal complex co-evolutionary histories within their respective host species. For example, multiple instances have been characterized of ERVs having been 'borrowed' for normal physiology, from single copies to ones involved in various regulatory networks such as innate immunity and during early development. Within the cell, the accessibility of ERVs is normally tightly controlled by epigenetic mechanisms such as DNA methylation or histone modifications. However, these silencing mechanisms of ERVs are reversible, and epigenetic alterations to the chromatin landscape can thus lead to their aberrant expression, as is observed in abnormal cellular environments such as in tumors. In this review, we focus on ERV transcriptional control and draw parallels and distinctions concerning the loss of regulation in disease, as well as their precise regulation in early development.
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Affiliation(s)
- Abigail S. Jarosz
- Science and Mathematics Division, Lorrain County Community College, Lorrain, OH 44035, USA;
| | - Julia V. Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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24
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Tandon D, Kubinyi E, Sándor S, Faughnan H, Miklósi Á, vonHoldt BM. Canine hyper-sociability structural variants associated with altered three-dimensional chromatin state. BMC Genomics 2024; 25:767. [PMID: 39112925 PMCID: PMC11305043 DOI: 10.1186/s12864-024-10614-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/11/2024] [Indexed: 08/11/2024] Open
Abstract
Strong selection on complex traits can lead to skewed trait means and reduced trait variability in populations. An example of this phenomenon can be evidenced in allele frequency changes and skewed trait distributions driven by persistent human-directed selective pressures in domesticated species. Dog domestication is linked to several genomic variants; however, the functional impacts of these variants may not always be straightforward when found in non-coding regions of the genome. Four polymorphic transposable elements (TE) found within non-coding sites along a 5 Mb region on canine CFA6 have evolved due to directional selection associated with heightened human-directed hyper-sociability in domesticated dogs. We found that the polymorphic TE in intron 17 of the canine GTF2I gene, which was previously reported to be negatively correlated with canid human-directed hyper-sociability, is associated with altered chromatin looping and hence distinct cis-regulatory landscapes. We reported supporting evidence of an E2F1-DNA binding peak concordant with the altered loop and higher expression of GTF2I exon 18, indicative of alternative splicing. Globally, we discovered differences in pathways regulating the extra-cellular matrix with respect to TE copy number. Overall, we reported evidence suggesting an intriguing molecular convergence between the emergence of hypersocial behaviors in dogs and the same genes that, when hemizygous, produce human Williams Beuren Syndrome characterized by cranio-facial defects and heightened social behaviors. Our results additionally emphasize the often-overlooked potential role of chromatin architecture in social evolution.
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Affiliation(s)
- Dhriti Tandon
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Enikő Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE Lendület "Momentum" Companion Animal Research Group, Budapest, Hungary
- ELTE NAP Canine Brain Research Group, Budapest, Hungary
| | - Sára Sándor
- MTA-ELTE Lendület "Momentum" Companion Animal Research Group, Budapest, Hungary
| | - Hannah Faughnan
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Ádám Miklósi
- Department of Ethology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
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25
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Dziulko AK, Allen H, Chuong EB. An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140. Hum Mol Genet 2024; 33:1454-1464. [PMID: 38751339 PMCID: PMC11305685 DOI: 10.1093/hmg/ddae084] [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: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 07/26/2024] Open
Abstract
Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn's disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family and is regulated by oncogenic mitogen-activated protein kinase (MAPK) signaling. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.
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Affiliation(s)
- Adam K Dziulko
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Holly Allen
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
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26
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Betancourt AJ, Wei KHC, Huang Y, Lee YCG. Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective. Annu Rev Genomics Hum Genet 2024; 25:1-25. [PMID: 38603565 DOI: 10.1146/annurev-genom-120822-105708] [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] [Indexed: 04/13/2024]
Abstract
Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new genomic locations. TE activity varies at multiple levels, from between taxa to within individuals. The rapidly accumulating evidence of the influence of TE activity on human health, as well as the rapid growth of new tools to study it, motivated an evaluation of what we know about TE activity thus far. Here, we discuss why TE activity varies, and the consequences of this variation, from an evolutionary perspective. By studying TE activity in nonhuman organisms in the context of evolutionary theories, we can shed light on the factors that affect TE activity. While the consequences of TE activity are usually deleterious, some have lasting evolutionary impacts by conferring benefits on the host or affecting other evolutionary processes.
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Affiliation(s)
- Andrea J Betancourt
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kevin H-C Wei
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Yuh Chwen G Lee
- Center for Complex Biological Systems, University of California, Irvine, California, USA;
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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27
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Cappucci U, Proietti M, Casale AM, Schiavo S, Chiavarini S, Accardo S, Manzo S, Piacentini L. Assessing genotoxic effects of plastic leachates in Drosophila melanogaster. CHEMOSPHERE 2024; 361:142440. [PMID: 38821133 DOI: 10.1016/j.chemosphere.2024.142440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
Plastic polymers were largely added with chemical substances to be utilized in the items and product manufacturing. The leachability of these substances is a matter of concern given the wide amount of plastic waste, particularly in terrestrial environments, where soil represents a sink for these novel contaminants and a possible pathway of human health risk. In this study, we integrated genetic, molecular, and behavioral approaches to comparatively evaluate toxicological effects of plastic leachates, virgin and oxodegradable polypropylene (PP) and polyethylene (PE), in Drosophila melanogaster, a novel in vivo model organism for environmental monitoring studies and (eco)toxicological research. The results of this study revealed that while conventional toxicological endpoints such as developmental times and longevity remain largely unaffected, exposure to plastic leachates induces chromosomal abnormalities and transposable element (TE) activation in neural tissues. The combined effects of DNA damage and TE mobilization contribute to genome instability and increase the likelihood of LOH events, thus potentiating tumor growth and metastatic behavior ofRasV12 clones. Collectively, these findings indicate that plastic leachates exert genotoxic effects in Drosophila thus highlighting potential risks associated with leachate-related plastic pollution and their implications for ecosystems and human health.
