1
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Schartl M, Woltering JM, Irisarri I, Du K, Kneitz S, Pippel M, Brown T, Franchini P, Li J, Li M, Adolfi M, Winkler S, de Freitas Sousa J, Chen Z, Jacinto S, Kvon EZ, Correa de Oliveira LR, Monteiro E, Baia Amaral D, Burmester T, Chalopin D, Suh A, Myers E, Simakov O, Schneider I, Meyer A. The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 2024:10.1038/s41586-024-07830-1. [PMID: 39143221 DOI: 10.1038/s41586-024-07830-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 07/15/2024] [Indexed: 08/16/2024]
Abstract
The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.
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Affiliation(s)
- Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria.
| | | | - Iker Irisarri
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum of Nature, Hamburg, Germany
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Pippel
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Thomas Brown
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- DRESDEN-concept Genome Center (DcGC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
- Leibniz Institute for Zoo & Wildlife Research, Berlin, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Jing Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Ming Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Mateus Adolfi
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sylke Winkler
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Zhuoxin Chen
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental & Cell Biology, University of California, Irvine, CA, USA
| | | | - Erika Monteiro
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | | | - Domitille Chalopin
- Institute of Cellular Biochemistry and Genetics, CNRS, University of Bordeaux, Bordeaux, France
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eugene Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center of Systems Biology Dresden, Dresden, Germany
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Igor Schneider
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
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2
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Srivastav SP, Feschotte C, Clark AG. Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary. Genome Res 2024; 34:711-724. [PMID: 38749655 PMCID: PMC11216404 DOI: 10.1101/gr.278062.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/07/2024] [Indexed: 05/28/2024]
Abstract
The piRNA pathway is a highly conserved mechanism to repress transposable element (TE) activity in the animal germline via a specialized class of small RNAs called piwi-interacting RNAs (piRNAs). piRNAs are produced from discrete genomic regions called piRNA clusters (piCs). Although the molecular processes by which piCs function are relatively well understood in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster with high-quality long-read genome assemblies. We perform annotations of ovary piCs and genome-wide TE content in each strain. Our analysis uncovers extensive variation in piC activity across strains and signatures of rapid birth and death of piCs. Most TEs inferred to be recently active show an enrichment of insertions into old and large piCs, consistent with the previously proposed "trap" model of piC evolution. In contrast, a small subset of active LTR families is enriched for the formation of new piCs, suggesting that these TEs have higher proclivity to form piCs. Thus, our findings uncover processes leading to the origin of piCs. We propose that piC evolution begins with the emergence of piRNAs from individual insertions of a few select TE families prone to seed new piCs that subsequently expand by accretion of insertions from most other TE families during evolution to form larger "trap" clusters. Our study shows that TEs themselves are the major force driving the rapid evolution of piCs.
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Affiliation(s)
- Satyam P Srivastav
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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Carpinteyro-Ponce J, Machado CA. The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes. Genome Biol Evol 2024; 16:evae047. [PMID: 38482945 PMCID: PMC10980976 DOI: 10.1093/gbe/evae047] [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] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence.
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Affiliation(s)
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
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Chen Z, Shi Q, Zhao Y, Xu M, Liu Y, Li X, Liu L, Sun M, Wu X, Shao Z, Xu Y, Wang L, He X. Long-read transcriptome landscapes of primary and metastatic liver cancers at transcript resolution. Biomark Res 2024; 12:4. [PMID: 38185659 PMCID: PMC10773130 DOI: 10.1186/s40364-023-00554-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/29/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND The liver ranks as the sixth most prevalent site of primary cancer in humans, and it frequently experiences metastases from cancers originating in other organs. To facilitate the development of effective treatments and improve survival rates, it is crucial to comprehend the intricate and diverse transcriptome landscape of primary and metastatic liver cancers. METHODS We conducted long-read isoform sequencing and short-read RNA sequencing using a cohort of 95 patients with primary and secondary liver cancer who underwent hepatic resection. We compared the transcriptome landscapes of primary and metastatic liver cancers and systematically investigated hepatocellular carcinoma (HCC), paired primary tumours and liver metastases, and matched nontumour liver tissues. RESULTS We elucidated the full-length isoform-level transcriptome of primary and metastatic liver cancers in humans. Our analysis revealed isoform-level diversity in HCC and identified transcriptome variations associated with liver metastatis. Specific RNA transcripts and isoform switching events with clinical implications were profound in liver cancer. Moreover, we defined metastasis-specific transcripts that may serve as predictors of risk of metastasis. Additionally, we observed abnormalities in adjacent paracancerous liver tissues and characterized the immunological and metabolic alterations occurring in the liver. CONCLUSIONS Our findings underscore the power of full-length transcriptome profiling in providing novel biological insights into the molecular mechanisms underlying tumourigenesis. These insights will further contribute to improving treatment strategies for primary and metastatic liver cancers.
