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[PMID]:29224130
[Au] Autor:Wang M; Wang Y; Baloch AR; Pan Y; Xu F; Tian L; Zeng Q
[Ad] Endereço:College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China.
[Ti] Título:Molecular epidemiology and characterization of bovine leukemia virus in domestic yaks (Bos grunniens) on the Qinghai-Tibet Plateau, China.
[So] Source:Arch Virol;163(3):659-670, 2018 Mar.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:Bovine leukemia virus (BLV) is a member of the genus Deltaretrovirus of the family Retroviridae and cause a chronic lymphosarcoma, which is extensive in cattle. In yaks (Bos grunniens), the distribution, strains and genetic characteristics of BLV have rarely been studied. The aim of our study was to investigate BLV infections in domestic yaks and determine the genetic variability of BLV circulating in a region of the Qinghai Tibet Plateau, China. Blood samples were collected from 798 yaks, which were from different farms from Gansu, Qinghai and Sichuan provinces surrounding the Qinghai-Tibet Plateau. Nested PCR targeting BLV long terminal repeats was used to detect the BLV provirus. The highest prevalence of BLV infection was in Gansu province, where it was 18.93% (39/206) in white yaks from Tianzhu City and 19.14% (31/162) in black yaks from Gannan City. In Qinghai and Sichuan provinces, the prevalence of BLV in black yaks was 14.83% (35/236) and 14.94% (29/194), respectively. The prevalence of BLV was not significantly different in yaks up to one year old than in older animals. Phylogenetic analysis was performed using 16 different env-gp51 (497-bp) gene sequences from the three provinces and 71 known BLV strains, which revealed that in both Gansu and Qinghai provinces, genotypes 6 and 10 of the BLV strains were at high levels, whereas only genotype 10 was prevalent in Sichuan Province. Phylogenetic analysis and sequence comparisons revealed 95.7-99.8% sequence identity among the full-length env genes of 16 strains, nearly full-length genome sequences of six BLV strains, and those of the known genotypes 6 and 10 of BLV. This study provides comprehensive information is regarding the widespread infection of domestic yaks with BLV on the Qinghai-Tibet Plateau of China, and shows that at least two BLV genotypes (genotypes 6 and 10) are circulating in this population.
[Mh] Termos MeSH primário: Leucose Enzoótica Bovina/epidemiologia
Genes env
Genótipo
Vírus da Leucemia Bovina/classificação
Vírus da Leucemia Bovina/genética
Filogenia
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Bovinos
Leucose Enzoótica Bovina/transmissão
Leucose Enzoótica Bovina/virologia
Expressão Gênica
Vírus da Leucemia Bovina/isolamento & purificação
Epidemiologia Molecular
Prevalência
Alinhamento de Sequência
Homologia de Sequência do Ácido Nucleico
Sequências Repetidas Terminais
Tibet/epidemiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171211
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3658-9


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[PMID]:29232693
[Au] Autor:Rai SK; Sangesland M; Lee M; Esnault C; Cui Y; Chatterjee AG; Levin HL
[Ad] Endereço:Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America.
[Ti] Título:Host factors that promote retrotransposon integration are similar in distantly related eukaryotes.
[So] Source:PLoS Genet;13(12):e1006775, 2017 12.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements.
[Mh] Termos MeSH primário: Fatores Hospedeiros de Integração/genética
Recombinação Genética
Retroelementos/genética
Sequências Repetidas Terminais/genética
Ubiquitina-Proteína Ligases/genética
[Mh] Termos MeSH secundário: Reparo do DNA/genética
Eucariotos/genética
Regulação Fúngica da Expressão Gênica
Integrases/genética
Regiões Promotoras Genéticas
DNA Polimerase Dirigida por RNA/genética
Retroviridae/genética
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/genética
Schizosaccharomyces/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Integration Host Factors); 0 (Retroelements); 0 (Saccharomyces cerevisiae Proteins); 0 (Spp382 protein, S cerevisiae); EC 2.3.2.27 (Rhp18 protein, S pombe); EC 2.3.2.27 (Ubiquitin-Protein Ligases); EC 2.7.7.- (Integrases); EC 2.7.7.49 (RNA-Directed DNA Polymerase); EC 2.7.7.49 (reverse transcriptase Ty3, S cerevisiae)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180111
[Lr] Data última revisão:
180111
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171213
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006775