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Affiliation(s)
- Ugo Cappucci
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Mirena Proietti
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Assunta Maria Casale
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Simona Schiavo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Salvatore Chiavarini
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Sara Accardo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Sonia Manzo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy.
| | - Lucia Piacentini
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy.
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28
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Zhou B, Hu P, Liu G, Chang Z, Dong Z, Li Z, Yin Y, Tian Z, Han G, Wang W, Li X. Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements. Nat Commun 2024; 15:6303. [PMID: 39060230 PMCID: PMC11282110 DOI: 10.1038/s41467-024-50529-0] [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: 11/28/2023] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Chromosome rearrangements may distort 3D chromatin architectures and thus change gene regulation, yet how 3D chromatin structures evolve in insects is largely unknown. Here, we obtain chromosome-level genomes for four butterfly species, Graphium cloanthus, Graphium sarpedon, Graphium eurypylus with 2n = 30, 40, and 60, respectively, and Papilio bianor with 2n = 60. Together with large-scale Hi-C data, we find that inter-chromosome rearrangements very rarely disrupted the pre-existing 3D chromatin structure of ancestral chromosomes. However, some intra-chromosome rearrangements changed 3D chromatin structures compared to the ancestral configuration. We find that new TADs and subTADs have emerged across the rearrangement sites where their adjacent compartments exhibit uniform types. Two intra-chromosome rearrangements altered Rel and lft regulation, potentially contributing to wing patterning differentiation and host plant choice. Notably, butterflies exhibited chromatin loops between Hox gene cluster ANT-C and BX-C, unlike Drosophila. Our CRISPR-Cas9 experiments in butterflies confirm that knocking out the CTCF binding site of the loops in BX-C affected the phenotypes regulated by Antp in ANT-C, resulting in legless larva. Our results reveal evolutionary patterns of insect 3D chromatin structures and provide evidence that 3D chromatin structure changes can play important roles in the evolution of traits.
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Affiliation(s)
- Botong Zhou
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ping Hu
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Guichun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zhou Chang
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zhiwei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China
| | - Zihe Li
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Yuan Yin
- NHC Key Laboratory of Nuclear Technology Medical Transformation, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Mianyang, 621000, China
| | - Zunzhe Tian
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Ge Han
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wen Wang
- School of Ecology and Environment, New Cornerstone Science Laboratory, Northwestern Polytechnical University, Xi'an, 710072, China.
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xueyan Li
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Kunming, 650223, China.
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
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29
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Russo A, Alessandrini M, El Baidouri M, Frei D, Galise TR, Gaidusch L, Oertel HF, Garcia Morales SE, Potente G, Tian Q, Smetanin D, Bertrand JAM, Onstein RE, Panaud O, Frey JE, Cozzolino S, Wicker T, Xu S, Grossniklaus U, Schlüter PM. Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation. Nat Commun 2024; 15:6308. [PMID: 39060266 PMCID: PMC11282089 DOI: 10.1038/s41467-024-50622-4] [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: 11/06/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Ophrys orchids mimic female insects to lure male pollinators into pseudocopulation. This strategy, called sexual deception, is species-specific, thereby providing strong premating reproductive isolation. Identifying the genomic architecture underlying pollinator adaptation and speciation may shed light on the mechanisms of angiosperm diversification. Here, we report the 5.2 Gb chromosome-scale genome sequence of Ophrys sphegodes. We find evidence for transposable element expansion that preceded the radiation of the O. sphegodes group, and for gene duplication having contributed to the evolution of chemical mimicry. We report a highly differentiated genomic candidate region for pollinator-mediated evolution on chromosome 2. The Ophrys genome will prove useful for investigations into the repeated evolution of sexual deception, pollinator adaptation and the genomic architectures that facilitate evolutionary radiations.
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Affiliation(s)
- Alessia Russo
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
| | - Mattia Alessandrini
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Moaine El Baidouri
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Daniel Frei
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Lara Gaidusch
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Hannah F Oertel
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Sara E Garcia Morales
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Qin Tian
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Joris A M Bertrand
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Renske E Onstein
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena - Leipzig, Leipzig, Germany
| | - Olivier Panaud
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Jürg E Frey
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Thomas Wicker
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution, University of Mainz, Mainz, Germany
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Philipp M Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
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30
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Yang Y, Liu J, Singer SD, Yan G, Bennet DR, Liu Y, Hily JM, Xu W, Yang Y, Wang X, Zhong GY, Liu Z, An YC, Liu H, Liu Z. Ectopic enhancer-enhancer interactions as causal forces driving RNA-directed DNA methylation in gene regulatory regions. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39021281 DOI: 10.1111/pbi.14435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/21/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024]
Abstract
Cis-regulatory elements (CREs) are integral to the spatiotemporal and quantitative expression dynamics of target genes, thus directly influencing phenotypic variation and evolution. However, many of these CREs become highly susceptible to transcriptional silencing when in a transgenic state, particularly when organised as tandem repeats. We investigated the mechanism of this phenomenon and found that three of the six selected flower-specific CREs were prone to transcriptional silencing when in a transgenic context. We determined that this silencing was caused by the ectopic expression of non-coding RNAs (ncRNAs), which were processed into 24-nt small interfering RNAs (siRNAs) that drove RNA-directed DNA methylation (RdDM). Detailed analyses revealed that aberrant ncRNA transcription within the AGAMOUS enhancer (AGe) in a transgenic context was significantly enhanced by an adjacent CaMV35S enhancer (35Se). This particular enhancer is known to mis-activate the regulatory activities of various CREs, including the AGe. Furthermore, an insertion of 35Se approximately 3.5 kb upstream of the AGe in its genomic locus also resulted in the ectopic induction of ncRNA/siRNA production and de novo methylation specifically in the AGe, but not other regions, as well as the production of mutant flowers. This confirmed that interactions between the 35Se and AGe can induce RdDM activity in both genomic and transgenic states. These findings highlight a novel epigenetic role for CRE-CRE interactions in plants, shedding light on the underlying forces driving hypermethylation in transgenes, duplicate genes/enhancers, and repetitive transposons, in which interactions between CREs are inevitable.