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Affiliation(s)
- Zhiao Chen
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Qili Shi
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Yiming Zhao
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Midie Xu
- Department of Pathology, biobank, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yizhe Liu
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Xinrong Li
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Li Liu
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China
| | - Menghong Sun
- Department of Pathology, biobank, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Zhimin Shao
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 200032, Shanghai, China.
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China.
| | - Xianghuo He
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University Shanghai Cancer Center, Fudan University, 302 Rm., 7# Bldg., 270 Dong An Road, 200032, Shanghai, China.
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China.
- Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, 200032, Shanghai, China.
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Gu X, Wang M, Zhang XO. TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS). Nucleic Acids Res 2024; 52:D322-D333. [PMID: 37956335 PMCID: PMC10767810 DOI: 10.1093/nar/gkad1048] [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: 08/13/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.
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Affiliation(s)
- Xiaobing Gu
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Mingdong Wang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao-Ou Zhang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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6
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Lawson HA, Liang Y, Wang T. Transposable elements in mammalian chromatin organization. Nat Rev Genet 2023; 24:712-723. [PMID: 37286742 DOI: 10.1038/s41576-023-00609-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2023] [Indexed: 06/09/2023]
Abstract
Transposable elements (TEs) are mobile DNA elements that comprise almost 50% of mammalian genomic sequence. TEs are capable of making additional copies of themselves that integrate into new positions in host genomes. This unique property has had an important impact on mammalian genome evolution and on the regulation of gene expression because TE-derived sequences can function as cis-regulatory elements such as enhancers, promoters and silencers. Now, advances in our ability to identify and characterize TEs have revealed that TE-derived sequences also regulate gene expression by both maintaining and shaping 3D genome architecture. Studies are revealing how TEs contribute raw sequence that can give rise to the structures that shape chromatin organization, and thus gene expression, allowing for species-specific genome innovation and evolutionary novelty.
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Affiliation(s)
- Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
| | - Yonghao Liang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, Saint Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO, USA.
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7
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Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci 2023; 24:11591. [PMID: 37511347 PMCID: PMC10380595 DOI: 10.3390/ijms241411591] [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: 07/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements.
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Affiliation(s)
| | - Federica Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (E.C.); (M.B.); (A.C.); (M.A.B.)
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8
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Wang J, Yuan L, Tang J, Liu J, Sun C, Itgen MW, Chen G, Sessions SK, Zhang G, Mueller RL. Transposable element and host silencing activity in gigantic genomes. Front Cell Dev Biol 2023; 11:1124374. [PMID: 36910142 PMCID: PMC9998948 DOI: 10.3389/fcell.2023.1124374] [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: 12/15/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of Ranodon sibiricus, a salamander species with a ∼21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both ovaries and testes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 to 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Testes have higher TE expression than ovaries, suggesting that they may contribute more to the species' high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently "on the attack" in the arms race dynamic.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Liang Yuan
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Jiaxing Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Jiongyu Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Guiying Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | | | - Guangpu Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
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9
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Pasquesi GIM, Kelly CJ, Ordonez AD, Chuong EB. Transcriptional dynamics of transposable elements in the type I IFN response in Myotis lucifugus cells. Mob DNA 2022; 13:22. [PMID: 36068622 PMCID: PMC9446614 DOI: 10.1186/s13100-022-00277-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/09/2022] [Indexed: 12/02/2022] Open
Abstract
Background Bats are a major reservoir of zoonotic viruses, and there has been growing interest in characterizing bat-specific features of innate immunity and inflammation. Recent studies have revealed bat-specific adaptations affecting interferon (IFN) signaling and IFN-stimulated genes (ISGs), but we still have a limited understanding of the genetic mechanisms that have shaped the evolution of bat immunity. Here we investigated the transcriptional and epigenetic dynamics of transposable elements (TEs) during the type I IFN response in little brown bat (Myotis lucifugus) primary embryonic fibroblast cells, using RNA-seq and CUT&RUN. Results We found multiple bat-specific TEs that undergo both locus-specific and family-level transcriptional induction in response to IFN. Our transcriptome reassembly identified multiple ISGs that have acquired novel exons from bat-specific TEs, including NLRC5, SLNF5 and a previously unannotated isoform of the IFITM2 gene. We also identified examples of TE-derived regulatory elements, but did not find strong evidence supporting genome-wide epigenetic activation of TEs in response to IFN. Conclusion Collectively, our study uncovers numerous TE-derived transcripts, proteins, and alternative isoforms that are induced by IFN in Myotis lucifugus cells, highlighting candidate loci that may contribute to bat-specific immune function. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00277-z.
