المؤلفون: Ghosh, Tanay, Almeida, Rafael G, Zhao, Chao, Mannioui, Abdelkrim, Martin, Elodie, Fleet, Alex, Chen, Civia Z, Assinck, Peggy, Ellams, Sophie, Gonzalez, Ginez A, Graham, Stephen C, Rowitch, David H, Stott, Katherine, Adams, Ian, Zalc, Bernard, Goldman, Nick, Lyons, David A, Franklin, Robin JM

مصطلحات موضوعية: ERV, LTR, convergent evolution, endogenous retrovirus, long terminal repeat, myelination, oligodendrocyte, oligodendrocyte progenitor cells, retrotransposon, transposable element, Animals, Gene Expression, Myelin Sheath, Oligodendroglia, Retroelements, RNA, Zebrafish, Anura

الوصف: Myelin, the insulating sheath that surrounds neuronal axons, is produced by oligodendrocytes in the central nervous system (CNS). This evolutionary innovation, which first appears in jawed vertebrates, enabled rapid transmission of nerve impulses, more complex brains, and greater morphological diversity. Here, we report that RNA-level expression of RNLTR12-int, a retrotransposon of retroviral origin, is essential for myelination. We show that RNLTR12-int-encoded RNA binds to the transcription factor SOX10 to regulate transcription of myelin basic protein (Mbp, the major constituent of myelin) in rodents. RNLTR12-int-like sequences (which we name RetroMyelin) are found in all jawed vertebrates, and we further demonstrate their function in regulating myelination in two different vertebrate classes (zebrafish and frogs). Our study therefore suggests that retroviral endogenization played a prominent role in the emergence of vertebrate myelin.

وصف الملف: application/pdf

العلاقة: https://www.repository.cam.ac.uk/handle/1810/363325Test; https://doi.org/10.17863/CAM.105438Test

الإتاحة: https://doi.org/10.17863/CAM.105438Test
https://www.repository.cam.ac.uk/handle/1810/363325Test

المؤلفون: Alicia C. Salinero, Simey Emerson, Tayla C. Cormier, John Yin, Randall H. Morse, M. Joan Curcio

مصطلحات موضوعية: Biochemistry, Molecular Biology, Structural Biology, Enzymes, Protein Trafficking, Proteomics and Intermolecular Interactions (excl. Medical Proteomics), Receptors and Membrane Biology, Signal Transduction, Structural Biology (incl. Macromolecular Modelling), Synthetic Biology, Ty1, retrotransposon, long terminal repeat, promoter, retromobility, co-factor, restriction factor, Saccharomyces cerevisiae

الوصف: The Ty1 retrotransposon family is maintained in a functional but dormant state by its host, Saccharomyces cerevisiae. Several hundred RHF and RTT genes encoding co-factors and restrictors of Ty1 retromobility, respectively, have been identified. Well-characterized examples include MED3 and MED15, encoding subunits of the Mediator transcriptional co-activator complex; control of retromobility by Med3 and Med15 requires the Ty1 promoter in the U3 region of the long terminal repeat. To characterize the U3-dependence of other Ty1 regulators, we screened a library of 188 known rhf and rtt mutants for altered retromobility of Ty1his3AI expressed from the strong, TATA-less TEF1 promoter or the weak, TATA-containing U3 promoter. Two classes of genes, each including both RHFs and RTTs, were identified. The first class comprising 82 genes that regulated Ty1his3AI retromobility independently of U3 is enriched for RHF genes that restrict the G1 phase of the cell cycle and those involved in transcriptional elongation and mRNA catabolism. The second class of 51 genes regulated retromobility of Ty1his3AI driven only from the U3 promoter. Nineteen U3-dependent regulators (U3DRs) also controlled retromobility of Ty1his3AI driven by the weak, TATA-less PSP2 promoter, suggesting reliance on the low activity of U3. Thirty-one U3DRs failed to modulate P PSP2 -Ty1his3AI retromobility, suggesting dependence on the architecture of U3. To further investigate the U3-dependency of Ty1 regulators, we developed a novel fluorescence-based assay to monitor expression of p22-Gag, a restriction factor expressed from the internal Ty1i promoter. Many U3DRs had minimal effects on levels of Ty1 RNA, Ty1i RNA or p22-Gag. These findings uncover a role for the Ty1 promoter in integrating signals from diverse host factors to modulate Ty1 RNA biogenesis or fate.