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Affiliation(s)
- Yazhou Yang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Jia Liu
- College of Landscape, Architecture and Life science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, Canada
| | - Guohua Yan
- The Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Dennis R Bennet
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jean-Michel Hily
- Institut Français de la Vigne et du Vin (IFV), Le Grau du Roi, France
| | - Weirong Xu
- School of Food & Wine, Ningxia University, Yinchuan, Ningxia, China
| | - Yingzhen Yang
- USDA-ARS, Grape Genetic Research Unit, Geneva, New York, USA
| | - Xiping Wang
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Gan-Yuan Zhong
- USDA-ARS, Grape Genetic Research Unit, Geneva, New York, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Yong-Chiang An
- USDA-ARS, Plant Genetics Research Unit, Donald Danforth Plant Science Center, St Louis, Missouri, USA
| | - Huawei Liu
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Zongrang Liu
- USDA-ARS Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
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31
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van den Bos E, Gadau J, Schrader L. Molecular identification of polymorphic transposable elements in populations of the invasive ant Cardiocondyla obscurior. Biol Methods Protoc 2024; 9:bpae050. [PMID: 39050818 PMCID: PMC11268152 DOI: 10.1093/biomethods/bpae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
Transposable elements (TEs) are found in virtually every eukaryotic genome and are important for generating de novo genetic variation. However, outside of costly and time-consuming whole-genome sequencing approaches, the set of available methods to study TE polymorphisms in non-model species is very limited. The Transposon Display (TD) is a simple yet effective technique to characterize polymorphisms across samples by identifying amplified fragment length polymorphisms using primers targeting specific TE families. So far, this technique has almost exclusively been used in plants. Here, we present an optimized TD protocol for insect species with small genomes such as ants (ca. 200-600 Mb). We characterized TE polymorphisms between two distinct genetic lineages of the invasive ant Cardiocondyla obscurior, as well as between neighboring populations of the New World lineage. We found active LTR/Ty3 retrotransposons, that contributed to the genetic diversification of populations in this species.
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Affiliation(s)
- Esther van den Bos
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
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32
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Harder CB, Miyauchi S, Virágh M, Kuo A, Thoen E, Andreopoulos B, Lu D, Skrede I, Drula E, Henrissat B, Morin E, Kohler A, Barry K, LaButti K, Salamov A, Lipzen A, Merényi Z, Hegedüs B, Baldrian P, Stursova M, Weitz H, Taylor A, Koriabine M, Savage E, Grigoriev IV, Nagy LG, Martin F, Kauserud H. Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations. CELL GENOMICS 2024; 4:100586. [PMID: 38942024 PMCID: PMC11293592 DOI: 10.1016/j.xgen.2024.100586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/28/2024] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.
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Affiliation(s)
- Christoffer Bugge Harder
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway; Department of Biology, Microbial Ecology Group, Biology Department, Lund University, Lund, Sweden; University of Copenhagen, Department of Biology, Section of Terrestrial Ecology, 2100 Copenhagen Ø, Denmark.
| | - Shingo Miyauchi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ella Thoen
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Bill Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dabao Lu
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Inger Skrede
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France; INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, 13009 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix Marseille Université, 163 avenue de Luminy, 13288 Marseille, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Annegret Kohler
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Asaf Salamov
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Martina Stursova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Hedda Weitz
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Andy Taylor
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK; The James Hutton Institute, Aberdeen, UK
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - László G Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, HUN-REN Szeged, 6726 Szeged, Hungary
| | - Francis Martin
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est Nancy, 54280 Champenoux, France.
| | - Håvard Kauserud
- Department of Biosciences, University of Oslo, Box 1066 Blindern, 0316 Oslo, Norway
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Li Y, Lyu R, Chen S, Wang Y, Sun MA. TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms. Nucleic Acids Res 2024; 52:W126-W131. [PMID: 38747349 PMCID: PMC11223789 DOI: 10.1093/nar/gkae411] [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: 02/26/2024] [Revised: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 07/06/2024] Open
Abstract
Transposable elements (TEs) are abundant in the genomes of various eukaryote organisms. Increasing evidence suggests that TEs can play crucial regulatory roles-usually by creating cis-elements (e.g. enhancers and promoters) bound by distinct transcription factors (TFs). TE-derived cis-elements have gained unprecedented attentions recently, and one key step toward their understanding is to identify the enriched TEs in distinct genomic intervals (e.g. a set of enhancers or TF binding sites) as candidates for further study. Nevertheless, such analysis remains challenging for researchers unfamiliar with TEs or lack strong bioinformatic skills. Here, we present TEENA (Transposable Element ENrichment Analyzer) to streamline TE enrichment analysis in various organisms. It implements an optimized pipeline, hosts the genome/gene/TE annotations of almost one hundred species, and provides multiple parameters to enable its flexibility. Taking genomic interval data as the only user-supplied file, it can automatically retrieve the corresponding annotations and finish a routine analysis in a couple minutes. Multiple case studies demonstrate that it can produce highly reliable results matching previous knowledge. TEENA can be freely accessed at: https://sun-lab.yzu.edu.cn/TEENA. Due to its easy-to-use design, we expect it to facilitate the studies of the regulatory function of TEs in various model and non-model organisms.