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Affiliation(s)
- Giulia Irene Maria Pasquesi
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
| | - Conor J Kelly
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
| | - Andrea D Ordonez
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA
| | - Edward B Chuong
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, 596 UCB, Boulder, CO, 80309, USA.
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10
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Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y, Lawson HA, Yang H, Yue F, Wang T. Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish. Genome Res 2022; 32:1424-1436. [PMID: 35649578 PMCID: PMC9341505 DOI: 10.1101/gr.276052.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/27/2022] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) encode regulatory elements that impact gene expression in multiple species, yet a comprehensive analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory elements in the zebrafish genome and that 37% of TEs are positioned in active regulatory states in adult zebrafish tissues. We identify TE subfamilies enriched in highly specific regulatory elements among different tissues. We use transcript assembly to discover TE-derived transcriptional units expressed across tissues. Finally, we show that novel TE-derived promoters can initiate tissue-specific transcription of alternate gene isoforms. This work provides a comprehensive profile of TE activity across normal zebrafish tissues, shedding light on mechanisms underlying the regulation of gene expression in this widely used model organism.
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Affiliation(s)
- Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Ju Heon Maeng
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Nakul M Shah
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, Illinois 60611, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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11
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Femenias MM, Santos JC, Sites JW, Avila LJ, Morando M. ExplorATE: A new pipeline to explore active transposable elements from RNA-seq data. Bioinformatics 2022; 38:3361-3366. [PMID: 35608310 DOI: 10.1093/bioinformatics/btac354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 05/03/2022] [Accepted: 05/19/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Transposable elements (TEs) are ubiquitous in genomes and many remain active. TEs comprise an important fraction of the transcriptomes with potential effects on the host genome, either by generating deleterious mutations or promoting evolutionary novelties. However, their functional study is limited by the difficulty in their identification and quantification, particularly in non-model organisms. RESULTS We developed a new pipeline (ExplorATE or Explore Active Transposable Elements) implemented in R and bash that allows the quantification of active TEs in both model and non-model organisms. ExplorATE creates TE-specific indexes and uses the Selective Alignment (SA) to filter out co-transcribed transposons within genes based on alignment scores. Moreover, our software incorporates a Wicker-like criteria to refine a set of target TEs and avoid spurious mapping. Based on simulated and real data, we show that the SA strategy adopted by ExplorATE achieved better estimates of non-co-transcribed elements than other available alignment-based or mapping-based software. ExplorATE results showed high congruence with alignment-based tools with and without a reference genome, yet ExplorATE required less execution time. Likewise, ExplorATE expands and complements most previous TE analyses by incorporating the co-transcription and multi-mapping effects during quantification, and provides a seamless integration with other downstream tools within the R environment. AVAILABILITY Source code is available at https://github.com/FemeniasM/ExplorATEproject and https://github.com/FemeniasM/ExplorATE_shell_script. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Martin M Femenias
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Juan C Santos
- Department of Biological Sciences, St. John's University, Queens, NY, 11439, USA
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University (BYU), Provo, UT, 84602, USA
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Boulevard Almirante Brown 2915, Puerto Madryn, CT U9120ACD, Argentina
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12