العلاقة: https://figshare.com/articles/presentation/Presentation1_Reliance_of_Host-Encoded_Regulators_of_Retromobility_on_Ty1_Promoter_Activity_or_Architecture_PPTX/20207279Test

الإتاحة: https://doi.org/10.3389/fmolb.2022.896215.s004Test
https://figshare.com/articles/presentation/Presentation1_Reliance_of_Host-Encoded_Regulators_of_Retromobility_on_Ty1_Promoter_Activity_or_Architecture_PPTX/20207279Test

المؤلفون: Alicia C. Salinero, Simey Emerson, Tayla C. Cormier, John Yin, Randall H. Morse, M. Joan Curcio

المصدر: Frontiers in Molecular Biosciences, Vol 9 (2022)

مصطلحات موضوعية: Ty1, retrotransposon, long terminal repeat, promoter, retromobility, co-factor, Biology (General), QH301-705.5

الوصف: The Ty1 retrotransposon family is maintained in a functional but dormant state by its host, Saccharomyces cerevisiae. Several hundred RHF and RTT genes encoding co-factors and restrictors of Ty1 retromobility, respectively, have been identified. Well-characterized examples include MED3 and MED15, encoding subunits of the Mediator transcriptional co-activator complex; control of retromobility by Med3 and Med15 requires the Ty1 promoter in the U3 region of the long terminal repeat. To characterize the U3-dependence of other Ty1 regulators, we screened a library of 188 known rhf and rtt mutants for altered retromobility of Ty1his3AI expressed from the strong, TATA-less TEF1 promoter or the weak, TATA-containing U3 promoter. Two classes of genes, each including both RHFs and RTTs, were identified. The first class comprising 82 genes that regulated Ty1his3AI retromobility independently of U3 is enriched for RHF genes that restrict the G1 phase of the cell cycle and those involved in transcriptional elongation and mRNA catabolism. The second class of 51 genes regulated retromobility of Ty1his3AI driven only from the U3 promoter. Nineteen U3-dependent regulators (U3DRs) also controlled retromobility of Ty1his3AI driven by the weak, TATA-less PSP2 promoter, suggesting reliance on the low activity of U3. Thirty-one U3DRs failed to modulate PPSP2-Ty1his3AI retromobility, suggesting dependence on the architecture of U3. To further investigate the U3-dependency of Ty1 regulators, we developed a novel fluorescence-based assay to monitor expression of p22-Gag, a restriction factor expressed from the internal Ty1i promoter. Many U3DRs had minimal effects on levels of Ty1 RNA, Ty1i RNA or p22-Gag. These findings uncover a role for the Ty1 promoter in integrating signals from diverse host factors to modulate Ty1 RNA biogenesis or fate.

وصف الملف: electronic resource

العلاقة: https://www.frontiersin.org/articles/10.3389/fmolb.2022.896215/fullTest; https://doaj.org/toc/2296-889XTest

الوصول الحر: https://doaj.org/article/f67f326371e141368fdd4062ddb64daeTest

المؤلفون: Marwa M. Ghonaim, Ruslan Kalendar, Heba Barakat, Nahla A. El‐Sherif, Naglaa A. Ashry, Alan H. Schulman

مصطلحات موضوعية: Genome Evolution and Polyploidy in Plants, Plant Science, Agricultural and Biological Sciences, Life Sciences, RNA Sequencing Data Analysis, Molecular Biology, Biochemistry, Genetics and Molecular Biology, Genetics and Epidemiology of Plant Pathogens, Genetic Mapping, Transcriptome Analysis, Retrotransposon, Biology, Germplasm, Genetic diversity, Genome, Genetics, FOS Biological sciences, Long terminal repeat, Amplicon, Genetic variation, Polymerase chain reaction, Computational biology, Gene, Transposable element, Botany, Population, Demography, FOS Sociology, Sociology