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Affiliation(s)
- Yuzhuo Li
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
| | - Renzhe Lyu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
| | - Shuai Chen
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
| | - Yejun Wang
- Youth Innovation Team of Medical Bioinformatics, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Ming-an Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009 Jiangsu, China
- Joint International Research Laboratory of Important Animal Infectious Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009 Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009 Jiangsu, China
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Lebherz MK, Fouks B, Schmidt J, Bornberg-Bauer E, Grandchamp A. DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs. Genome Biol Evol 2024; 16:evae134. [PMID: 38934893 PMCID: PMC11264136 DOI: 10.1093/gbe/evae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 06/11/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
De novo genes emerge from noncoding regions of genomes via succession of mutations. Among others, such mutations activate transcription and create a new open reading frame (ORF). Although the mechanisms underlying ORF emergence are well documented, relatively little is known about the mechanisms enabling new transcription events. Yet, in many species a continuum between absent and very prominent transcription has been reported for essentially all regions of the genome. In this study, we searched for de novo transcripts by using newly assembled genomes and transcriptomes of seven inbred lines of Drosophila melanogaster, originating from six European and one African population. This setup allowed us to detect sample specific de novo transcripts, and compare them to their homologous nontranscribed regions in other samples, as well as genic and intergenic control sequences. We studied the association with transposable elements (TEs) and the enrichment of transcription factor motifs upstream of de novo emerged transcripts and compared them with regulatory elements. We found that de novo transcripts overlap with TEs more often than expected by chance. The emergence of new transcripts correlates with regions of high guanine-cytosine content and TE expression. Moreover, upstream regions of de novo transcripts are highly enriched with regulatory motifs. Such motifs are more enriched in new transcripts overlapping with TEs, particularly DNA TEs, and are more conserved upstream de novo transcripts than upstream their 'nontranscribed homologs'. Overall, our study demonstrates that TE insertion is important for transcript emergence, partly by introducing new regulatory motifs from DNA TE families.
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Affiliation(s)
| | - Bertrand Fouks
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
| | - Julian Schmidt
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
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Skalon EK, Panyushev NV, Podgornaya OI, Smolyaninova AR, Solovyeva AI. Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle. Noncoding RNA 2024; 10:39. [PMID: 39051373 PMCID: PMC11270206 DOI: 10.3390/ncrna10040039] [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: 04/29/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of eukaryotic genomes. The extensive body of evidence suggests that although they were once considered "genomic parasites", transposons and their transcripts perform specific functions, such as regulation of early embryo development. Understanding the role of TEs in such parasites as trematodes is becoming critically important. Fasciola hepatica, a parasite affecting humans and livestock, undergoes a complex life cycle in diverse environments and hosts, and knowledge about its life cycle regulation is scarce so far. METHODS We summarized the data regarding the repetitive elements in F. hepatica and conducted bulk RNA-seq analysis across its life cycle stages. TE expression profiles were analyzed, focusing on differential expression and potential homology with previously described long non-coding RNAs (lncRNAs). RESULTS Differential expression analysis revealed stage-specific TE transcription patterns, notably peaking during egg and metacercariae stages. Some TEs showed homology with known lncRNAs and contained putative transcription factor binding sites. Interestingly, TE transcription levels were highest in eggs and metacercariae compared to adults, suggesting regulatory roles in trematode life cycle transitions. CONCLUSIONS These findings suggest that TEs may play roles in regulating trematode life cycle transitions. Moreover, TE homology with lncRNAs underscores their significance in gene regulation.
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Affiliation(s)
- Elizaveta K. Skalon
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
| | | | - Olga I. Podgornaya
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
| | - Anastasia R. Smolyaninova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
| | - Anna I. Solovyeva
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (O.I.P.); (A.R.S.)
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Sun D, Zhu Y, Peng W, Zheng S, Weng J, Dong S, Li J, Chen Q, Ge C, Liao L, Dong Y, Liu Y, Meng W, Jiang Y. SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells. Genome Biol 2024; 25:175. [PMID: 38961490 PMCID: PMC11221086 DOI: 10.1186/s13059-024-03327-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Transposable elements play a critical role in maintaining genome architecture during neurodevelopment. Short Interspersed Nuclear Elements (SINEs), a major subtype of transposable elements, are known to harbor binding sites for the CCCTC-binding factor (CTCF) and pivotal in orchestrating chromatin organization. However, the regulatory mechanisms controlling the activity of SINEs in the developing brain remains elusive. RESULTS In our study, we conduct a comprehensive genome-wide epigenetic analysis in mouse neural precursor cells using ATAC-seq, ChIP-seq, whole genome bisulfite sequencing, in situ Hi-C, and RNA-seq. Our findings reveal that the SET domain bifurcated histone lysine methyltransferase 1 (SETDB1)-mediated H3K9me3, in conjunction with DNA methylation, restricts chromatin accessibility on a selective subset of SINEs in neural precursor cells. Mechanistically, loss of Setdb1 increases CTCF access to these SINE elements and contributes to chromatin loop reorganization. Moreover, de novo loop formation contributes to differential gene expression, including the dysregulation of genes enriched in mitotic pathways. This leads to the disruptions of cell proliferation in the embryonic brain after genetic ablation of Setdb1 both in vitro and in vivo. CONCLUSIONS In summary, our study sheds light on the epigenetic regulation of SINEs in mouse neural precursor cells, suggesting their role in maintaining chromatin organization and cell proliferation during neurodevelopment.