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Vandewege MW, Patt RN, Merriman DK, Ray DA, Hoffmann FG. The PIWI/piRNA response is relaxed in a rodent that lacks mobilizing transposable elements. RNA (NEW YORK, N.Y.) 2022; 28:609-621. [PMID: 35064043 PMCID: PMC8925971 DOI: 10.1261/rna.078862.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs) are genomic parasites that can propagate throughout host genomes. Mammalian genomes are typically dominated by LINE retrotransposons and their associated SINEs, and germline mobilization is a challenge to genome integrity. There are defenses against TE proliferation and the PIWI/piRNA defense is among the most well understood. However, the PIWI/piRNA system has been investigated largely in animals with actively mobilizing TEs and it is unclear how the PIWI/piRNA system functions in the absence of mobilizing TEs. The 13-lined ground squirrel provides the opportunity to examine PIWI/piRNA and TE dynamics within the context of minimal, and possibly nonexistent, TE accumulation. To do so, we compared the PIWI/piRNA dynamics in squirrels to observations from the rabbit and mouse. Despite a lack of young insertions in squirrels, TEs were still actively transcribed at higher levels compared to mouse and rabbit. All three Piwi genes were not expressed, prior to P8 in squirrel testis, and there was little TE expression change with the onset of Piwi expression. We also demonstrated there was not a major expression change in the young squirrel LINE families in the transition from juvenile to adult testis in contrast to young mouse and rabbit LINE families. These observations lead us to conclude that PIWI suppression, was weaker for squirrel LINEs and SINEs and did not strongly reduce their transcription. We speculate that, although the PIWI/piRNA system is adaptable to novel TE threats, transcripts from TEs that are no longer threatening receive less attention from PIWI proteins.
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Affiliation(s)
- Michael W Vandewege
- Department of Biology, Eastern New Mexico University, Portales, New Mexico 88130, USA
| | - Roy N Patt
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas 78245-0549, USA
| | - Dana K Merriman
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, Wisconsin 54901, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39762, USA
- Institute of Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39762, USA
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13
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Zheng J, Wei Y, Han GZ. The diversity and evolution of retroviruses: perspectives from viral “fossils”. Virol Sin 2022; 37:11-18. [PMID: 35234634 PMCID: PMC8922424 DOI: 10.1016/j.virs.2022.01.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/12/2021] [Indexed: 01/19/2023] Open
Abstract
Retroviruses exclusively infect vertebrates, causing a variety of diseases. The replication of retroviruses requires reverse transcription and integration into host genomes. When infecting germline cells, retroviruses become inherited vertically, forming endogenous retroviruses (ERVs). ERVs document past viral infections, providing molecular fossils for studying the evolutionary history of retroviruses. In this review, we summarize the recent advances in understanding the diversity and evolution of retroviruses from the perspectives of viral fossils, and discuss the effects of ERVs on the evolution of host biology. Recent advances in understanding the diversity and evolution of retroviruses. Methods to analyze ERVs. The effects of ERVs on the evolution of host biology.
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Affiliation(s)
- Jialu Zheng
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yutong Wei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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14
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A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements. J Genet Genomics 2021; 48:1007-1019. [PMID: 34531149 DOI: 10.1016/j.jgg.2021.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
Enhancers modulate gene expression by interacting with promoters. Models of enhancer-promoter interactions (EPIs) in the literature involve the activity of many components, including transcription factors and nucleic acid. However, the role that sequence similarity plays in EPIs remains largely unexplored. Herein, we report that Alu-derived sequences dominate sequence similarity between enhancers and promoters. After rejecting alternative DNA:DNA and DNA:RNA triplex models, we propose that enhancer-associated RNAs (eRNAs) may directly contact their targeted promoters by forming trans-acting R-loops at those Alu sequences. We show how the characteristic distribution of functional genomic data, such as RNA-DNA proximate ligation reads, binding of transcription factors, and RNA-binding proteins, all align with the Alu sequences of EPIs. We also show that these aligned Alu sequences may be subject to the constraint of coevolution, further implying the functional significance of these R-loop hybrids. Finally, our results imply that eRNA and Alu elements associate in a manner previously unrecognized in EPIs and the evolution of gene regulation networks in mammals.