الوصف: Maize is one of the world's most important crops and a model for grass genome research. Long terminal repeat (LTR) retrotransposons comprise most of the maize genome; their ability to produce new copies makes them efficient high-throughput genetic markers. Inter-retrotransposon-amplified polymorphisms (IRAPs) were used to study the genetic diversity of maize germplasm. Five LTR retrotransposons ( Huck , Tekay , Opie , Ji , and Grande ) were chosen, based on their large number of copies in the maize genome, whereas polymerase chain reaction primers were designed based on consensus LTR sequences. The LTR primers showed high quality and reproducible DNA fingerprints, with a total of 677 bands including 392 polymorphic bands showing 58% polymorphism between maize hybrid lines. These markers were used to identify genetic similarities among all lines of maize. Analysis of genetic similarity was carried out based on polymorphic amplicon profiles and genetic similarity phylogeny analysis. This diversity was ... : الذرة الصفراء هي واحدة من أهم المحاصيل في العالم ونموذج لأبحاث جينوم العشب. تشكل عمليات النقل الرجعية ذات التكرار الطرفي الطويل (LTR) معظم جينوم الذرة ؛ وقدرتها على إنتاج نسخ جديدة تجعلها علامات وراثية فعالة عالية الإنتاجية. تم استخدام تعدد الأشكال المضخم بين البدائل (IRAPs) لدراسة التنوع الجيني للجبلة الجرثومية للذرة. تم اختيار خمسة مناقلات خلفية لتر ( هاك ، تيكاي، أوبي، جي، وغراندي )، بناءً على عدد كبير من النسخ في جينوم الذرة، في حين تم تصميم بادئات تفاعل سلسلة البلمرة بناءً على متواليات لتر الإجماع. أظهرت برايمر LTR بصمات الحمض النووي عالية الجودة والقابلة للتكرار، مع ما مجموعه 677 شريطًا بما في ذلك 392 شريطًا متعدد الأشكال يظهر 58 ٪ من تعدد الأشكال بين خطوط الذرة الهجينة. تم استخدام هذه العلامات لتحديد أوجه التشابه الوراثية بين جميع خطوط الذرة. تم إجراء تحليل التشابه الجيني بناءً على ملامح أمبليكون متعددة الأشكال وتحليل سلالة التشابه الجيني. كان من المتوقع أن يعرض هذا التنوع أنماطًا جغرافية بيئية من التباين والتكيف المحلي. أظهرت طريقة التجميع العنقودي أن الأصناف تم تجميعها في ثلاث مجموعات تختلف في الأصل ...

العلاقة: https://dx.doi.org/10.60692/5dked-deq95Test

الإتاحة: https://doi.org/10.60692/pbw7y-hq50910.60692/5dked-deq95Test

المؤلفون: Hayashi, Sakura, Shimizu, Konami, Honda, Yusuke, Katsura, Yukako, Koga, Akihiko

المصدر: Genome. 65:277-286

مصطلحات موضوعية: Macropodidae, viruses, retrotransposon, Endogenous Retroviruses, Terminal Repeat Sequences, albinism, marsupial, General Medicine, long terminal repeat, Proviruses, endogenous retrovirus, Genetics, Animals, Amino Acid Sequence, Molecular Biology, Biotechnology

الوصف: An albino infant wallaby was born to a mother with the wild-type body color. PCR and sequencing analyses of TYR (encoding tyrosinase, which is essential for melanin biosynthesis) of this albino wallaby revealed a 7.1-kb-long DNA fragment inserted in the first exon. Because the fragment carried long terminal repeats, we assumed it to be a copy of an endogenous retrovirus, which we named walb. We cloned other walb copies residing in the genomes of this species and another wallaby species. The copies exhibited length variation, and the longest copy (>8.0 kb) contained open reading frames whose deduced amino acid sequences were well aligned with those of gag, pol, and env of retroviruses. It is not known through which of the following likely processes the walb copy was inserted into TYR: endogenization (infection of a germline cell by an exogenous virus), reinfection (infection by a virus produced from a previously endogenized provirus), or retrotransposition (intracellular relocation of a provirus). In any case, the insertion into TYR is considered to have been a recent event on an evolutionary timescale because albino mutant alleles generally do not persist for long because of their deleterious effects in wild circumstances.
白いワラビーの遺伝的原因を初めて解明 --世界各地の動物園で相次いで誕生--. 京都大学プレスリリース. 2022-01-18.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::01cd47c424d41eec22953019cf54c065Test
https://doi.org/10.1139/gen-2021-0047Test

المؤلفون: Artem Babaian, Dixie L. Mager

المصدر: Mobile DNA, Vol 7, Iss 1, Pp 1-21 (2016)

مصطلحات موضوعية: Gene regulation, Endogenous retrovirus, Long terminal repeat, Retrotransposon, Epigenetics, Cancer, Genetics, QH426-470

الوصف: Abstract Cancer arises from a series of genetic and epigenetic changes, which result in abnormal expression or mutational activation of oncogenes, as well as suppression/inactivation of tumor suppressor genes. Aberrant expression of coding genes or long non-coding RNAs (lncRNAs) with oncogenic properties can be caused by translocations, gene amplifications, point mutations or other less characterized mechanisms. One such mechanism is the inappropriate usage of normally dormant, tissue-restricted or cryptic enhancers or promoters that serve to drive oncogenic gene expression. Dispersed across the human genome, endogenous retroviruses (ERVs) provide an enormous reservoir of autonomous gene regulatory modules, some of which have been co-opted by the host during evolution to play important roles in normal regulation of genes and gene networks. This review focuses on the “dark side” of such ERV regulatory capacity. Specifically, we discuss a growing number of examples of normally dormant or epigenetically repressed ERVs that have been harnessed to drive oncogenes in human cancer, a process we term onco-exaptation, and we propose potential mechanisms that may underlie this phenomenon.