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Affiliation(s)
- Daijing Sun
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yueyan Zhu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Wenzhu Peng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Shenghui Zheng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Jie Weng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Shulong Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiaqi Li
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Qi Chen
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Chuanhui Ge
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Liyong Liao
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yuhao Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yun Liu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Weida Meng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China.
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37
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Singh PP, Reeves GA, Contrepois K, Papsdorf K, Miklas JW, Ellenberger M, Hu CK, Snyder MP, Brunet A. Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape. Cell 2024; 187:3338-3356.e30. [PMID: 38810644 DOI: 10.1016/j.cell.2024.04.048] [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: 11/24/2021] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.
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Affiliation(s)
| | - G Adam Reeves
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| | | | - Jason W Miklas
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Chi-Kuo Hu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.
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38
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Fu B, Ma H, Liu D. Pioneer Transcription Factors: The First Domino in Zygotic Genome Activation. Biomolecules 2024; 14:720. [PMID: 38927123 PMCID: PMC11202083 DOI: 10.3390/biom14060720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Zygotic genome activation (ZGA) is a pivotal event in mammalian embryogenesis, marking the transition from maternal to zygotic control of development. During the ZGA process that is characterized by the intricate cascade of gene expression, who tipped the first domino in a meticulously arranged sequence is a subject of paramount interest. Recently, Dux, Obox and Nr5a2 were identified as pioneer transcription factors that reside at the top of transcriptional hierarchy. Through co-option of retrotransposon elements as hubs for transcriptional activation, these pioneer transcription factors rewire the gene regulatory network, thus initiating ZGA. In this review, we provide a snapshot of the mechanisms underlying the functions of these pioneer transcription factors. We propose that ZGA is the starting point where the embryo's own genome begins to influence development trajectory, therefore in-depth dissecting the functions of pioneer transcription factors during ZGA will form a cornerstone of our understanding for early embryonic development, which will pave the way for advancing our grasp of mammalian developmental biology and optimizing in vitro production (IVP) techniques.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of Agricultural Sciences, Harbin 150086, China; (B.F.); (H.M.)
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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39
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Adler GL, Le K, Fu Y, Kim WS. Human Endogenous Retroviruses in Neurodegenerative Diseases. Genes (Basel) 2024; 15:745. [PMID: 38927681 PMCID: PMC11202925 DOI: 10.3390/genes15060745] [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: 05/10/2024] [Revised: 05/25/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are DNA transposable elements that have integrated into the human genome via an ancestral germline infection. The potential importance of HERVs is underscored by the fact that they comprise approximately 8% of the human genome. HERVs have been implicated in the pathogenesis of neurodegenerative diseases, a group of CNS diseases characterized by a progressive loss of structure and function of neurons, resulting in cell death and multiple physiological dysfunctions. Much evidence indicates that HERVs are initiators or drivers of neurodegenerative processes in multiple sclerosis and amyotrophic lateral sclerosis, and clinical trials have been designed to target HERVs. In recent years, the role of HERVs has been explored in other major neurodegenerative diseases, including frontotemporal dementia, Alzheimer's disease and Parkinson's disease, with some interesting discoveries. This review summarizes and evaluates the past and current research on HERVs in neurodegenerative diseases. It discusses the potential role of HERVs in disease manifestation and neurodegeneration. It critically reviews antiretroviral strategies used in the therapeutic intervention of neurodegenerative diseases.
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Affiliation(s)
- Gabrielle L. Adler
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Kelvin Le
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - YuHong Fu
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Woojin Scott Kim
- Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2050, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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40
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Hatanaka R, Tamagawa K, Haruta N, Sugimoto A. The impact of differential transposition activities of autonomous and nonautonomous hAT transposable elements on genome architecture and gene expression in Caenorhabditis inopinata. Genetics 2024; 227:iyae052. [PMID: 38577765 DOI: 10.1093/genetics/iyae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/08/2024] [Accepted: 03/28/2024] [Indexed: 04/06/2024] Open
Abstract
Transposable elements are DNA sequences capable of moving within genomes and significantly influence genomic evolution. The nematode Caenorhabditis inopinata exhibits a much higher transposable element copy number than its sister species, Caenorhabditis elegans. In this study, we identified a novel autonomous transposable element belonging to the hAT superfamily from a spontaneous transposable element-insertion mutant in C. inopinata and named this transposon Ci-hAT1. Further bioinformatic analyses uncovered 3 additional autonomous hAT elements-Ci-hAT2, Ci-hAT3, and Ci-hAT4-along with over 1,000 copies of 2 nonautonomous miniature inverted-repeat transposable elements, mCi-hAT1 and mCi-hAT4, likely derived from Ci-hAT1 and Ci-hAT4 through internal deletion. We tracked at least 3 sequential transpositions of Ci-hAT1 over several years. However, the transposition rates of the other 3 autonomous hAT elements were lower, suggesting varying activity levels. Notably, the distribution patterns of the 2 miniature inverted-repeat transposable element families differed significantly: mCi-hAT1 was primarily located in the chromosome arms, a pattern observed in the transposable elements of other Caenorhabditis species, whereas mCi-hAT4 was more evenly distributed across chromosomes. Additionally, interspecific transcriptome analysis indicated that C. inopinata genes with upstream or intronic these miniature inverted-repeat transposable element insertions tend to be more highly expressed than their orthologous genes in C. elegans. These findings highlight the significant role of de-silenced transposable elements in driving the evolution of genomes and transcriptomes, leading to species-specific genetic diversity.