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15
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Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet 2021; 22:691-711. [PMID: 34354263 DOI: 10.1038/s41576-021-00385-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.
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Affiliation(s)
- Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
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16
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Modzelewski AJ, Shao W, Chen J, Lee A, Qi X, Noon M, Tjokro K, Sales G, Biton A, Anand A, Speed TP, Xuan Z, Wang T, Risso D, He L. A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell 2021; 184:5541-5558.e22. [PMID: 34644528 PMCID: PMC8787082 DOI: 10.1016/j.cell.2021.09.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transient retrotransposon induction during preimplantation development of eight mammals. Induced retrotransposons exhibit similar preimplantation profiles across species, conferring gene regulatory activities, particularly through long terminal repeat (LTR) retrotransposon promoters. A mouse-specific MT2B2 retrotransposon promoter generates an N-terminally truncated Cdk2ap1ΔN that peaks in preimplantation embryos and promotes proliferation. In contrast, the canonical Cdk2ap1 peaks in mid-gestation and represses cell proliferation. This MT2B2 promoter, whose deletion abolishes Cdk2ap1ΔN production, reduces cell proliferation and impairs embryo implantation, is developmentally essential. Intriguingly, Cdk2ap1ΔN is evolutionarily conserved in sequence and function yet is driven by different promoters across mammals. The distinct preimplantation Cdk2ap1ΔN expression in each mammalian species correlates with the duration of its preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.
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Affiliation(s)
- Andrew J Modzelewski
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wanqing Shao
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jingqi Chen
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Angus Lee
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xin Qi
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mackenzie Noon
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kristy Tjokro
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabriele Sales
- Department of Biology, University of Padova, Padova 35122, Italy
| | - Anne Biton
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA; Bioinformatics and Biostatistics, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris 75015, France
| | - Aparna Anand
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Terence P Speed
- Bioinformatics Division, WEHI, Parkville, VIC 3052, Australia
| | - Zhenyu Xuan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova 35122, Italy.
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA.
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17
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Ludwig A, Schemberger MO, Gazolla CB, de Moura Gama J, Duarte I, Lopes ALK, Mathias C, Petters-Vandresen DAL, Zattera ML, Bruschi DP. Transposable elements expression in Rhinella marina (cane toad) specimens submitted to immune and stress challenge. Genetica 2021; 149:335-342. [PMID: 34383169 DOI: 10.1007/s10709-021-00130-w] [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: 03/11/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
Transposable elements (TEs) are important components of eukaryotic genomes and compose around 30% of the genome of Rhinella marina, an invasive toad species. Considering the possible role of TEs in the adaptation of populations, we have analyzed the expression of TEs in publicly available spleen tissue transcriptomic data generated for this species after immune and stress challenge. By analyzing the transcriptome assembly, we detected a high number of TE segments. Moreover, some distinct TE families were differentially expressed in some conditions. Our result shows that several TEs are capable of being transcribed in R. marina and they could help to generate a rapid response of specimens to the environment. Also, we can suggest that these TEs could be activated in the germinative cells as well producing variability to be selected and shaped by the evolutionary processes behind the success of this invasive species. Thus, the TEs are important targets for investigation in the context of R. marina adaptation.
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Affiliation(s)
- Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas - Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Michelle Orane Schemberger
- Laboratório de Biotecnologia Aplicada a Fruticultura, Departamento de Fitotecnia e Fitossanidade, Universidade Estadual de Ponta Grossa (UEPG), Ponta Grossa, Paraná, Brazil
| | - Camilla Borges Gazolla
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Joana de Moura Gama
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Iraine Duarte
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Ana Luisa Kalb Lopes
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas - Fiocruz-PR, Curitiba, Paraná, Brazil
- Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Carolina Mathias
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | | | - Michelle Louise Zattera
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil
| | - Daniel Pacheco Bruschi
- Programa de Pós-Graduação em Genética (PPG-GEN), Universidade Federal do Paraná (UFPR), Curitiba, Brazil.
- Laboratório de Citogenética Evolutiva e Conservação Animal (LabCECA), Departamento de Genética, Universidade Federal do Paraná (UFPR), Curitiba, Brazil.
