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Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [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: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
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Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
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2
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Mizgier NA, Jones CE, Furano AV. Co-expression of distinct L1 retrotransposon coiled coils can lead to their entanglement. Mob DNA 2023; 14:16. [PMID: 37864180 PMCID: PMC10588031 DOI: 10.1186/s13100-023-00303-8] [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: 08/31/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023] Open
Abstract
L1 (LINE1) non-LTR retrotransposons are ubiquitous genomic parasites and the dominant transposable element in humans having generated about 40% of their genomic DNA during their ~ 100 million years (Myr) of activity in primates. L1 replicates in germ line cells and early embryos, causing genetic diversity and defects, but can be active in some somatic stem cells, tumors and during aging. L1 encodes two proteins essential for retrotransposition: ORF2p, a reverse transcriptase that contains an endonuclease domain, and ORF1p, a coiled coil mediated homo trimer, which functions as a nucleic acid chaperone. Both proteins contain highly conserved domains and preferentially bind their encoding transcript to form an L1 ribonucleoprotein (RNP), which mediates retrotransposition. However, the coiled coil has periodically undergone episodes of substantial amino acid replacement to the extent that a given L1 family can concurrently express multiple ORF1s that differ in the sequence of their coiled coils. Here we show that such distinct ORF1p sequences can become entangled forming heterotrimers when co-expressed from separate vectors and speculate on how coiled coil entanglement could affect coiled coil evolution.
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Affiliation(s)
- Nikola A. Mizgier
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Charlie E. Jones
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
| | - Anthony V. Furano
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892 USA
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3
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Luqman-Fatah A, Miyoshi T. Human LINE-1 retrotransposons: impacts on the genome and regulation by host factors. Genes Genet Syst 2023; 98:121-154. [PMID: 36436935 DOI: 10.1266/ggs.22-00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genome sequencing revealed that nearly half of the human genome is comprised of transposable elements. Although most of these elements have been rendered inactive due to mutations, full-length intact long interspersed element-1 (LINE-1 or L1) copies retain the ability to mobilize through RNA intermediates by a so-called "copy-and-paste" mechanism, termed retrotransposition. L1 is the only known autonomous mobile genetic element in the genome, and its retrotransposition contributes to inter- or intra-individual genetic variation within the human population. However, L1 retrotransposition also poses a threat to genome integrity due to gene disruption and chromosomal instability. Moreover, recent studies suggest that aberrant L1 expression can impact human health by causing diseases such as cancer and chronic inflammation that might lead to autoimmune disorders. To counteract these adverse effects, the host cells have evolved multiple layers of defense mechanisms at the epigenetic, RNA and protein levels. Intriguingly, several host factors have also been reported to facilitate L1 retrotransposition, suggesting that there is competition between negative and positive regulation of L1 by host factors. Here, we summarize the known host proteins that regulate L1 activity at different stages of the replication cycle and discuss how these factors modulate disease-associated phenotypes caused by L1.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
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4
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Martelossi J, Nicolini F, Subacchi S, Pasquale D, Ghiselli F, Luchetti A. Multiple and diversified transposon lineages contribute to early and recent bivalve genome evolution. BMC Biol 2023; 21:145. [PMID: 37365567 DOI: 10.1186/s12915-023-01632-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) can represent one of the major sources of genomic variation across eukaryotes, providing novel raw materials for species diversification and innovation. While considerable effort has been made to study their evolutionary dynamics across multiple animal clades, molluscs represent a substantially understudied phylum. Here, we take advantage of the recent increase in mollusc genomic resources and adopt an automated TE annotation pipeline combined with a phylogenetic tree-based classification, as well as extensive manual curation efforts, to characterize TE repertories across 27 bivalve genomes with a particular emphasis on DDE/D class II elements, long interspersed nuclear elements (LINEs), and their evolutionary dynamics. RESULTS We found class I elements as highly dominant in bivalve genomes, with LINE elements, despite less represented in terms of copy number per genome, being the most common retroposon group covering up to 10% of their genome. We mined 86,488 reverse transcriptases (RVT) containing LINE coming from 12 clades distributed across all known superfamilies and 14,275 class II DDE/D-containing transposons coming from 16 distinct superfamilies. We uncovered a previously underestimated rich and diverse bivalve ancestral transposon complement that could be traced back to their most recent common ancestor that lived ~ 500 Mya. Moreover, we identified multiple instances of lineage-specific emergence and loss of different LINEs and DDE/D lineages with the interesting cases of CR1- Zenon, Proto2, RTE-X, and Academ elements that underwent a bivalve-specific amplification likely associated with their diversification. Finally, we found that this LINE diversity is maintained in extant species by an equally diverse set of long-living and potentially active elements, as suggested by their evolutionary history and transcription profiles in both male and female gonads. CONCLUSIONS We found that bivalves host an exceptional diversity of transposons compared to other molluscs. Their LINE complement could mainly follow a "stealth drivers" model of evolution where multiple and diversified families are able to survive and co-exist for a long period of time in the host genome, potentially shaping both recent and early phases of bivalve genome evolution and diversification. Overall, we provide not only the first comparative study of TE evolutionary dynamics in a large but understudied phylum such as Mollusca, but also a reference library for ORF-containing class II DDE/D and LINE elements, which represents an important genomic resource for their identification and characterization in novel genomes.
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Affiliation(s)
- Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Filippo Nicolini
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
- Fano Marine Center, Department of Biological, Geological and Environmental Sciences, University of Bologna, Viale Adriatico 1/N, 61032, Fano, Italy
| | - Simone Subacchi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniela Pasquale
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy.
| | - Andrea Luchetti
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
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5
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Garcia-Cañadas M, Sanchez-Luque FJ, Sanchez L, Rojas J, Garcia Perez JL. LINE-1 Retrotransposition Assays in Embryonic Stem Cells. Methods Mol Biol 2023; 2607:257-309. [PMID: 36449167 DOI: 10.1007/978-1-0716-2883-6_13] [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: 06/17/2023]
Abstract
The ongoing mobilization of active non-long terminal repeat (LTR) retrotransposons continues to impact the genomes of most mammals, including humans and rodents. Non-LTR retrotransposons mobilize using an intermediary RNA and a copy-and-paste mechanism termed retrotransposition. Non-LTR retrotransposons are subdivided into long and short interspersed elements (LINEs and SINEs, respectively), depending on their size and autonomy; while active class 1 LINEs (LINE-1s or L1s) encode the enzymatic machinery required to mobilize in cis, active SINEs use the enzymatic machinery of active LINE-1s to mobilize in trans. The mobilization mechanism used by LINE-1s/SINEs was exploited to develop ingenious plasmid-based retrotransposition assays in cultured cells, which typically exploit a reporter gene that can only be activated after a round of retrotransposition. Retrotransposition assays, in cis or in trans, are instrumental tools to study the biology of mammalian LINE-1s and SINEs. In fact, these and other biochemical/genetic assays were used to uncover that endogenous mammalian LINE-1s/SINEs naturally retrotranspose during early embryonic development. However, embryonic stem cells (ESCs) are typically used as a cellular model in these and other studies interrogating LINE-1/SINE expression/regulation during early embryogenesis. Thus, human and mouse ESCs represent an excellent model to understand how active retrotransposons are regulated and how their activity impacts the germline. Here, we describe robust and quantitative protocols to study human/mouse LINE-1 (in cis) and SINE (in trans) retrotransposition using (human and mice) ESCs. These protocols are designed to study the mobilization of active non-LTR retrotransposons in a cellular physiologically relevant context.
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Affiliation(s)
- Marta Garcia-Cañadas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Laura Sanchez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Johana Rojas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Jose L Garcia Perez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
- MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC)/University of Edinburgh, Western General Hospital Campus, Edinburgh, UK.
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6
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Cashen BA, Naufer M, Morse M, Jones CE, Williams M, Furano A. The L1-ORF1p coiled coil enables formation of a tightly compacted nucleic acid-bound complex that is associated with retrotransposition. Nucleic Acids Res 2022; 50:8690-8699. [PMID: 35871298 PMCID: PMC9410894 DOI: 10.1093/nar/gkac628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Long interspersed nuclear element 1 (L1) parasitized most vertebrates and constitutes ∼20% of the human genome. It encodes ORF1p and ORF2p which form an L1-ribonucleoprotein (RNP) with their encoding transcript that is copied into genomic DNA (retrotransposition). ORF1p binds single-stranded nucleic acid (ssNA) and exhibits NA chaperone activity. All vertebrate ORF1ps contain a coiled coil (CC) domain and we previously showed that a CC-retrotransposition null mutant prevented formation of stably bound ORF1p complexes on ssNA. Here, we compared CC variants using our recently improved method that measures ORF1p binding to ssDNA at different forces. Bound proteins decrease ssDNA contour length and at low force, retrotransposition-competent ORF1ps (111p and m14p) exhibit two shortening phases: the first is rapid, coincident with ORF1p binding; the second is slower, consistent with formation of tightly compacted complexes by NA-bound ORF1p. In contrast, two retrotransposition-null CC variants (151p and m15p) did not attain the second tightly compacted state. The C-terminal half of the ORF1p trimer (not the CC) contains the residues that mediate NA-binding. Our demonstrating that the CC governs the ability of NA-bound retrotransposition-competent trimers to form tightly compacted complexes reveals the biochemical phenotype of these coiled coil mutants.