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Affiliation(s)
- Ryuhei Hatanaka
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Katsunori Tamagawa
- Laboratory of Evolutionary Genomics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Nami Haruta
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Asako Sugimoto
- Laboratory of Developmental Dynamics, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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41
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Shao F, Zeng M, Xu X, Zhang H, Peng Z. FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. Database (Oxford) 2024; 2024:baae044. [PMID: 38829853 PMCID: PMC11146639 DOI: 10.1093/database/baae044] [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: 09/08/2023] [Revised: 04/04/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
We launched the initial version of FishTEDB in 2018, which aimed to establish an open-source, user-friendly, data-rich transposable element (TE) database. Over the past 5 years, FishTEDB 1.0 has gained approximately 10 000 users, accumulating more than 450 000 interactions. With the unveiling of extensive fish genome data and the increasing emphasis on TE research, FishTEDB needs to extend the richness of data and functions. To achieve the above goals, we introduced 33 new fish species to FishTEDB 2.0, encompassing a wide array of fish belonging to 48 orders. To make the updated database more functional, we added a genome browser to visualize the positional relationship between TEs and genes and the estimated TE insertion time in different species. In conclusion, we released a new version of the fish TE database, FishTEDB 2.0, designed to assist researchers in the future study of TE functions and promote the progress of biological theories related to TEs. Database URL: https://www.fishtedb.com/.
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Affiliation(s)
- Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Minzhi Zeng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
| | - Xiaofei Xu
- School of Computing Technologies, RMIT University, 124 La Trobe Street, Victoria 3000, Australia
| | - Huahao Zhang
- College of Pharmacy and Life Science, Jiujiang University, 551 Qianjin East Road, Jiujiang 332005, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, 2 Tiansheng Road, Chongqing 400715, China
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42
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Wong EWP, Sahin M, Yang R, Lee U, Zhan YA, Misra R, Tomas F, Alomran N, Polyzos A, Lee CJ, Trieu T, Fundichely AM, Wiesner T, Rosowicz A, Cheng S, Liu C, Lallo M, Merghoub T, Hamard PJ, Koche R, Khurana E, Apostolou E, Zheng D, Chen Y, Leslie CS, Chi P. TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596845. [PMID: 38895201 PMCID: PMC11185511 DOI: 10.1101/2024.05.31.596845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.
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Kerckhofs E, Schubert D. Conserved functions of chromatin regulators in basal Archaeplastida. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1301-1311. [PMID: 37680033 DOI: 10.1111/tpj.16446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Chromatin is a dynamic network that regulates genome organization and gene expression. Different types of chromatin regulators are highly conserved among Archaeplastida, including unicellular algae, while some chromatin genes are only present in land plant genomes. Here, we review recent advances in understanding the function of conserved chromatin factors in basal land plants and algae. We focus on the role of Polycomb-group genes which mediate H3K27me3-based silencing and play a role in balancing gene dosage and regulating haploid-to-diploid transitions by tissue-specific repression of the transcription factors KNOX and BELL in many representatives of the green lineage. Moreover, H3K27me3 predominantly occupies repetitive elements which can lead to their silencing in a unicellular alga and basal land plants, while it covers mostly protein-coding genes in higher land plants. In addition, we discuss the role of nuclear matrix constituent proteins as putative functional lamin analogs that are highly conserved among land plants and might have an ancestral function in stress response regulation. In summary, our review highlights the importance of studying chromatin regulation in a wide range of organisms in the Archaeplastida.
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Affiliation(s)
- Elise Kerckhofs
- Epigenetics of Plants, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Daniel Schubert
- Epigenetics of Plants, Institute for Biology, Freie Universität Berlin, Berlin, Germany
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Radrizzani S, Kudla G, Izsvák Z, Hurst LD. Selection on synonymous sites: the unwanted transcript hypothesis. Nat Rev Genet 2024; 25:431-448. [PMID: 38297070 DOI: 10.1038/s41576-023-00686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2023] [Indexed: 02/02/2024]
Abstract
Although translational selection to favour codons that match the most abundant tRNAs is not readily observed in humans, there is nonetheless selection in humans on synonymous mutations. We hypothesize that much of this synonymous site selection can be explained in terms of protection against unwanted RNAs - spurious transcripts, mis-spliced forms or RNAs derived from transposable elements or viruses. We propose not only that selection on synonymous sites functions to reduce the rate of creation of unwanted transcripts (for example, through selection on exonic splice enhancers and cryptic splice sites) but also that high-GC content (but low-CpG content), together with intron presence and position, is both particular to functional native mRNAs and used to recognize transcripts as native. In support of this hypothesis, transcription, nuclear export, liquid phase condensation and RNA degradation have all recently been shown to promote GC-rich transcripts and suppress AU/CpG-rich ones. With such 'traps' being set against AU/CpG-rich transcripts, the codon usage of native genes has, in turn, evolved to avoid such suppression. That parallel filters against AU/CpG-rich transcripts also affect the endosomal import of RNAs further supports the unwanted transcript hypothesis of synonymous site selection and explains the similar design rules that have enabled the successful use of transgenes and RNA vaccines.