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18
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Hermant C, Torres-Padilla ME. TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev 2021; 35:22-39. [PMID: 33397727 PMCID: PMC7778262 DOI: 10.1101/gad.344473.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Hermant and Torres-Padilla summarize and discuss the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific transposable element families or subfamilies. Transposable elements (TEs) are genetic elements capable of changing position within the genome. Although their mobilization can constitute a threat to genome integrity, nearly half of modern mammalian genomes are composed of remnants of TE insertions. The first critical step for a successful transposition cycle is the generation of a full-length transcript. TEs have evolved cis-regulatory elements enabling them to recruit host-encoded factors driving their own, selfish transcription. TEs are generally transcriptionally silenced in somatic cells, and the mechanisms underlying their repression have been extensively studied. However, during germline formation, preimplantation development, and tumorigenesis, specific TE families are highly expressed. Understanding the molecular players at stake in these contexts is of utmost importance to establish the mechanisms regulating TEs, as well as the importance of their transcription to the biology of the host. Here, we review the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific TE families or subfamilies. We discuss the diversity of TE regulatory elements within mammalian genomes and highlight the importance of TE mobilization in the dispersal of transcription factor-binding sites over the course of evolution.
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Affiliation(s)
- Clara Hermant
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany.,Faculty of Biology, Ludwig-Maximilians Universität München, D-82152 Planegg-Martinsried, Germany
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19
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Sun MA, Wolf G, Wang Y, Senft AD, Ralls S, Jin J, Dunn-Fletcher CE, Muglia LJ, Macfarlan TS. Endogenous retroviruses drive lineage-specific regulatory evolution across primate and rodent placentae. Mol Biol Evol 2021; 38:4992-5004. [PMID: 34320657 DOI: 10.1093/molbev/msab223] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In mammals, the placenta mediates maternal-fetal nutrient and waste exchange and acts in an immunomodulatory way to facilitate maternal-fetal tolerance. The placenta is highly diverse across mammalian species, yet the molecular mechanisms that distinguish the placenta of human from other mammals are not fully understood. Using an interspecies transcriptomic comparison of human, macaque, and mouse late-gestation placentae, we identified hundreds of genes with lineage-specific expression-including dozens that are placentally-enriched and potentially related to pregnancy. We further annotated the enhancers for different human tissues using epigenomic data and demonstrate that the placenta and chorion are unique in that their enhancers display the least conservation. We identified numerous lineage-specific human placental enhancers and found they highly overlap with specific families of endogenous retroviruses (ERVs), including MER21A, MER41A/B and MER39B that were previously linked to immune response and placental function. Among these ERV families, we further demonstrate that MER41A/B insertions create dozens of lineage-specific Serum Response Factor (SRF) binding loci in human, including one adjacent to FBN2, a placenta-specific gene with increased expression in humans that produces the peptide hormone placensin to stimulate glucose secretion and trophoblast invasion. Overall, our results demonstrate the prevalence of lineage-specific placental enhancers which are frequently associated with ERV insertions and likely facilitate the lineage-specific evolution of the mammalian placenta.
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Affiliation(s)
- Ming-An Sun
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD, 20892, USA.,Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Gernot Wolf
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD, 20892, USA
| | - Yejun Wang
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Anna D Senft
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD, 20892, USA
| | - Sherry Ralls
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD, 20892, USA
| | - Jinpu Jin
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD, 20892, USA
| | - Caitlin E Dunn-Fletcher
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Physician-Scientist Training Program in Pediatrics, Department of Pediatrics, University of Texas Southwestern, Dallas, Texas, USA
| | - Louis J Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Burroughs Wellcome Fund, Research Triangle Park, NC, 27709, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD, 20892, USA
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20
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Stow EC, Kaul T, deHaro DL, Dem MR, Beletsky AG, Morales ME, Du Q, LaRosa AJ, Yang H, Smither E, Baddoo M, Ungerleider N, Deininger P, Belancio VP. Organ-, sex- and age-dependent patterns of endogenous L1 mRNA expression at a single locus resolution. Nucleic Acids Res 2021; 49:5813-5831. [PMID: 34023901 PMCID: PMC8191783 DOI: 10.1093/nar/gkab369] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Expression of L1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability. We used a reported stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. This analysis determined that mRNA expression of L1 loci in rodents exhibits striking organ specificity with less than 0.8% of loci shared between organs of the same organism. This organ specificity in L1 mRNA expression is preserved in male and female mice and across age groups. We discovered notable differences in L1 mRNA expression between sexes with only 5% of expressed L1 loci shared between male and female mice. Moreover, we report that the levels of total L1 mRNA expression and the number and spectrum of expressed L1 loci fluctuate with age as independent variables, demonstrating different patterns in different organs and sexes. Overall, our comparisons between organs and sexes and across ages ranging from 2 to 22 months establish previously unforeseen dynamic changes in L1 mRNA expression in vivo. These findings establish the beginning of an atlas of endogenous L1 mRNA expression across a broad range of biological variables that will guide future studies.