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Affiliation(s)
- Ben A Cashen
- Northeastern University, Department of Physics, Boston, MA02115, USA
| | - M Nabuan Naufer
- Northeastern University, Department of Physics, Boston, MA02115, USA
| | - Michael Morse
- Northeastern University, Department of Physics, Boston, MA02115, USA
| | - Charles E Jones
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA02115, USA
| | - Anthony V Furano
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
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7
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On the Base Composition of Transposable Elements. Int J Mol Sci 2022; 23:ijms23094755. [PMID: 35563146 PMCID: PMC9099904 DOI: 10.3390/ijms23094755] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Transposable elements exhibit a base composition that is often different from the genomic average and from hosts’ genes. The most common compositional bias is towards Adenosine and Thymine, although this bias is not universal, and elements with drastically different base composition can coexist within the same genome. The AT-richness of transposable elements is apparently maladaptive because it results in poor transcription and sub-optimal translation of proteins encoded by the elements. The cause(s) of this unusual base composition remain unclear and have yet to be investigated. Here, I review what is known about the nucleotide content of transposable elements and how this content can affect the genome of their host as well as their own replication. The compositional bias of transposable elements could result from several non-exclusive processes including horizontal transfer, mutational bias, and selection. It appears that mutation alone cannot explain the high AT-content of transposons and that selection plays a major role in the evolution of the compositional bias. The reason why selection would favor a maladaptive nucleotide content remains however unexplained and is an area of investigation that clearly deserves attention.
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8
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Cytosolic Self-DNA—A Potential Source of Chronic Inflammation in Aging. Cells 2021; 10:cells10123544. [PMID: 34944052 PMCID: PMC8700131 DOI: 10.3390/cells10123544] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Aging is the consequence of a lifelong accumulation of stochastic damage to tissues and cellular components. Advancing age closely associates with elevated markers of innate immunity and low-grade chronic inflammation, probably reflecting steady increasing incidents of cellular and tissue damage over the life course. The DNA sensing cGAS-STING signaling pathway is activated by misplaced cytosolic self-DNA, which then initiates the innate immune responses. Here, we hypothesize that the stochastic release of various forms of DNA from the nucleus and mitochondria, e.g., because of DNA damage, altered nucleus integrity, and mitochondrial damage, can result in chronic activation of inflammatory responses that characterize the aging process. This cytosolic self-DNA-innate immunity axis may perturb tissue homeostasis and function that characterizes human aging and age-associated pathology. Proper techniques and experimental models are available to investigate this axis to develop therapeutic interventions.
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9
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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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10
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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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11
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Choi IS, Wojciechowski MF, Ruhlman TA, Jansen RK. In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae). Mol Phylogenet Evol 2021; 163:107236. [PMID: 34147655 DOI: 10.1016/j.ympev.2021.107236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | | | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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12
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Blythe MJ, Kocer A, Rubio-Roldan A, Giles T, Abakir A, Ialy-Radio C, Wheldon LM, Bereshchenko O, Bruscoli S, Kondrashov A, Drevet JR, Emes RD, Johnson AD, McCarrey JR, Gackowski D, Olinski R, Cocquet J, Garcia-Perez JL, Ruzov A. LINE-1 transcription in round spermatids is associated with accretion of 5-carboxylcytosine in their open reading frames. Commun Biol 2021; 4:691. [PMID: 34099857 PMCID: PMC8184969 DOI: 10.1038/s42003-021-02217-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
Chromatin of male and female gametes undergoes a number of reprogramming events during the transition from germ cell to embryonic developmental programs. Although the rearrangement of DNA methylation patterns occurring in the zygote has been extensively characterized, little is known about the dynamics of DNA modifications during spermatid maturation. Here, we demonstrate that the dynamics of 5-carboxylcytosine (5caC) correlate with active transcription of LINE-1 retroelements during murine spermiogenesis. We show that the open reading frames of active and evolutionary young LINE-1s are 5caC-enriched in round spermatids and 5caC is eliminated from LINE-1s and spermiogenesis-specific genes during spermatid maturation, being simultaneously retained at promoters and introns of developmental genes. Our results reveal an association of 5caC with activity of LINE-1 retrotransposons suggesting a potential direct role for this DNA modification in fine regulation of their transcription.
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Affiliation(s)
- Martin J Blythe
- Deep Seq, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Ayhan Kocer
- GReD Laboratory, CNRS UMR 6293 - INSERM U1103 - Clermont Université, Aubière, France
| | - Alejandro Rubio-Roldan
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Tom Giles
- Digital Research Service, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Leicestershire, UK
| | - Abdulkadir Abakir
- School of Medicine, University of Nottingham, University Park, Nottingham, UK
| | - Côme Ialy-Radio
- INSERM U1016, Institut Cochin - CNRS UMR8104 - Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Lee M Wheldon
- Medical Molecular Sciences, University of Nottingham, University Park, Nottingham, UK
| | - Oxana Bereshchenko
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - Stefano Bruscoli
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | | | - Joël R Drevet
- GReD Laboratory, CNRS UMR 6293 - INSERM U1103 - Clermont Université, Aubière, France
| | - Richard D Emes
- Digital Research Service, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Leicestershire, UK. .,School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Leicestershire, UK.
| | - Andrew D Johnson
- School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | | | - Daniel Gackowski
- Department of Clinical Biochemistry, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Ryszard Olinski
- Department of Clinical Biochemistry, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Julie Cocquet
- INSERM U1016, Institut Cochin - CNRS UMR8104 - Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jose L Garcia-Perez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Alexey Ruzov
- School of Medicine, University of Nottingham, University Park, Nottingham, UK.
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13
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Chen Y, Ding X, Wang S, Ding P, Xu Z, Li J, Wang M, Xiang R, Wang X, Wang H, Feng Q, Qiu J, Wang F, Huang Z, Zhang X, Tang G, Tang S. A single-cell atlas of mouse olfactory bulb chromatin accessibility. J Genet Genomics 2021; 48:147-162. [PMID: 33926839 DOI: 10.1016/j.jgg.2021.02.007] [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: 08/06/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 10/21/2022]
Abstract
Olfaction, the sense of smell, is a fundamental trait crucial to many species. The olfactory bulb (OB) plays pivotal roles in processing and transmitting odor information from the environment to the brain. The cellular heterogeneity of the mouse OB has been studied using single-cell RNA sequencing. However, the epigenetic landscape of the mOB remains mostly unexplored. Herein, we apply single-cell assay for transposase-accessible chromatin sequencing to profile the genome-wide chromatin accessibility of 9,549 single cells from the mOB. Based on single-cell epigenetic signatures, mOB cells are classified into 21 clusters corresponding to 11 cell types. We identify distinct sets of putative regulatory elements specific to each cell cluster from which putative target genes and enriched potential functions are inferred. In addition, the transcription factor motifs enriched in each cell cluster are determined to indicate the developmental fate of each cell lineage. Our study provides a valuable epigenetic data set for the mOB at single-cell resolution, and the results can enhance our understanding of regulatory circuits and the therapeutic capacity of the OB at the single-cell level.
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Affiliation(s)
- Yin Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiangning Ding
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Shiyou Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Peiwen Ding
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Zaoxu Xu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiankang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Mingyue Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Rong Xiang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoling Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Haoyu Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Qikai Feng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Jiaying Qiu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China
| | - Feiyue Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China; School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhen Huang
- Southern Center for Biomedical Research and Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Xingliang Zhang
- Shenzhen Children's Hospital, Shenzhen 518083, China; Department of Pediatrics, the Affiliated Hospital of Guangdong Medical University, Zhanjiang 524000, China.
| | - Gen Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China.
| | - Shengping Tang
- Shenzhen Children's Hospital, Shenzhen 518083, China; Zunyi Medical University, Zunyi, Guizhou 563099, China; China Medical University, Shenyang, Liaoning 110122, China.
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14
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R2 and Non-Site-Specific R2-Like Retrotransposons of the German Cockroach, Blattella germanica. Genes (Basel) 2020; 11:genes11101202. [PMID: 33076367 PMCID: PMC7650587 DOI: 10.3390/genes11101202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 11/17/2022] Open
Abstract
The structural and functional organization of the ribosomal RNA gene cluster and the full-length R2 non-LTR retrotransposon (integrated into a specific site of 28S ribosomal RNA genes) of the German cockroach, Blattella germanica, is described. A partial sequence of the R2 retrotransposon of the cockroach Rhyparobia maderae is also analyzed. The analysis of previously published next-generation sequencing data from the B. germanica genome reveals a new type of retrotransposon closely related to R2 retrotransposons but with a random distribution in the genome. Phylogenetic analysis reveals that these newly described retrotransposons form a separate clade. It is shown that proteins corresponding to the open reading frames of newly described retrotransposons exhibit unequal structural domains. Within these retrotransposons, a recombination event is described. New mechanism of transposition activity is discussed. The essential structural features of R2 retrotransposons are conserved in cockroaches and are typical of previously described R2 retrotransposons. However, the investigation of the number and frequency of 5′-truncated R2 retrotransposon insertion variants in eight B. germanica populations suggests recent mobile element activity. It is shown that the pattern of 5′-truncated R2 retrotransposon copies can be an informative molecular genetic marker for revealing genetic distances between insect populations.