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Affiliation(s)
- Sofia Radrizzani
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Grzegorz Kudla
- MRC Human Genetics Unit, Institute for Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK.
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Chen M, Yang C, Zhai X, Wang C, Liu M, Zhang B, Guo X, Wang Y, Li H, Liu Y, Han J, Wang X, Li J, Jia L, Li L. Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome. Viruses 2024; 16:892. [PMID: 38932184 PMCID: PMC11209481 DOI: 10.3390/v16060892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Endogenous retroviruses (ERVs) are related to long terminal repeat (LTR) retrotransposons, comprising gene sequences of exogenous retroviruses integrated into the host genome and inherited according to Mendelian law. They are considered to have contributed greatly to the evolution of host genome structure and function. We previously characterized HERV-K HML-9 in the human genome. However, the biological function of this type of element in the genome of the chimpanzee, which is the closest living relative of humans, largely remains elusive. Therefore, the current study aims to characterize HML-9 in the chimpanzee genome and to compare the results with those in the human genome. Firstly, we report the distribution and genetic structural characterization of the 26 proviral elements and 38 solo LTR elements of HML-9 in the chimpanzee genome. The results showed that the distribution of these elements displayed a non-random integration pattern, and only six elements maintained a relatively complete structure. Then, we analyze their phylogeny and reveal that the identified elements all cluster together with HML-9 references and with those identified in the human genome. The HML-9 integration time was estimated based on the 2-LTR approach, and the results showed that HML-9 elements were integrated into the chimpanzee genome between 14 and 36 million years ago and into the human genome between 18 and 49 mya. In addition, conserved motifs, cis-regulatory regions, and enriched PBS sequence features in the chimpanzee genome were predicted based on bioinformatics. The results show that pathways significantly enriched for ERV LTR-regulated genes found in the chimpanzee genome are closely associated with disease development, including neurological and neurodevelopmental psychiatric disorders. In summary, the identification, characterization, and genomics of HML-9 presented here not only contribute to our understanding of the role of ERVs in primate evolution but also to our understanding of their biofunctional significance.
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Affiliation(s)
- Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan 430068, China;
| | - Caiqin Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiuli Zhai
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Chunlei Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Mengying Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Bohan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xing Guo
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yanglan Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
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Kotov AA, Adashev VE, Kombarov IA, Bazylev SS, Shatskikh AS, Olenina LV. Molecular Insights into Female Hybrid Sterility in Interspecific Crosses between Drosophila melanogaster and Drosophila simulans. Int J Mol Sci 2024; 25:5681. [PMID: 38891872 PMCID: PMC11172174 DOI: 10.3390/ijms25115681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/19/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Species of the genus Drosophila have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent defect of oogenesis in hybrid ovaries. Because of the differential expression of genes encoding piRNA pathway components, rhino and deadlock, the functional RDCmel complex in hybrid ovaries was not assembled. However, the activity of the RDCsim complex was maintained in hybrids independent of the genomic origin of piRNA clusters. Despite the identification of a cohort of overexpressed TEs in hybrid ovaries, we found no evidence that their activity can be considered the main cause of hybrid sterility. We revealed a complicated pattern of Vasa protein expression in the hybrid germline, including partial AT-chX piRNA targeting of the vasasim allele and a significant zygotic delay in vasamel expression. We arrived at the conclusion that the hybrid sterility phenotype was caused by intricate multi-locus differences between the species.
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Affiliation(s)
- Alexei A. Kotov
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Vladimir E. Adashev
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Ilia A. Kombarov
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Sergei S. Bazylev
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Aleksei S. Shatskikh
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
| | - Ludmila V. Olenina
- Department of Molecular Mechanisms for Realization of Genetic Information, National Research Centre “Kurchatov Institute”, Moscow 123182, Russia; (A.A.K.); (V.E.A.); (S.S.B.)
- Laboratory of Functional Genomics, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow 119334, Russia; (I.A.K.); (A.S.S.)
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Münch L, Helmprobst F, Volff JN, Chalopin D, Schartl M, Kneitz S. Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus. Genes (Basel) 2024; 15:620. [PMID: 38790249 PMCID: PMC11121471 DOI: 10.3390/genes15050620] [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: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Transposable elements (TEs) are characterized by their ability to change their genomic position. Through insertion or recombination leading to deletions and other chromosomal aberrations, they can cause genetic instability. The extent to which they thereby exert regulatory influence on cellular functions is unclear. To better characterize TEs in processes such as carcinogenesis, we used the well-established Xiphophorus melanoma model. By transcriptome sequencing, we show that an increasing total number in transposons correlates with progression of malignancy in melanoma samples from Xiphophorus interspecific hybrids. Further, by comparing the presence of TEs in the parental genomes of Xiphophorus maculatus and Xiphophorus hellerii, we could show that even in closely related species, genomic location and spectrum of TEs are considerably different.