وصف الملف: electronic resource

العلاقة: http://link.springer.com/article/10.1186/s13100-016-0080-xTest; https://doaj.org/toc/1759-8753Test

الوصول الحر: https://doaj.org/article/042f60385651489298600e4e1fc54d37Test

المؤلفون: Beatrice Weber, Tony Heitkam, Kathrin M. Seibt, Sedat Serçe, Gerhard Menzel, Sònia Garcia, Nusrat Sultana

المصدر: Digital.CSIC. Repositorio Institucional del CSIC
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مصطلحات موضوعية: In silico, LTR retrotransposon, Soil Science, Sequence assembly, Retrotransposon, Plant Science, Computational biology, Repetitive DNA, Ty1-copia, Horticulture, Biology, Biochemistry, Genome, food, Vaccinium macrocarpon, Cranberry, Shotgun sequencing, fungi, food and beverages, Long terminal repeat, American cranberry, food.food, Agronomy and Crop Science, Ty3-gypsy, Food Science

الوصف: [BACKGROUND] Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they may be beneficial for current berry breeding efforts. [OBJECTIVE] Exemplarily focusing on the genome of American cranberry (Vaccinium macrocarpon Aiton), we aim to generate an overview of the LTR retrotransposon landscape, highlighting the abundance, transcriptional activity, sequence, and structure of the major retrotransposon lineages. [METHODS] Graph-based clustering of whole genome shotgun Illumina reads was performed to identify the most abundant LTR retrotransposons and to reconstruct representative in silico full-length elements. To generate insights into the LTR retrotransposon diversity in V. macrocarpon, we also queried the genome assembly for presence of reverse transcriptases (RTs), the key domain of LTR retrotransposons. Using transcriptomic data, transcriptional activity of retrotransposons corresponding to the consensuses was analyzed. [RESULTS] We provide an in-depth characterization of the LTR retrotransposon landscape in the V. macrocarpon genome. Based on 475 RTs harvested from the genome assembly, we detect a high retrotransposon variety, with all major lineages present. To better understand their structural hallmarks, we reconstructed 26 Ty1-copia and 28 Ty3-gypsy in silico consensuses that capture the detected diversity. Accordingly, we frequently identify association with tandemly repeated motifs, extra open reading frames, and specialized, lineage-typical domains. Based on the overall high genomic abundance and transcriptional activity, we suggest that retrotransposons of the Ale and Athila lineages are most promising to monitor retrotransposon-derived polymorphisms across accessions. [CONCLUSIONS]We conclude that LTR retrotransposons are major components of the V. macrocarpon genome. The representative consensuses provide an entry point for further Vaccinium genome analyses and may be applied to derive molecular markers for enhancing cranberry selection and breeding.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::60c637552c9c91b487ab5845c5a5abf4Test
http://hdl.handle.net/10261/275419Test

المؤلفون: Yue Liang, Jochen B. W. Wolf, Fang Suo, Li-Lin Du, Sergio Tusso

المصدر: Genome Research. 32:324-336

مصطلحات موضوعية: Transposable element, education.field_of_study, Retroelements, Population, Terminal Repeat Sequences, Retrotransposon, Biology, biology.organism_classification, Genome, Long terminal repeat, Evolution, Molecular, Negative selection, Evolutionary biology, Schizosaccharomyces, Schizosaccharomyces pombe, DNA Transposable Elements, Genetics, Humans, Genome, Fungal, Homologous recombination, education, Genetics (clinical)

الوصف: Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this ‘genomic shock hypothesis’ in the fission yeast Schizosaccharomyces pombe. In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. Sequence analysis of active full-length elements, as well as solo-LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo-LTRs prior to the split of the Sp and Sk lineages. Most full-length elements were inserted more recently after hybridization. With the exception of a single full-length element with signs of positive selection, both solo-LTRs, and in particular, full-length elements carried signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increased with the degree of genomic admixture. This study gives a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements and provides evidence for the ‘genomic shock hypothesis’.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::71f4e1d7189bc5959fce8ca7c0101db0Test
https://doi.org/10.1101/gr.276056.121Test