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15
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Furano AV, Jones CE, Periwal V, Callahan KE, Walser JC, Cook PR. Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p. PLoS Genet 2020; 16:e1008991. [PMID: 32797042 PMCID: PMC7449397 DOI: 10.1371/journal.pgen.1008991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/26/2020] [Accepted: 07/13/2020] [Indexed: 11/18/2022] Open
Abstract
Accounting for continual evolution of deleterious L1 retrotransposon families, which can contain hundreds to thousands of members remains a major issue in mammalian biology. L1 activity generated upwards of 40% of some mammalian genomes, including humans where they remain active, causing genetic defects and rearrangements. L1 encodes a coiled coil-containing protein that is essential for retrotransposition, and the emergence of novel primate L1 families has been correlated with episodes of extensive amino acid substitutions in the coiled coil. These results were interpreted as an adaptive response to maintain L1 activity, however its mechanism remained unknown. Although an adventitious mutation can inactivate coiled coil function, its effect could be buffered by epistatic interactions within the coiled coil, made more likely if the family contains a diverse set of coiled coil sequences-collectively referred to as the coiled coil sequence space. Amino acid substitutions that do not affect coiled coil function (i.e., its phenotype) could be "hidden" from (not subject to) purifying selection. The accumulation of such substitutions, often referred to as cryptic genetic variation, has been documented in various proteins. Here we report that this phenomenon was in effect during the latest episode of primate coiled coil evolution, which occurred 30-10 MYA during the emergence of primate L1Pa7-L1Pa3 families. First, we experimentally demonstrated that while coiled coil function (measured by retrotransposition) can be eliminated by single epistatic mutations, it nonetheless can also withstand extensive amino acid substitutions. Second, principal component and cluster analysis showed that the coiled coil sequence space of each of the L1Pa7-3 families was notably increased by the presence of distinct, coexisting coiled coil sequences. Thus, sampling related networks of functional sequences rather than traversing discrete adaptive states characterized the persistence L1 activity during this evolutionary event.
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Affiliation(s)
- Anthony V. Furano
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Charlie E. Jones
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vipul Periwal
- Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathryn E. Callahan
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jean-Claude Walser
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Pamela R. Cook
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
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16
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Del Re B, Giorgi G. Long INterspersed element-1 mobility as a sensor of environmental stresses. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:465-493. [PMID: 32144842 DOI: 10.1002/em.22366] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 06/10/2023]
Abstract
Long INterspersed element (LINE-1, L1) retrotransposons are the most abundant transposable elements in the human genome, constituting approximately 17%. They move by a "copy-paste" mechanism, involving reverse transcription of an RNA intermediate and insertion of its cDNA copy at a new site in the genome. L1 retrotransposition (L1-RTP) can cause insertional mutations, alter gene expression, transduce exons, and induce epigenetic dysregulation. L1-RTP is generally repressed; however, a number of observations collected over about 15 years revealed that it can occur in response to environmental stresses. Moreover, emerging evidence indicates that L1-RTP can play a role in the onset of several neurological and oncological diseases in humans. In recent years, great attention has been paid to the exposome paradigm, which proposes that health effects of an environmental factor should be evaluated considering both cumulative environmental exposures and the endogenous processes resulting from the biological response. L1-RTP could be an endogenous process considered for this application. Here, we summarize the current understanding of environmental factors that can affect the retrotransposition of human L1 elements. Evidence indicates that L1-RTP alteration is triggered by numerous and various environmental stressors, such as chemical agents (heavy metals, carcinogens, oxidants, and drugs), physical agents (ionizing and non-ionizing radiations), and experiential factors (voluntary exercise, social isolation, maternal care, and environmental light/dark cycles). These data come from in vitro studies on cell lines and in vivo studies on transgenic animals: future investigations should be focused on physiologically relevant models to gain a better understanding of this topic.
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Affiliation(s)
- Brunella Del Re
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Gianfranco Giorgi
- Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy
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17
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Celarain N, Tomas-Roig J. Changes in Deoxyribonucleic Acid Methylation Contribute to the Pathophysiology of Multiple Sclerosis. Front Genet 2019; 10:1138. [PMID: 31798633 PMCID: PMC6874160 DOI: 10.3389/fgene.2019.01138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/21/2019] [Indexed: 12/02/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by loss of coordination, weakness, dysfunctions in bladder capacity, bowel movement, and cognitive impairment. Thus, the disease leads to a significant socioeconomic burden. In the pathophysiology of the disease, both genetic and environmental risk factors are involved. Gene x environment interaction is modulated by epigenetic mechanisms. Epigenetics refers to a sophisticated system that regulates gene expression with no changes in the DNA sequence. The most studied epigenetic mechanism is the DNA methylation. In this review, we summarize the data available from the current literature by grouping sets of differentially methylated genes in distinct biological categories: the immune system including innate and adaptive response, the DNA damage, and the central nervous system.
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Affiliation(s)
- Naiara Celarain
- Girona Neuroimmunology and Multiple Sclerosis Unit (UNIEM), Dr. Josep Trueta University Hospital, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jordi Tomas-Roig
- Girona Neuroimmunology and Multiple Sclerosis Unit (UNIEM), Dr. Josep Trueta University Hospital, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
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18
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Matsuno Y, Yamashita T, Wagatsuma M, Yamakage H. Convergence in LINE-1 nucleotide variations can benefit redundantly forming triplexes with lncRNA in mammalian X-chromosome inactivation. Mob DNA 2019; 10:33. [PMID: 31384315 PMCID: PMC6664574 DOI: 10.1186/s13100-019-0173-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/08/2019] [Indexed: 01/01/2023] Open
Abstract
Background Associations between X-inactive transcript (Xist)–long noncoding RNA (lncRNA) and chromatin are critical intermolecular interactions in the X-chromosome inactivation (XCI) process. Despite high-resolution analyses of the Xist RNA-binding sites, specific interaction sequences are yet to be identified. Based on elusive features of the association between Xist RNA and chromatin and the possible existence of multiple low-affinity binding sites in Xist RNA, we defined short motifs (≥5 nucleotides), termed as redundant UC/TC (r-UC/TC) or AG (r-AG) motifs, which may help in the mediation of triplex formation between the lncRNAs and duplex DNA. Results The study showed that r-UC motifs are densely dispersed throughout mouse and human Xist/XIST RNAs, whereas r-AG motifs are even more densely dispersed along opossum RNA-on-the-silent X (Rsx) RNA, and also along both full-length and truncated long interspersed nuclear elements (LINE-1s, L1s) of the three species. Predicted secondary structures of the lncRNAs showed that the length range of these sequence motifs available for forming triplexes was even shorter, mainly 5- to 9-nucleotides long. Quartz crystal microbalance (QCM) measurements and Monte Carlo (MC) simulations indicated that minimum-length motifs can reinforce the binding state by increasing the copy number of the motifs in the same RNA or DNA molecule. Further, r-AG motifs in L1s had a similar length-distribution pattern, regardless of the similarities in the length or sequence of L1s across the three species; this also applies to high-frequency mutations in r-AG motifs, which suggests convergence in L1 sequence variations. Conclusions Multiple short motifs in both RNA and duplex DNA molecules could be brought together to form triplexes with either Hoogsteen or reverse Hoogsteen hydrogen bonding, by which their associations are cooperatively enhanced. This novel triplex interaction could be involved in associations between lncRNA and chromatin in XCI, particularly at the sites of L1s. Potential binding of Xist/XIST/Rsx RNAs specifically at L1s is most likely preserved through the r-AG motifs conserved in mammalian L1s through convergence in L1 nucleotide variations and by maintaining a particular r-UC/r-AG motif ratio in each of these lncRNAs, irrespective of their poorly conserved sequences. Electronic supplementary material The online version of this article (10.1186/s13100-019-0173-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoko Matsuno
- 1Division of Clinical Preventive Medicine, Niigata University, Niigata, Japan
| | - Takefumi Yamashita
- 2Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
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19
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Yang L, Scott L, Wichman HA. Tracing the history of LINE and SINE extinction in sigmodontine rodents. Mob DNA 2019; 10:22. [PMID: 31139266 PMCID: PMC6530004 DOI: 10.1186/s13100-019-0164-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background L1 retrotransposons have co-evolved with their mammalian hosts for the entire history of mammals and currently compose ~ 20% of a mammalian genome. B1 retrotransposons are dependent on L1 for retrotransposition and span the evolutionary history of rodents since their radiation. L1s were found to have lost their activity in a group of South American rodents, the Sigmodontinae, and B1 inactivation preceded the extinction of L1 in the same group. Consequently, a basal group of sigmodontines have active L1s but inactive B1s and a derived clade have both inactive L1s and B1s. It has been suggested that B1s became extinct during a long period of L1 quiescence and that L1s subsequently reemerged in the basal group. Results Here we investigate the evolutionary histories of L1 and B1 in the sigmodontine rodents and show that L1 activity continued until after the L1-extinct clade and the basal group diverged. After the split, L1 had a small burst of activity in the former group, followed by extinction. In the basal group, activity was initially low but was followed by a dramatic increase in L1 activity. We found the last wave of B1 retrotransposition was large and probably preceded the split between the two rodent clades. Conclusions Given that L1s had been steadily retrotransposing during the time corresponding to B1 extinction and that the burst of B1 activity preceding B1 extinction was large, we conclude that B1 extinction was not a result of L1 quiescence. Rather, the burst of B1 activity may have contributed to L1 extinction both by competition with L1 and by putting strong selective pressure on the host to control retrotransposition. Electronic supplementary material The online version of this article (10.1186/s13100-019-0164-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lei Yang
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
| | - LuAnn Scott
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
| | - Holly A Wichman
- 1Department of Biological Sciences, University of Idaho, Moscow, ID USA.,2Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID USA
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20
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Blumenstiel JP. Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation. Genes (Basel) 2019; 10:genes10050336. [PMID: 31058854 PMCID: PMC6562965 DOI: 10.3390/genes10050336] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66049, USA.