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Affiliation(s)
- Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Dawn L deHaro
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Madeleine R Dem
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Anna G Beletsky
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Maria E Morales
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Qianhui Du
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Alexis J LaRosa
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Hanlin Yang
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Emily Smither
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
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21
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Zhang XO, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annu Rev Genomics Hum Genet 2021; 22:199-218. [PMID: 33792357 DOI: 10.1146/annurev-genom-111620-100736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Short interspersed nuclear elements (SINEs) are nonautonomous retrotransposons that occupy approximately 13% of the human genome. They are transcribed by RNA polymerase III and can be retrotranscribed and inserted back into the genome with the help of other autonomous retroelements. Because they are preferentially located close to or within gene-rich regions, they can regulate gene expression by various mechanisms that act at both the DNA and the RNA levels. In this review, we summarize recent findings on the involvement of SINEs in different types of gene regulation and discuss the potential regulatory functions of SINEs that are in close proximity to genes, Pol III-transcribed SINE RNAs, and embedded SINE sequences within Pol II-transcribed genes in the human genome. These discoveries illustrate how the human genome has exapted some SINEs into functional regulatory elements.
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Affiliation(s)
- Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA; .,Current affiliation: School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
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22
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Magnani E, Macchi F, Madakashira BP, Zhang C, Alaydaroos F, Sadler KC. uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements. Front Immunol 2021; 12:627926. [PMID: 33854502 PMCID: PMC8039153 DOI: 10.3389/fimmu.2021.627926] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/23/2021] [Indexed: 12/13/2022] Open
Abstract
Activation of transposable elements (TEs) can cause cellular damage. Cytoplasmic nucleic acid sensing pathways evolved to detect pathogens, but can also serve to cull cells with inappropriate TE activation as TEs can be viral mimetics. Epigenetic silencing of TEs is mediated in part by DNA methylation, but it is not clear if TE activation or the immune system contribute to the cellular damage caused by loss of DNA methylation. Here, we provide mechanistic insight into the observation of an activated interferon response in the liver of zebrafish larvae with deletion in critical components of the DNA methylation machinery, uhrf1 and dnmt1. We focus on dissecting the relationship between DNA methylation, TE activation and induction of an immune response through cytoplasmic DNA and double stranded RNA sensing pathways and identify tnfa as a mediator of cell death in the liver of these mutants. Integrated RNAseq and methylome analysis identified LTR transposons as the most upregulated in these mutants and also the most methylated in control larvae, indicating a direct role of DNA methylation in suppressing this TE subclass. RNAseq analysis from these same samples revealed expression signatures of a type-I interferon response and of tnfa activation, mimicking the pattern of gene expression in virally infected cells. CRISPR/Cas9 mediated depletion of the cellular antiviral sensors sting and mavs reduced expression of interferon response genes and tnfa depletion dramatically reduced cell death in uhrf1 mutant livers. This suggests that the antiviral response induced by DNA hypomethylation and TE activation in the liver is mediated by the signaling pathways activated by both cytoplasmic double stranded RNA and DNA and that tnfa mediates cell death as a potential mechanism to eliminate these damaged cells.
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Affiliation(s)
- Elena Magnani
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Filippo Macchi
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | | | - Chi Zhang
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Fatima Alaydaroos
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kirsten C Sadler
- Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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23
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Palacios-Gimenez OM, Koelman J, Palmada-Flores M, Bradford TM, Jones KK, Cooper SJB, Kawakami T, Suh A. Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats. BMC Biol 2020; 18:199. [PMID: 33349252 PMCID: PMC7754599 DOI: 10.1186/s12915-020-00925-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the "repeatome", are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. RESULTS We obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. CONCLUSION This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.