المؤلفون: Seung Cho Lee, Robert A. Martienssen

المصدر: Biochemical Society Transactions. 49:2241-2251

مصطلحات موضوعية: DNA Replication, Transcriptional Activation, Genetics, Transposable element, Regulation of gene expression, Small RNA, Retroelements, fungi, Arabidopsis, food and beverages, Retrotransposon, Biology, Genes, Plant, biology.organism_classification, Biochemistry, Long terminal repeat, Epigenesis, Genetic, Gene Expression Regulation, Plant, Gene Silencing, Gene, Reference genome

الوصف: Plant genomes are largely comprised of retrotransposons which can replicate through ‘copy and paste' mechanisms. Long terminal repeat (LTR) retrotransposons are the major class of retrotransposons in plant species, and importantly they broadly affect the expression of nearby genes. Although most LTR retrotransposons are non-functional, active retrotranspositions have been reported in plant species or mutants under normal growth condition and environmental stresses. With the well-defined reference genome and numerous mutant alleles, Arabidopsis studies have significantly expanded our understanding of retrotransposon regulation. Active LTR retrotransposon loci produce virus-like particles to perform reverse transcription, and their complementary DNA can be inserted into new genomic loci. Due to the detrimental consequences of retrotransposition, plants like animals, have developed transcriptional and post-transcriptional silencing mechanisms. Recently several different genome-wide techniques have been developed to understand LTR retrotransposition in Arabidopsis and different plant species. Transposome, methylome, transcriptome, translatome and small RNA sequencing data have revealed how host silencing mechanisms can affect multiple steps of retrotransposition. These recent advances shed light on future mechanistic studies of retrotransposition as well as retrotransposon diversity.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1b65f03f8157cc469cd9566cd9694a6Test
https://doi.org/10.1042/bst20210337Test

المؤلفون: Beckers J, Marco Thines, Gunther Doehlemann, Julia Kruse, Bilal Ökmen, Malaika K. Ebert, Jasper R L Depotter

المصدر: Microbiology spectrum. 10(5)

مصطلحات موضوعية: Microbiology (medical), Transposable element, Retroelements, Physiology, Retrotransposon, Locus (genetics), Genome, Evolution, Molecular, Genetics, Amino Acids, Gene, Secretome, Cell Proliferation, General Immunology and Microbiology, Ecology, Ustilago hordei, biology, Nucleotides, Point mutation, Terminal Repeat Sequences, food and beverages, Cell Biology, biology.organism_classification, Long terminal repeat, Infectious Diseases, DNA Transposable Elements

الوصف: Transposable elements (TEs) play a pivotal role in shaping diversity in eukaryotic genomes. The covered smut pathogen on barley, Ustilago hordei, encountered a recent genome expansion. Using long reads, we assembled genomes of 6 U. hordei strains and 3 sister species, to study this genome expansion. We found that larger genome sizes can mainly be attributed to a higher genome fraction of long terminal repeat retrotransposons (LTR-RTs). In the studied smut genomes, LTR-RTs fractions are the largest in U. hordei and are positively correlated to the mating-type locus sizes, which is up to ∼560 kb in U. hordei. Furthermore, LTR-RTs were found to be associated with higher nucleotide substitution levels, as these higher levels occur more clustered in smut species with a recent LTR-RT proliferation. Moreover, genes in genome regions with higher nucleotide substitution levels generally reside closer to LTR-RTs than other genome regions. Genome regions with many nucleotide substitutions encountered an especially high fraction of CG substitutions, which is not observed for LTR-RT sequences. The high nucleotide substitution levels particularly accelerate the evolution of secretome genes, as their more flexible nature results that substitutions often lead to amino acid alterations.ImportanceGenomic alteration can be generated through various means, in which transposable elements (TEs) can play a pivotal role. Their mobility causes mutagenesis in itself and can disrupt the function of the sequences they insert into. Indirectly, they also impact genome evolution as their repetitive nature facilitates non-homologous recombination. Furthermore, TEs have been linked to specific epigenetic genome organizations. We report a recent TE proliferation in the genome of the barley covered smut fungus, Ustilago hordei. This proliferation is associated with a distinct nucleotide substitution regime that has a higher rate and a higher fraction of CG substitutions. This different regime shapes the evolution of genes in subjected genome regions. Our findings highlight that TEs may influence the error-rate of DNA polymerase in a hitherto unknown fashion.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::08db5a0b25f0930ef02c6103070b8455Test
https://pubmed.ncbi.nlm.nih.gov/35972267Test