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21
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Wang GD, Shao XJ, Bai B, Wang J, Wang X, Cao X, Liu YH, Wang X, Yin TT, Zhang SJ, Lu Y, Wang Z, Wang L, Zhao W, Zhang B, Ruan J, Zhang YP. Structural variation during dog domestication: insights from gray wolf and dhole genomes. Natl Sci Rev 2019; 6:110-122. [PMID: 34694297 PMCID: PMC8291444 DOI: 10.1093/nsr/nwy076] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/27/2018] [Accepted: 07/17/2018] [Indexed: 12/11/2022] Open
Abstract
Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations (SVs) in the genome. Here, we present high-quality draft genomes of the gray wolf (Canis lupus) and dhole (Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1B1 (Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies.
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Affiliation(s)
- Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiu-Juan Shao
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Bing Bai
- Medical Faculty, Kunming University of Science and Technology, Kunming 650504, China
- Department of Pediatrics, the First People's Hospital of Yunnan Province, Kunming 650032, China
| | - Junlong Wang
- College of Pharmacology, Soochow University, Suzhou 215123, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaobo Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xue Cao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming 650500, China
| | - Yan-Hu Liu
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Shao-Jie Zhang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Yan Lu
- Beijing Zoo, Beijing 100044, China
| | | | - Lu Wang
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
| | - Wenming Zhao
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jue Ruan
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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22
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Wagstaff BJ, Wang L, Lai S, Derbes RS, Roy-Engel AM. Reviving a 60 million year old LINE-1 element. GENE REPORTS 2018; 11:74-78. [PMID: 30221208 DOI: 10.1016/j.genrep.2018.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Mobile elements have significantly impacted genome structure of most organisms. The continued activity of the mobile element, LINE-1 (L1), through time has contributed to the accumulation of over half a million L1 copies in the human genome. Most copies in the human genome belong to evolutionary older extinct L1s. Here we apply our previous published approach to "revive" the extinct L1 PA13A; an L1 family that was active about 60 million year ago (mya). The reconstructed L1PA13A is retrocompentent in culture, but shows a significantly lower level of activity in HeLa cells when compared to the modern L1 element (L1PA1) and a 40 million year old L1PA8. L1 elements code for two proteins (ORF1p and ORF2p) that are necessary for retrotransposition. Using PA13A-PA1 and PA13A-PA8 L1 chimeric elements, we determined that both the ORF1p and ORF2p contribute to the observed decrease in retrotransposition efficiency of L1PA13A. The lower retrotransposition rate of L1PA13A is consistent in both human and rodent cell lines. However, in rodent cells, the chimeric element L1PA:1-13 containing the modern L1PA1 ORF1p shows a recovery in the retrotransposition rate, suggestive that the L1PA13A ORF2p efficiently drives retrotransposition in these cells. The functionality of the L1PA13A ORF2p was further confirmed by demonstrating its ability to drive Alu retrotransposition in rodent cells. The variation in L1PA13A retrotransposition rates observed between rodent and human cells are suggestive that cellular environment significantly affects retrotransposition efficiency, which may be mediated through an interaction with ORF1p. Based on these observations, we speculate that the observed differences between cell lines may reflect an evolutionary adaptation of the L1 element to its host cell.
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Affiliation(s)
- Bradley J Wagstaff
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Linda Wang
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Susan Lai
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
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23
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Szafranski P, Kośmider E, Liu Q, Karolak JA, Currie L, Parkash S, Kahler SG, Roeder E, Littlejohn RO, DeNapoli TS, Shardonofsky FR, Henderson C, Powers G, Poisson V, Bérubé D, Oligny L, Michaud JL, Janssens S, De Coen K, Van Dorpe J, Dheedene A, Harting MT, Weaver MD, Khan AM, Tatevian N, Wambach J, Gibbs KA, Popek E, Gambin A, Stankiewicz P. LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV. Hum Mutat 2018; 39:1916-1925. [PMID: 30084155 DOI: 10.1002/humu.23608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/20/2023]
Abstract
Transposable elements modify human genome by inserting into new loci or by mediating homology-, microhomology-, or homeology-driven DNA recombination or repair, resulting in genomic structural variation. Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal neonatal developmental lung disorder caused by point mutations or copy-number variant (CNV) deletions of FOXF1 or its distant tissue-specific enhancer. Eighty-five percent of 45 ACDMPV-causative CNV deletions, of which junctions have been sequenced, had at least one of their two breakpoints located in a retrotransposon, with more than half of them being Alu elements. We describe a novel ∼35 kb-large genomic instability hotspot at 16q24.1, involving two evolutionarily young LINE-1 (L1) elements, L1PA2 and L1PA3, flanking AluY, two AluSx, AluSx1, and AluJr elements. The occurrence of L1s at this location coincided with the branching out of the Homo-Pan-Gorilla clade, and was preceded by the insertion of AluSx, AluSx1, and AluJr. Our data show that, in addition to mediating recurrent CNVs, L1 and Alu retrotransposons can predispose the human genome to formation of variably sized CNVs, both of clinical and evolutionary relevance. Nonetheless, epigenetic or other genomic features of this locus might also contribute to its increased instability.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ewelina Kośmider
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Lauren Currie
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Sandhya Parkash
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Stephen G Kahler
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | | | - Thomas S DeNapoli
- Department of Pathology, Children's Hospital of San Antonio, San Antonio, Texas
| | - Felix R Shardonofsky
- Pediatric Pulmonary Center, Children's Hospital of San Antonio, San Antonio, Texas
| | - Cody Henderson
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | - George Powers
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | | | | | | | | | - Sandra Janssens
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Kris De Coen
- Department of Neonatal Intensive Care, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent, Belgium
| | | | | | | | - Amir M Khan
- McGovern Medical School at UTHealth, Houston, Texas
| | | | - Jennifer Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Kathleen A Gibbs
- Children's Hospital of Philadelphia, and University of Pennsylvania, Philadelphia, Pennsylvania
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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24
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Sookdeo A, Ruiz-García M, Schneider H, Boissinot S. Contrasting Rates of LINE-1 Amplification among New World Primates of the Atelidae Family. Cytogenet Genome Res 2018; 154:217-228. [PMID: 29991050 DOI: 10.1159/000490481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2018] [Indexed: 11/19/2022] Open
Abstract
LINE-1 (L1) retrotransposons constitute the dominant category of transposons in mammalian genomes. L1 elements are active in the vast majority of mammals, and only a few cases of L1 extinction have been documented. The only possible case of extinction in primates was suggested for South American spider monkeys. However, these previous studies were based on a single species. We revisited this question with a larger phylogenetic sample, covering all 4 genera of Atelidae and 3 species of spider monkeys. We used an enrichment method to clone recently inserted L1 elements and performed an evolutionary analysis of the sequences. We were able to identify young L1 elements in all taxa, suggesting that L1 is probably still active in all Atelidae examined. However, we also detected considerable variations in the proportion of recent elements indicating that the rate of L1 amplification varies among Atelidae by a 3-fold factor. The extent of L1 amplification in Atelidae remains overall lower than in other New World monkeys. Multiple factors can affect the amplification of L1, such as the demography of the host and the control of transposition. These factors are discussed in the context of host life history.
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25
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Giorgi G, Virgili M, Monti B, Del Re B. Long INterspersed nuclear Elements (LINEs) in brain and non-brain tissues of the rat. Cell Tissue Res 2018; 374:17-24. [PMID: 29725769 DOI: 10.1007/s00441-018-2843-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/11/2018] [Indexed: 10/17/2022]
Abstract
Long INterspersed Element-1 (L1) is a transposable element that can insert copies of itself in new genomic locations causing genomic instability. In somatic cells, L1 retrotransposition activity is usually repressed but somatic L1 retrotransposition has recently been observed during neuronal differentiation. In this study, we evaluate whether L1 elements are differentially active in rat tissues during postnatal development. To this purpose, we quantified L1 in genomic DNA extracted from the olfactory bulb (OB), cerebellum (CE), cortex (CO) and heart (H). Each analysis was repeated on rats aged 7, 21 and 60 days. We found that L1 content in OB and CE tissue was significantly higher than H tissue, in rats of all three ages studied, suggesting that L1 activity could be modulated in postnatal development and neurogenesis.