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Affiliation(s)
- Octavio M Palacios-Gimenez
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
| | - Julia Koelman
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Marc Palmada-Flores
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
| | - Tessa M Bradford
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences and Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Karl K Jones
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia
| | - Steven J B Cooper
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences and Australian Centre for Evolutionary Biology and Biodiversity, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Takeshi Kawakami
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- Embark Veterinary, Inc., Boston, MA, USA.
| | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
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24
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Kirov I, Omarov M, Merkulov P, Dudnikov M, Gvaramiya S, Kolganova E, Komakhin R, Karlov G, Soloviev A. Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower ( Helianthus annuus L.). Int J Mol Sci 2020; 21:E9331. [PMID: 33297579 PMCID: PMC7730604 DOI: 10.3390/ijms21239331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/21/2022] Open
Abstract
LTR retrotransposons (RTEs) play a crucial role in plant genome evolution and adaptation. Although RTEs are generally silenced in somatic plant tissues under non-stressed conditions, some expressed RTEs (exRTEs) escape genome defense mechanisms. As our understanding of exRTE organization in plants is rudimentary, we systematically surveyed the genomic and transcriptomic organization and mobilome (transposition) activity of sunflower (Helianthus annuus L.) exRTEs. We identified 44 transcribed RTEs in the sunflower genome and demonstrated their distinct genomic features: more recent insertion time, longer open reading frame (ORF) length, and smaller distance to neighboring genes. We showed that GAG-encoding ORFs are present at significantly higher frequencies in exRTEs, compared with non-expressed RTEs. Most exRTEs exhibit variation in copy number among sunflower cultivars and one exRTE Gagarin produces extrachromosomal circular DNA in seedling, demonstrating recent and ongoing transposition activity. Nanopore direct RNA sequencing of full-length RTE RNA revealed complex patterns of alternative splicing in RTE RNAs, resulting in isoforms that carry ORFs for distinct RTE proteins. Together, our study demonstrates that tens of expressed sunflower RTEs with specific genomic organization shape the hidden layer of the transcriptome, pointing to the evolution of specific strategies that circumvent existing genome defense mechanisms.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Murad Omarov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Faculty of Computer Science, National Research University Higher School of Economics, Pokrovsky Boulvar 11, 109028 Moscow, Russia
| | - Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| | - Sofya Gvaramiya
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Elizaveta Kolganova
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Roman Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (M.O.); (P.M.); (M.D.); (S.G.); (E.K.); (R.K.); (G.K.); (A.S.)
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25
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Miao B, Fu S, Lyu C, Gontarz P, Wang T, Zhang B. Tissue-specific usage of transposable element-derived promoters in mouse development. Genome Biol 2020; 21:255. [PMID: 32988383 PMCID: PMC7520981 DOI: 10.1186/s13059-020-02164-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are a significant component of eukaryotic genomes and play essential roles in genome evolution. Mounting evidence indicates that TEs are highly transcribed in early embryo development and contribute to distinct biological functions and tissue morphology. RESULTS We examine the epigenetic dynamics of mouse TEs during the development of five tissues: intestine, liver, lung, stomach, and kidney. We found that TEs are associated with over 20% of open chromatin regions during development. Close to half of these accessible TEs are only activated in a single tissue and a specific developmental stage. Most accessible TEs are rodent-specific. Across these five tissues, 453 accessible TEs are found to create the transcription start sites of downstream genes in mouse, including 117 protein-coding genes and 144 lincRNA genes, 93.7% of which are mouse-specific. Species-specific TE-derived transcription start sites are found to drive the expression of tissue-specific genes and change their tissue-specific expression patterns during evolution. CONCLUSION Our results suggest that TE insertions increase the regulatory potential of the genome, and some TEs have been domesticated to become a crucial component of gene and regulate tissue-specific expression during mouse tissue development.
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Affiliation(s)
- Benpeng Miao
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Department of Genetics, Edison Family Center for Genomic Sciences and Systems Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Shuhua Fu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Cheng Lyu
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Paul Gontarz
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genomic Sciences and Systems Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Bo Zhang
- Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63108, USA.
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