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Affiliation(s)
- Luca Münch
- Neurology Asklepios Klinik Barmbek, Rübenkamp 220, 22307 Hamburg, Germany;
| | - Frederik Helmprobst
- Institute of Neuropathology, Philipps-University Marburg, 35037 Marburg, Germany;
| | | | | | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 786666, USA
- Developmental Biochemistry, University of Würzburg, 97974 Würzburg, Germany
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
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48
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Zhang YR, Yin Y, Guo SM, Wang YF, Zhao GN, Ji DM, Zhou LQ. The landscape of transcriptional profiles in human oocytes with different chromatin configurations. J Ovarian Res 2024; 17:99. [PMID: 38730385 PMCID: PMC11088011 DOI: 10.1186/s13048-024-01431-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
With increasingly used assisted reproductive technology (ART), the acquisition of high-quality oocytes and early embryos has become the focus of much attention. Studies in mice have found that the transition of chromatin conformation from non-surrounded nucleolus (NSN) to surrounded nucleolus (SN) is essential for oocyte maturation and early embryo development, and similar chromatin transition also exists in human oocytes. In this study, we collected human NSN and SN oocytes and investigated their transcriptome. The analysis of differentially expressed genes showed that epigenetic functions, cyclin-dependent kinases and transposable elements may play important roles in chromatin transition during human oocyte maturation. Our findings provide new insights into the molecular mechanism of NSN-to-SN transition of human oocyte and obtained new clues for improvement of oocyte in vitro maturation technique.
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Affiliation(s)
- Yi-Ran Zhang
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Anhui, China
| | - Ying Yin
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shi-Meng Guo
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu-Fan Wang
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guang-Nian Zhao
- Department of Obstetrics and Gynecology, National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Key Laboratory of Cancer Invasion and Metastasis (Ministry of Education), Hubei Key Laboratory of Tumor Invasion and Metastasis, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Dong-Mei Ji
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Anhui, China.
| | - Li-Quan Zhou
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Anhui, China.
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49
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Guo P, Yu Y, Kang H, Liu Y, Zhu D, Sun C, Xing Z, Tang Z, Chen K, Tan A. GASZ is indispensable for gametogenesis in the silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38728119 DOI: 10.1111/imb.12921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
The prominent role of the P-element induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway in animals is to silence transposable elements and maintain genome stability, ensuring proper gametogenesis in gonads. GASZ (Germ cell protein with Ankyrin repeats, Sterile alpha motif, and leucine Zipper) is an evolutionarily conserved protein located on the outer mitochondrial membrane of germ cells and plays vital roles in the piRNA pathway and spermatogenesis in mammals. In the model insect Drosophila melanogaster, GASZ is essential for piRNA biogenesis and oogenesis, whereas its biological functions in non-drosophilid insects are still unknown. Here, we describe a comprehensive investigation of GASZ functions in the silkworm, Bombyx mori, a lepidopteran model insect, by using a binary transgenic CRISPR/Cas9 system. The BmGASZ mutation did not affect growth and development, but led to sterility in both males and females. Eupyrene sperm bundles of mutant males exhibited developmental defects, while the apyrene sperm bundles were normal, which were further confirmed through double copulation experiments with sex-lethal mutants, which males possess functional eupyrene sperm and abnormal apyrene sperm. In female mutant moths, ovarioles were severely degenerated and the eggs in ovarioles were deformed compared with that of wild type (WT). Further RNA-seq and RT-qPCR analysis revealed that amounts of piRNAs and transposon expression were dysregulated in gonads of mutants. In summary, this study has demonstrated vital roles of BmGASZ in gametogenesis through regulating the piRNA pathway in B. mori.
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Affiliation(s)
- Peilin Guo
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ye Yu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Hongxia Kang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Yutong Liu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Dalin Zhu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Chenxin Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Zhiping Xing
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ziyue Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Kai Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Anjiang Tan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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50
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Wang B, Saleh AA, Yang N, Asare E, Chen H, Wang Q, Chen C, Song C, Gao B. High Diversity of Long Terminal Repeat Retrotransposons in Compact Vertebrate Genomes: Insights from Genomes of Tetraodontiformes. Animals (Basel) 2024; 14:1425. [PMID: 38791643 PMCID: PMC11117352 DOI: 10.3390/ani14101425] [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: 03/25/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
This study aimed to investigate the evolutionary profile (including diversity, activity, and abundance) of retrotransposons (RTNs) with long terminal repeats (LTRs) in ten species of Tetraodontiformes. These species, Arothron firmamentum, Lagocephalus sceleratus, Pao palembangensis, Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, Takifugu rubripes, Tetraodon nigroviridis, Mola mola, and Thamnaconus septentrionalis, are known for having the smallest genomes among vertebrates. Data mining revealed a high diversity and wide distribution of LTR retrotransposons (LTR-RTNs) in these compact vertebrate genomes, with varying abundances among species. A total of 819 full-length LTR-RTN sequences were identified across these genomes, categorized into nine families belonging to four different superfamilies: ERV (Orthoretrovirinae and Epsilon retrovirus), Copia, BEL-PAO, and Gypsy (Gmr, Mag, V-clade, CsRN1, and Barthez). The Gypsy superfamily exhibited the highest diversity. LTR family distribution varied among species, with Takifugu bimaculatus, Takifugu flavidus, Takifugu ocellatus, and Takifugu rubripes having the highest richness of LTR families and sequences. Additionally, evidence of recent invasions was observed in specific tetraodontiform genomes, suggesting potential transposition activity. This study provides insights into the evolution of LTR retrotransposons in Tetraodontiformes, enhancing our understanding of their impact on the structure and evolution of host genomes.
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Affiliation(s)
- Bingqing Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Ahmed A. Saleh
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
- Animal and Fish Production Department, Faculty of Agriculture (Al-Shatby), Alexandria University, Alexandria 11865, Egypt
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Emmanuel Asare
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Hong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Quan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
| | - Bo Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (B.W.); (A.A.S.); (N.Y.); (E.A.); (H.C.); (Q.W.); (C.C.); (C.S.)
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