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Affiliation(s)
- Gianfranco Giorgi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Marco Virgili
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Barbara Monti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Brunella Del Re
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, via Selmi 3, 40126, Bologna, Italy.
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26
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Schauer SN, Carreira PE, Shukla R, Gerhardt DJ, Gerdes P, Sanchez-Luque FJ, Nicoli P, Kindlova M, Ghisletti S, Santos AD, Rapoud D, Samuel D, Faivre J, Ewing AD, Richardson SR, Faulkner GJ. L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Res 2018; 28:639-653. [PMID: 29643204 PMCID: PMC5932605 DOI: 10.1101/gr.226993.117] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/26/2018] [Indexed: 12/15/2022]
Abstract
The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is a continuing source of germline and somatic mutagenesis in mammals. Deregulated L1 activity is a hallmark of cancer, and L1 mutagenesis has been described in numerous human malignancies. We previously employed retrotransposon capture sequencing (RC-seq) to analyze hepatocellular carcinoma (HCC) samples from patients infected with hepatitis B or hepatitis C virus and identified L1 variants responsible for activating oncogenic pathways. Here, we have applied RC-seq and whole-genome sequencing (WGS) to an Abcb4 (Mdr2)-/- mouse model of hepatic carcinogenesis and demonstrated for the first time that L1 mobilization occurs in murine tumors. In 12 HCC nodules obtained from 10 animals, we validated four somatic L1 insertions by PCR and capillary sequencing, including TF subfamily elements, and one GF subfamily example. One of the TF insertions carried a 3' transduction, allowing us to identify its donor L1 and to demonstrate that this full-length TF element retained retrotransposition capacity in cultured cancer cells. Using RC-seq, we also identified eight tumor-specific L1 insertions from 25 HCC patients with a history of alcohol abuse. Finally, we used RC-seq and WGS to identify three tumor-specific L1 insertions among 10 intra-hepatic cholangiocarcinoma (ICC) patients, including one insertion traced to a donor L1 on Chromosome 22 known to be highly active in other cancers. This study reveals L1 mobilization as a common feature of hepatocarcinogenesis in mammals, demonstrating that the phenomenon is not restricted to human viral HCC etiologies and is encountered in murine liver tumors.
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Affiliation(s)
- Stephanie N Schauer
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ruchi Shukla
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- Invenra, Incorporated, Madison, Wisconsin 53719, USA
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Paola Nicoli
- Department of Experimental Oncology, European Institute of Oncology, 20146 Milan, Italy
| | - Michaela Kindlova
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | | | - Alexandre Dos Santos
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Delphine Rapoud
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Didier Samuel
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Pôle de Biologie Médicale, Paul-Brousse University Hospital, Villejuif 94800, France
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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27
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Xue AT, Ruggiero RP, Hickerson MJ, Boissinot S. Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling. Genome Biol Evol 2018; 10:1265-1281. [PMID: 29688421 PMCID: PMC5963298 DOI: 10.1093/gbe/evy083] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2018] [Indexed: 12/30/2022] Open
Abstract
Variation in LINE composition is one of the major determinants for the substantial size and structural differences among vertebrate genomes. In particular, the larger genomes of mammals are characterized by hundreds of thousands of copies from a single LINE clade, L1, whereas nonmammalian vertebrates possess a much greater diversity of LINEs, yet with orders of magnitude less in copy number. It has been proposed that such variation in copy number among vertebrates is due to differential effect of LINE insertions on host fitness. To investigate LINE selection, we deployed a framework of demographic modeling, coalescent simulations, and probabilistic inference against population-level whole-genome data sets for four model species: one population each of threespine stickleback, green anole, and house mouse, as well as three human populations. Specifically, we inferred a null demographic background utilizing SNP data, which was then exploited to simulate a putative null distribution of summary statistics that was compared with LINE data. Subsequently, we applied the inferred null demographic model with an additional exponential size change parameter, coupled with model selection, to test for neutrality as well as estimate the strength of either negative or positive selection. We found a robust signal for purifying selection in anole and mouse, but a lack of clear evidence for selection in stickleback and human. Overall, we demonstrated LINE insertion dynamics that are not in accordance to a mammalian versus nonmammalian dichotomy, and instead the degree of existing LINE activity together with host-specific demographic history may be the main determinants of LINE abundance.
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Affiliation(s)
- Alexander T Xue
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York
- Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, Piscataway
| | - Robert P Ruggiero
- New York University Abu Dhabi, Saadiyat Island Campus, United Arab Emirates
| | - Michael J Hickerson
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island Campus, United Arab Emirates
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28
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Naufer MN, Furano AV, Williams MC. Protein-nucleic acid interactions of LINE-1 ORF1p. Semin Cell Dev Biol 2018; 86:140-149. [PMID: 29596909 PMCID: PMC6428221 DOI: 10.1016/j.semcdb.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 11/03/2022]
Abstract
Long interspersed nuclear element 1 (LINE-1 or L1) is the dominant retrotransposon in mammalian genomes. L1 encodes two proteins ORF1p and ORF2p that are required for retrotransposition. ORF2p functions as the replicase. ORF1p is a coiled coil-mediated trimeric, high affinity RNA binding protein that packages its full- length coding transcript into an ORF2p-containing ribonucleoprotein (RNP) complex, the retrotransposition intermediate. ORF1p also is a nucleic acid chaperone that presumably facilitates the proposed nucleic acid remodeling steps involved in retrotransposition. Although detailed mechanistic understanding of ORF1p function in this process is lacking, recent studies showed that the rate at which ORF1p can form stable nucleic acid-bound oligomers in vitro is positively correlated with formation of an active L1 RNP as assayed in vivo using a cell culture-based retrotransposition assay. This rate was sensitive to minor amino acid changes in the coiled coil domain, which had no effect on nucleic acid chaperone activity. Additional studies linking the complex nucleic acid binding properties to the conformational changes of the protein are needed to understand how ORF1p facilitates retrotransposition.
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Affiliation(s)
- M Nabuan Naufer
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Anthony V Furano
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA.
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29
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Sookdeo A, Hepp CM, Boissinot S. Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction. Mob DNA 2018; 9:12. [PMID: 29610583 PMCID: PMC5872511 DOI: 10.1186/s13100-018-0117-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1. Results We found that multiple L1 lineages, carrying different 5’UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time. Conclusions The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms. Electronic supplementary material The online version of this article (10.1186/s13100-018-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Akash Sookdeo
- 1Department of Biology, New York University, New York, NY USA
| | - Crystal M Hepp
- 2School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ USA
| | - Stéphane Boissinot
- 3New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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30
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Boissinot S, Sookdeo A. The Evolution of LINE-1 in Vertebrates. Genome Biol Evol 2018; 8:3485-3507. [PMID: 28175298 PMCID: PMC5381506 DOI: 10.1093/gbe/evw247] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2016] [Indexed: 12/21/2022] Open
Abstract
The abundance and diversity of the LINE-1 (L1) retrotransposon differ greatly among vertebrates. Mammalian genomes contain hundreds of thousands L1s that have accumulated since the origin of mammals. A single group of very similar elements is active at a time in mammals, thus a single lineage of active families has evolved in this group. In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies. Why the pattern of diversity and abundance of L1 is so different among vertebrates remains unknown. To address this issue, we performed a detailed analysis of the evolution of active L1 in 14 mammals and in 3 non-mammalian vertebrate model species. We examined the evolution of base composition and codon bias, the general structure, and the evolution of the different domains of L1 (5′UTR, ORF1, ORF2, 3′UTR). L1s differ substantially in length, base composition, and structure among vertebrates. The most variation is found in the 5′UTR, which is longer in amniotes, and in the ORF1, which tend to evolve faster in mammals. The highly divergent L1 families of lizard, frog, and fish share species-specific features suggesting that they are subjected to the same functional constraints imposed by their host. The relative conservation of the 5′UTR and ORF1 in non-mammalian vertebrates suggests that the repression of transposition by the host does not act in a sequence-specific manner and did not result in an arms race, as is observed in mammals.
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31
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Richardson SR, Gerdes P, Gerhardt DJ, Sanchez-Luque FJ, Bodea GO, Muñoz-Lopez M, Jesuadian JS, Kempen MJHC, Carreira PE, Jeddeloh JA, Garcia-Perez JL, Kazazian HH, Ewing AD, Faulkner GJ. Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Res 2017; 27:1395-1405. [PMID: 28483779 PMCID: PMC5538555 DOI: 10.1101/gr.219022.116] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 05/02/2017] [Indexed: 12/31/2022]
Abstract
LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of ≥1 event per eight births. We traced heritable L1 insertions to pluripotent embryonic cells and, strikingly, to early primordial germ cells (PGCs). New L1 insertions bore structural hallmarks of target-site primed reverse transcription (TPRT) and mobilized efficiently in a cultured cell retrotransposition assay. Together, our results highlight the rate and evolutionary impact of heritable L1 retrotransposition and reveal retrotransposition-mediated genomic diversification as a fundamental property of pluripotent embryonic cells in vivo.
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Affiliation(s)
- Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia.,Invenra, Incorporated, Madison, Wisconsin 53719, USA
| | - Francisco J Sanchez-Luque
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia.,Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Gabriela-Oana Bodea
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Martin Muñoz-Lopez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - J Samuel Jesuadian
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | | | - Patricia E Carreira
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | | | - Jose L Garcia-Perez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Haig H Kazazian
- Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, Woolloongabba QLD 4102, Australia.,School of Biomedical Sciences.,Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia
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32
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Ruggiero RP, Bourgeois Y, Boissinot S. LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis. Front Genet 2017; 8:44. [PMID: 28450881 PMCID: PMC5389967 DOI: 10.3389/fgene.2017.00044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies. It is unclear why vertebrate genomes harbor such drastic differences in LINE composition. To address this issue, we conducted whole genome resequencing to investigate the population genomics of LINEs across 13 genomes of the lizard Anolis carolinensis sampled from two geographically and genetically distinct populations in the Eastern Florida and the Gulf Atlantic regions of the United States. We used the Mobile Element Locator Tool to identify and genotype polymorphic insertions from five major clades of LINEs (CR1, L1, L2, RTE and R4) and the 41 subfamilies that constitute them. Across these groups we found large variation in the frequency of polymorphic insertions and the observed length distributions of these insertions, suggesting these groups vary in their activity and how frequently they successfully generate full-length, potentially active copies. Though we found an abundance of polymorphic insertions (over 45,000) most of these were observed at low frequencies and typically appeared as singletons. Site frequency spectra for most LINEs showed a significant shift toward low frequency alleles compared to the spectra observed for total genomic single nucleotide polymorphisms. Using Tajima's D, FST and the mean number of pairwise differences in LINE insertion polymorphisms, we found evidence that negative selection is acting on LINE families in a length-dependent manner, its effects being stronger in the larger Eastern Florida population. Our results suggest that a large effective population size and negative selection limit the expansion of polymorphic LINE insertions across these populations and that the probability of LINE polymorphisms reaching fixation is extremely low.
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33
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Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL. LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. Genome Biol Evol 2016; 8:3301-3322. [PMID: 27702814 PMCID: PMC5203782 DOI: 10.1093/gbe/evw243] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to ‘jump’ around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterized domain organization. For the past 30 years, model organisms have been used to define L1s as 6–8 kb sequences containing a 5′-UTR, two open reading frames working harmoniously in cis, and a 3′-UTR with a polyA tail. In this study, we demonstrate the remarkable and overlooked diversity of L1s via a comprehensive phylogenetic analysis of elements from over 500 species from widely divergent branches of the tree of life. The rapid and recent growth of L1 elements in mammalian species is juxtaposed against the diverse lineages found in other metazoans and plants. In fact, some of these previously unexplored mammalian species (e.g. snub-nosed monkey, minke whale) exhibit L1 retrotranspositional ‘hyperactivity’ far surpassing that of human or mouse. In contrast, non-mammalian L1s have become so varied that the current classification system seems to inadequately capture their structural characteristics. Our findings illustrate how both long-term inherited evolutionary patterns and random bursts of activity in individual species can significantly alter genomes, highlighting the importance of L1 dynamics in eukaryotes.
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Affiliation(s)
- Atma M Ivancevic
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Terry Bertozzi
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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Penzkofer T, Jäger M, Figlerowicz M, Badge R, Mundlos S, Robinson PN, Zemojtel T. L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res 2016; 45:D68-D73. [PMID: 27924012 PMCID: PMC5210629 DOI: 10.1093/nar/gkw925] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022] Open
Abstract
LINE-1 (L1) insertions comprise as much as 17% of the human genome sequence, and similar proportions have been recorded for other mammalian species. Given the established role of L1 retrotransposons in shaping mammalian genomes, it becomes an important task to track and annotate the sources of this activity: full length elements, able to encode the cis and trans acting components of the retrotransposition machinery. The L1Base database (http://l1base.charite.de) contains annotated full-length sequences of LINE-1 transposons including putatively active L1s. For the new version of L1Base, a LINE-1 annotation tool, L1Xplorer, has been used to mine potentially active L1 retrotransposons from the reference genome sequences of 17 mammals. The current release of the human genome, GRCh38, contains 146 putatively active L1 elements or full length intact L1 elements (FLIs). The newest versions of the mouse, GRCm38 and the rat, Rnor_6.0, genomes contain 2811 and 492 FLIs, respectively. Most likely reflecting the current level of completeness of the genome project, the latest reference sequence of the common chimpanzee genome, PT 2.19, only contains 19 FLIs. Of note, the current assemblies of the dog, CF 3.1 and the sheep, OA 3.1, genomes contain 264 and 598 FLIs, respectively. Further developments in the new version of L1Base include an updated website with implementation of modern web server technologies. including a more responsive design for an improved user experience, as well as the addition of data sharing capabilities for L1Xplorer annotation.
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Affiliation(s)
- Tobias Penzkofer
- Department of Radiology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marten Jäger
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
| | - Richard Badge
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Stefan Mundlos
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.,The Jackson Laboratory for Genomic medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Tomasz Zemojtel
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
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Nascimento FF, Rodrigo AG. Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution. PLoS One 2016; 11:e0162454. [PMID: 27649303 PMCID: PMC5029938 DOI: 10.1371/journal.pone.0162454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/02/2016] [Indexed: 02/05/2023] Open
Abstract
Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM). In SMM only a single copy of a given TE lineage is able to replicate, and all other genomic copies of TEs are derived from that master copy. In TM, any element of a given family is able to replicate in the host genome. In this paper, we simulated ERV phylogenetic trees under variations of SMM and TM. To test whether current phylogenetic programs can recover the simulated ERV phylogenies, DNA sequence alignments were simulated and maximum likelihood trees were reconstructed and compared to the simulated phylogenies. Results indicate that visual inspection of phylogenetic trees alone can be misleading. However, if a set of statistical summaries is calculated, we are able to distinguish between models with high accuracy by using a data mining algorithm that we introduce here. We also demonstrate the use of our data mining algorithm with empirical data for the porcine endogenous retrovirus (PERV), an ERV that is able to replicate in human and pig cells in vitro.
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Affiliation(s)
| | - Allen G. Rodrigo
- National Evolutionary Synthesis Center, Durham, NC, United States of America
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Abstract
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA 212051
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Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S. AgIn: measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics 2016; 32:2911-9. [PMID: 27318202 PMCID: PMC5039925 DOI: 10.1093/bioinformatics/btw360] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/03/2016] [Indexed: 12/18/2022] Open
Abstract
Motivation: Determining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensitive to DNA modifications. Results: We propose a novel linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ∼30-fold from an inbred strain medaka (Oryzias latipes), we observed that both the sensitivity and precision of our method on individual CpG sites were ∼93.7%. We also observed a high correlation coefficient (R = 0.884) between our method and bisulfite sequencing, and for 92.0% of CpG sites, methylation levels ranging over [0,1] were in concordance within an acceptable difference 0.25. Using this method, we characterized the landscape of the methylation status of repetitive elements, such as LINEs, in the human genome, thereby revealing the strong correlation between CpG density and hypomethylation and detecting hypomethylation hot spots of LTRs and LINEs. We uncovered the methylation states for nearly identical active transposons, two novel LINE insertions of identity ∼99% and length 6050 base pairs (bp) in the human genome, and 16 Tol2 elements of identity >99.8% and length 4682 bp in the medaka genome. Availability and Implementation: AgIn (Aggregate on Intervals) is available at: https://github.com/hacone/AgIn Contact:ysuzuki@cb.k.u-tokyo.ac.jp or moris@cb.k.u-tokyo.ac.jp Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | | | | | - Tatsuya Tsukahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junko Taniguchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Hideaki Yurino
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Yuji Takahashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
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Alu SINE analyses of 3,000-year-old human skeletal remains: a pilot study. Mob DNA 2016; 7:7. [PMID: 27096009 PMCID: PMC4836192 DOI: 10.1186/s13100-016-0063-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/31/2016] [Indexed: 01/21/2023] Open
Abstract
Background As Short Interspersed Elements (SINEs), human-specific Alu elements can be used for population genetic studies. Very recent inserts are polymorphic within and between human populations. In a sample of 30 elements originating from three different Alu subfamilies, we investigated whether they are preserved in prehistorical skeletal human remains from the Bronze Age Lichtenstein cave in Lower Saxony, Germany. In the present study, we examined a prehistoric triad of father, mother and daughter. Results For 26 of the 30 Alu loci investigated, definite results were obtained. We were able to demonstrate that presence/absence analyses of Alu elements can be conducted on individuals who lived 3,000 years ago. The preservation of the ancient DNA (aDNA) is good enough in two out of three ancient individuals to routinely allow the amplification of 500 bp fragments. The third individual revealed less well-preserved DNA, which results in allelic dropout or complete amplification failures. We here present an alternative molecular approach to deal with these degradation phenomena by using internal Alu subfamily specific primers producing short fragments of approximately 150 bp. Conclusions Our data clearly show the possibility of presence/absence analyses of Alu elements in individuals from the Lichtenstein cave. Thus, we demonstrate that our method is reliably applicable for aDNA samples with good or moderate DNA preservation. This method will be very useful for further investigations with more Alu loci and larger datasets. Human population genetic studies and other large-scale investigations would provide insight into Alu SINE-based microevolutionary processes in humans during the last few thousand years and help us comprehend the evolutionary dynamics of our genome. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0063-y) contains supplementary material, which is available to authorized users.
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Mukherjee S, Sharma D, Upadhyaya KC. L1 Retrotransposons Are Transcriptionally Active in Hippocampus of Rat Brain. Prague Med Rep 2016; 117:42-53. [DOI: 10.14712/23362936.2016.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
LINE1 (L1) is an autonomous, non-LTR retrotransposon and the L1 family of retrotransposons constitute around 17%, 20% and 23% in the human, mouse and rat genomes respectively. Under normal physiological conditions, the retroelements remain by and large transcriptionally silent but are activated in response to biotic and abiotic stress conditions and during perturbation in cellular metabolism. They have also been shown to be transiently activated under certain developmental programs. Using RT-PCR, we show that the L1 elements are transcriptionally active in the hippocampus region of the brain of four-month-old rat under normal conditions without any apparent stress. Twenty non-redundant LINE1-specific reverse transcriptase (RTase) sequences form ORF2 region were isolated, cloned and sequenced. Full length L1 element sequences complementary to the isolated sequences were retrieved from the L1 database. In silico analysis was used to determine the presence of these retroelements proximal (up to 10 kb) to the genes transcriptionally active in the hippocampus. Many important genes were found to be in close proximity of the transcriptionally active L1 elements. Transcriptional activation of the elements possibly affects the expression of the neighbouring genes.
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Abstract
Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.
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Naufer MN, Callahan KE, Cook PR, Perez-Gonzalez CE, Williams MC, Furano AV. L1 retrotransposition requires rapid ORF1p oligomerization, a novel coiled coil-dependent property conserved despite extensive remodeling. Nucleic Acids Res 2015; 44:281-93. [PMID: 26673717 PMCID: PMC4705668 DOI: 10.1093/nar/gkv1342] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/17/2015] [Indexed: 12/16/2022] Open
Abstract
Detailed mechanistic understanding of L1 retrotransposition is sparse, particularly with respect to ORF1p, a coiled coil-mediated homotrimeric nucleic acid chaperone that can form tightly packed oligomers on nucleic acids. Although the coiled coil motif is highly conserved, it is uniquely susceptible to evolutionary change. Here we studied three ORF1 proteins: a modern human one (111p), its resuscitated primate ancestor (555p) and a mosaic modern protein (151p) wherein 9 of the 30 coiled coil substitutions retain their ancestral state. While 111p and 555p equally supported retrotransposition, 151p was inactive. Nonetheless, they were fully active in bulk assays of nucleic acid interactions including chaperone activity. However, single molecule assays showed that 151p trimers form stably bound oligomers on ssDNA at <1/10th the rate of the active proteins, revealing that oligomerization rate is a novel critical parameter of ORF1p activity in retrotransposition conserved for at least the last 25 Myr of primate evolution.
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Affiliation(s)
- M Nabuan Naufer
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Kathryn E Callahan
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela R Cook
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cesar E Perez-Gonzalez
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Anthony V Furano
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
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Furano AV, Cook PR. The challenge of ORF1p phosphorylation: Effects on L1 activity and its host. Mob Genet Elements 2015; 6:e1119927. [PMID: 27066302 DOI: 10.1080/2159256x.2015.1119927] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 01/09/2023] Open
Abstract
L1 non-LTR retrotransposons are autonomously replicating genetic elements that profoundly affected their mammalian hosts having generated upwards of 40% or more of their genomes. Although deleterious, they remain active in most mammalian species, and thus the nature and consequences of the interaction between L1 and its host remain major issues for mammalian biology. We recently showed that L1 activity requires phosphorylation of one of its 2 encoded proteins, ORF1p, a nucleic acid chaperone and the major component of the L1RNP retrotransposition intermediate. Reversible protein phosphorylation, which is effected by interacting cascades of protein kinases, phosphatases, and ancillary proteins, is a mainstay in the regulation and coordination of many basic biological processes. Therefore, demonstrating phosphorylation-dependence of L1 activity substantially enlarged our knowledge of the scope of L1 / host interaction. However, developing a mechanistic understanding of what this means for L1 or its host is a formidable challenge, which we discuss here.
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Affiliation(s)
- Anthony V Furano
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health , Bethesda, MD, USA
| | - Pamela R Cook
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health , Bethesda, MD, USA
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Yu Q, Carbone CJ, Katlinskaya YV, Zheng H, Zheng K, Luo M, Wang PJ, Greenberg RA, Fuchs SY. Type I interferon controls propagation of long interspersed element-1. J Biol Chem 2015; 290:10191-9. [PMID: 25716322 DOI: 10.1074/jbc.m114.612374] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Indexed: 01/01/2023] Open
Abstract
Type I interferons (IFN) including IFNα and IFNβ are critical for the cellular defense against viruses. Here we report that increased levels of IFNβ were found in testes from mice deficient in MOV10L1, a germ cell-specific RNA helicase that plays a key role in limiting the propagation of retrotransposons including Long Interspersed Element-1 (LINE-1). Additional experiments revealed that activation of LINE-1 retrotransposons increases the expression of IFNβ and of IFN-stimulated genes. Conversely, pretreatment of cells with IFN suppressed the replication of LINE-1. Furthermore, the efficacy of LINE-1 replication was increased in isogenic cell lines harboring inactivating mutations in diverse elements of the IFN signaling pathway. Knockdown of the IFN receptor chain IFNAR1 also stimulated LINE-1 propagation in vitro. Finally, a greater accumulation of LINE-1 was found in mice that lack IFNAR1 compared with wild type mice. We propose that LINE-1-induced IFN plays an important role in restricting LINE-1 propagation and discuss the putative role of IFN in preserving the genome stability.
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Affiliation(s)
- Qiujing Yu
- From the Departments of Animal Biology, School of Veterinary Medicine and
| | | | | | - Hui Zheng
- From the Departments of Animal Biology, School of Veterinary Medicine and
| | - Ke Zheng
- From the Departments of Animal Biology, School of Veterinary Medicine and
| | - Mengcheng Luo
- From the Departments of Animal Biology, School of Veterinary Medicine and
| | - P Jeremy Wang
- From the Departments of Animal Biology, School of Veterinary Medicine and
| | - Roger A Greenberg
- Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Serge Y Fuchs
- From the Departments of Animal Biology, School of Veterinary Medicine and
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Castro-Diaz N, Friedli M, Trono D. Drawing a fine line on endogenous retroelement activity. Mob Genet Elements 2015; 5:1-6. [PMID: 26442176 DOI: 10.1080/2159256x.2015.1006109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/22/2014] [Accepted: 01/07/2015] [Indexed: 01/05/2023] Open
Abstract
Endogenous retroelements (EREs) are essential motors of evolution yet require careful control to prevent genomic catastrophes, notably during the vulnerable phases of epigenetic reprogramming that occur immediately after fertilization and in germ cells. Accordingly, a variety of mechanisms restrict these mobile genetic units. Previous studies have revealed the importance of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor, KAP1, in the early embryonic silencing of endogenous retroviruses and so-called SVAs, but the implication of this transcriptional repression system in the control of LINE-1, the only known active autonomous retrotransposon in the human genome, was thought to be marginal. Two recent studies straighten the record by revealing that the KRAB/KAP system is key to the control of L1 in embryonic stem (ES) cells, and go further in demonstrating that DNA methylation and KRAB/KAP1-induced repression contribute to this process in an evolutionally dynamic fashion. These results shed light on the delicate equilibrium between higher vertebrates and endogenous retroelements, which are not just genetic invaders calling for strict control but rather a constantly renewed and nicely exploitable source of evolutionary potential.
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Affiliation(s)
- Nathaly Castro-Diaz
- School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL) ; Lausanne, Switzerland
| | - Marc Friedli
- School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL) ; Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences; École Polytechnique Fédérale de Lausanne (EPFL) ; Lausanne, Switzerland
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Rajan KS, Ramasamy S. Retrotransposons and piRNA: The missing link in central nervous system. Neurochem Int 2014; 77:94-102. [DOI: 10.1016/j.neuint.2014.05.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/25/2014] [Accepted: 05/29/2014] [Indexed: 01/17/2023]
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Yang L, Brunsfeld J, Scott L, Wichman H. Reviving the dead: history and reactivation of an extinct l1. PLoS Genet 2014; 10:e1004395. [PMID: 24968166 PMCID: PMC4072516 DOI: 10.1371/journal.pgen.1004395] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date, their activity was lost in the megabat family, Pteropodidae, ∼24 million years ago. To examine the characteristics of L1s prior to their extinction, we analyzed the evolutionary history of L1s in the genome of a megabat, Pteropus vampyrus, and found a pattern of periodic L1 expansion and quiescence. In contrast to the well-characterized L1s in human and mouse, megabat genomes have accommodated two or more simultaneously active L1 families throughout their evolutionary history, and major peaks of L1 deposition into the genome always involved multiple families. We compared the consensus sequences of the two major megabat L1 families at the time of their extinction to consensus L1s of a variety of mammalian species. Megabat L1s are comparable to the other mammalian L1s in terms of adenosine content and conserved amino acids in the open reading frames (ORFs). However, the intergenic region (IGR) of the reconstructed element from the more active family is dramatically longer than the IGR of well-characterized human and mouse L1s. We synthesized the reconstructed element from this L1 family and tested the ability of its components to support retrotransposition in a tissue culture assay. Both ORFs are capable of supporting retrotransposition, while the IGR is inhibitory to retrotransposition, especially when combined with either of the reconstructed ORFs. We dissected the inhibitory effect of the IGR by testing truncated and shuffled versions and found that length is a key factor, but not the only one affecting inhibition of retrotransposition. Although the IGR is inhibitory to retrotransposition, this inhibition does not account for the extinction of L1s in megabats. Overall, the evolution of the L1 sequence or the quiescence of L1 is unlikely the reason of L1 extinction.
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Affiliation(s)
- Lei Yang
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - John Brunsfeld
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Holly Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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De novo transcriptome hybrid assembly and validation in the European earwig (Dermaptera, Forficula auricularia). PLoS One 2014; 9:e94098. [PMID: 24722757 PMCID: PMC3983118 DOI: 10.1371/journal.pone.0094098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/10/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The European earwig (Forficula auricularia) is an established system for studies of sexual selection, social interactions and the evolution of parental care. Despite its scientific interest, little knowledge exists about the species at the genomic level, limiting the scope of molecular studies and expression analyses of genes of interest. To overcome these limitations, we sequenced and validated the transcriptome of the European earwig. METHODOLOGY AND PRINCIPAL FINDINGS To obtain a comprehensive transcriptome, we sequenced mRNA from various tissues and developmental stages of female and male earwigs using Roche 454 pyrosequencing and Illumina HiSeq. The reads were de novo assembled independently and screened for possible microbial contamination and repeated elements. The remaining contigs were combined into a hybrid assembly and clustered to reduce redundancy. A comparison with the eukaryotic core gene dataset indicates that we sequenced a substantial part of the earwig transcriptome with a low level of fragmentation. In addition, a comparative analysis revealed that more than 8,800 contigs of the hybrid assembly show significant similarity to insect-specific proteins and those were assigned for Gene Ontology terms. Finally, we established a quantitative PCR test for expression stability using commonly used housekeeping genes and applied the method to five homologs of known sex-biased genes of the honeybee. The qPCR pilot study confirmed sex specific expression and also revealed significant expression differences between the brain and antenna tissue samples. CONCLUSIONS By employing two different sequencing approaches and including samples obtained from different tissues, developmental stages, and sexes, we were able to assemble a comprehensive transcriptome of F. auricularia. The transcriptome presented here offers new opportunities to study the molecular bases and evolution of parental care and sociality in arthropods.
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Sironen A, Fischer D, Laiho A, Gyenesei A, Vilkki J. A recent L1 insertion withinSPEF2gene is associated with changes inPRLRexpression in sow reproductive organs. Anim Genet 2014; 45:500-7. [DOI: 10.1111/age.12153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2014] [Indexed: 12/01/2022]
Affiliation(s)
- A. Sironen
- Agrifood Research Finland; MTT; Biotechnology and Food Research, Genomics; FI-36100 Jokioinen Finland
| | - D. Fischer
- Agrifood Research Finland; MTT; Biotechnology and Food Research, Genomics; FI-36100 Jokioinen Finland
| | - A. Laiho
- The Finnish Microarray and Sequencing Centre; Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Tykistökatu 6 FI-20520 Turku Finland
| | - A. Gyenesei
- The Finnish Microarray and Sequencing Centre; Turku Centre for Biotechnology; University of Turku and Åbo Akademi University; Tykistökatu 6 FI-20520 Turku Finland
| | - J. Vilkki
- Agrifood Research Finland; MTT; Biotechnology and Food Research, Genomics; FI-36100 Jokioinen Finland
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Kumari V, Iyer LR, Roy R, Bhargava V, Panda S, Paul J, Verweij JJ, Clark CG, Bhattacharya A, Bhattacharya S. Genomic distribution of SINEs in Entamoeba histolytica strains: implication for genotyping. BMC Genomics 2013; 14:432. [PMID: 23815468 PMCID: PMC3716655 DOI: 10.1186/1471-2164-14-432] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 06/20/2013] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND The major clinical manifestations of Entamoeba histolytica infection include amebic colitis and liver abscess. However the majority of infections remain asymptomatic. Earlier reports have shown that some E. histolytica isolates are more virulent than others, suggesting that virulence may be linked to genotype. Here we have looked at the genomic distribution of the retrotransposable short interspersed nuclear elements EhSINE1 and EhSINE2. Due to their mobile nature, some EhSINE copies may occupy different genomic locations among isolates of E. histolytica possibly affecting adjacent gene expression; this variability in location can be exploited to differentiate strains. RESULTS We have looked for EhSINE1- and EhSINE2-occupied loci in the genome sequence of Entamoeba histolytica HM-1:IMSS and searched for homologous loci in other strains to determine the insertion status of these elements. A total of 393 EhSINE1 and 119 EhSINE2 loci were analyzed in the available sequenced strains (Rahman, DS4-868, HM1:CA, KU48, KU50, KU27 and MS96-3382. Seventeen loci (13 EhSINE1 and 4 EhSINE2) were identified where a EhSINE1/EhSINE2 sequence was missing from the corresponding locus of other strains. Most of these loci were unoccupied in more than one strain. Some of the loci were analyzed experimentally for SINE occupancy using DNA from strain Rahman. These data helped to correctly assemble the nucleotide sequence at three loci in Rahman. SINE occupancy was also checked at these three loci in 7 other axenically cultivated E. histolytica strains and 16 clinical isolates. Each locus gave a single, specific amplicon with the primer sets used, making this a suitable method for strain typing. Based on presence/absence of SINE and amplification with locus-specific primers, the 23 strains could be divided into eleven genotypes. The results obtained by our method correlated with the data from other typing methods. We also report a bioinformatic analysis of EhSINE2 copies. CONCLUSIONS Our results reveal several loci with extensive polymorphism of SINE occupancy among different strains of E. histolytica and prove the principle that the genomic distribution of SINEs is a valid method for typing of E. histolytica strains.
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Affiliation(s)
- Vandana Kumari
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Lakshmi Rani Iyer
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Riti Roy
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Varsha Bhargava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suchita Panda
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Jaishree Paul
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Jaco J Verweij
- Laboratory for Medical Microbiology and Immunology, Laboratory for Clinical Pathology, St. Elisabeth Hospital, Tilburg, The Netherlands
| | - C Graham Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Sookdeo A, Hepp CM, McClure MA, Boissinot S. Revisiting the evolution of mouse LINE-1 in the genomic era. Mob DNA 2013; 4:3. [PMID: 23286374 PMCID: PMC3600994 DOI: 10.1186/1759-8753-4-3] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/25/2012] [Indexed: 11/10/2022] Open
Abstract
Background LINE-1 (L1) is the dominant category of transposable elements in placental mammals. L1 has significantly affected the size and structure of all mammalian genomes and understanding the nature of the interactions between L1 and its mammalian host remains a question of crucial importance in comparative genomics. For this reason, much attention has been dedicated to the evolution of L1. Among the most studied elements is the mouse L1 which has been the subject of a number of studies in the 1980s and 1990s. These seminal studies, performed in the pre-genomic era when only a limited number of L1 sequences were available, have significantly improved our understanding of L1 evolution. Yet, no comprehensive study on the evolution of L1 in mouse has been performed since the completion of this genome sequence. Results Using the Genome Parsing Suite we performed the first evolutionary analysis of mouse L1 over the entire length of the element. This analysis indicates that the mouse L1 has recruited novel 5’UTR sequences more frequently than previously thought and that the simultaneous activity of non-homologous promoters seems to be one of the conditions for the co-existence of multiple L1 families or lineages. In addition the exchange of genetic information between L1 families is not limited to the 5’UTR as evidence of inter-family recombination was observed in ORF1, ORF2, and the 3’UTR. In contrast to the human L1, there was little evidence of rapid amino-acid replacement in the coiled-coil of ORF1, although this region is structurally unstable. We propose that the structural instability of the coiled-coil domain might be adaptive and that structural changes in this region are selectively equivalent to the rapid evolution at the amino-acid level reported in the human lineage. Conclusions The pattern of evolution of L1 in mouse shows some similarity with human suggesting that the nature of the interactions between L1 and its host might be similar in these two species. Yet, some notable differences, particularly in the evolution of ORF1, suggest that the molecular mechanisms involved in host-L1 interactions might be different in these two species.
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Affiliation(s)
- Akash Sookdeo
- Department of Biology, Queens College, the City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367-1597, USA.
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