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[PMID]:29198561
[Au] Autor:Chou HJ; Donnard E; Gustafsson HT; Garber M; Rando OJ
[Ad] Endereço:Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
[Ti] Título:Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation.
[So] Source:Mol Cell;68(5):978-992.e4, 2017 Dec 07.
[Is] ISSN:1097-4164
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Covalent nucleotide modifications in noncoding RNAs affect a plethora of biological processes, and new functions continue to be discovered even for well-known modifying enzymes. To systematically compare the functions of a large set of noncoding RNA modifications in gene regulation, we carried out ribosome profiling in budding yeast to characterize 57 nonessential genes involved in tRNA modification. Deletion mutants exhibited a range of translational phenotypes, with enzymes known to modify anticodons, or non-tRNA substrates such as rRNA, exhibiting the most dramatic translational perturbations. Our data build on prior reports documenting translational upregulation of the nutrient-responsive transcription factor Gcn4 in response to numerous tRNA perturbations, and identify many additional translationally regulated mRNAs throughout the yeast genome. Our data also uncover unexpected roles for tRNA-modifying enzymes in regulation of TY retroelements, and in rRNA 2'-O-methylation. This dataset should provide a rich resource for discovery of additional links between tRNA modifications and gene regulation.
[Mh] Termos MeSH primário: RNA Fúngico/metabolismo
RNA de Transferência/metabolismo
Ribossomos/enzimologia
Proteínas de Saccharomyces cerevisiae/metabolismo
Saccharomyces cerevisiae/enzimologia
Transcriptoma
tRNA Metiltransferases/metabolismo
[Mh] Termos MeSH secundário: Fatores de Transcrição de Zíper de Leucina Básica/biossíntese
Fatores de Transcrição de Zíper de Leucina Básica/genética
Perfilação da Expressão Gênica/métodos
Regulação Fúngica da Expressão Gênica
Genótipo
Metilação
Mutação
Fenótipo
RNA Fúngico/genética
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
RNA Ribossômico/genética
RNA Ribossômico/metabolismo
RNA de Transferência/genética
RNA não Traduzido/genética
RNA não Traduzido/metabolismo
Retroelementos
Ribossomos/genética
Saccharomyces cerevisiae/genética
Proteínas de Saccharomyces cerevisiae/biossíntese
Proteínas de Saccharomyces cerevisiae/genética
Sequências Repetidas Terminais
tRNA Metiltransferases/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Basic-Leucine Zipper Transcription Factors); 0 (GCN4 protein, S cerevisiae); 0 (RNA, Fungal); 0 (RNA, Messenger); 0 (RNA, Ribosomal); 0 (RNA, Untranslated); 0 (Retroelements); 0 (Saccharomyces cerevisiae Proteins); 9014-25-9 (RNA, Transfer); EC 2.1.1.- (Trm7 protein, S cerevisiae); EC 2.1.1.- (tRNA Methyltransferases)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:171226
[Lr] Data última revisão:
171226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171205
[St] Status:MEDLINE


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[PMID]:28867566
[Au] Autor:Jung YD; Lee HE; Jo A; Hiroo I; Cha HJ; Kim HS
[Ad] Endereço:Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 34141, Republic of Korea.
[Ti] Título:Activity analysis of LTR12C as an effective regulatory element of the RAE1 gene.
[So] Source:Gene;634:22-28, 2017 Nov 15.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Ribonucleic acid export 1 (RAE1) plays an important role in the export of mature mRNAs from the nucleus to the cytoplasm. Long terminal repeats (LTRs) became integrated into the human genome during primate evolution. One such repeat element, LTR12C, lies within a predicted regulatory region located upstream of the RAE1 gene. We examined the transcriptional activity of LTR12C by using the luciferase assay, and showed that the tandem repeat region (TRR) located within LTR12C was required for its regulatory function. A bioinformatics analysis revealed that the LTR12C element had multiple transcription factor binding sites specific for nuclear transcription factor Y (NF-Y), and the promoter activity of LTR12C was significantly decreased after NF-Y knockdown. Additionally, we discovered novel data indicating that LTR12C was initially inserted into the gorilla genome. Taken together, our results reveal that the TRR of LTR12C has powerful regulatory activity due to its NF-Y binding sites, and the integration of the LTR12C element into the primate genome during evolution may have affected RAE1 transcription.
[Mh] Termos MeSH primário: Fator de Ligação a CCAAT/metabolismo
Gorilla gorilla/genética
Proteínas Associadas à Matriz Nuclear/metabolismo
Proteínas de Transporte Nucleocitoplasmático/metabolismo
Sequências Repetidas Terminais
[Mh] Termos MeSH secundário: Células A549
Animais
Sítios de Ligação
Linhagem Celular
Evolução Molecular
Regulação da Expressão Gênica
Células HCT116
Células HEK293
Células Hep G2
Seres Humanos
Regiões Promotoras Genéticas
Sequências de Repetição em Tandem
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (CCAAT-Binding Factor); 0 (Nuclear Matrix-Associated Proteins); 0 (Nucleocytoplasmic Transport Proteins); 0 (RAE1 protein, human); 0 (Transcription Factors); 0 (nuclear factor Y)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171002
[Lr] Data última revisão:
171002
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170905
[St] Status:MEDLINE


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[PMID]:28867564
[Au] Autor:Mascagni F; Cavallini A; Giordani T; Natali L
[Ad] Endereço:Dept. of Agriculture, Food, and Environment, University of Pisa, Via delBorghetto 80, I-56124 Pisa, Italy.
[Ti] Título:Different histories of two highly variable LTR retrotransposons in sunflower species.
[So] Source:Gene;634:5-14, 2017 Nov 15.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution.
[Mh] Termos MeSH primário: Helianthus/classificação
Retroelementos
Sequências Repetidas Terminais
[Mh] Termos MeSH secundário: DNA de Plantas/genética
Evolução Molecular
Variação Genética
Helianthus/genética
Hibridização Genética
Análise de Sequência de DNA/métodos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant); 0 (Retroelements)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171002
[Lr] Data última revisão:
171002
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170905
[St] Status:MEDLINE


  6 / 2388 MEDLINE  
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[PMID]:28794032
[Au] Autor:Bamunusinghe D; Liu Q; Plishka R; Dolan MA; Skorski M; Oler AJ; Yedavalli VRK; Buckler-White A; Hartley JW; Kozak CA
[Ad] Endereço:Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA.
[Ti] Título:Recombinant Origins of Pathogenic and Nonpathogenic Mouse Gammaretroviruses with Polytropic Host Range.
[So] Source:J Virol;91(21), 2017 Nov 01.
[Is] ISSN:1098-5514
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Ecotropic, xenotropic, and polytropic mouse leukemia viruses (E-, X-, and P-MLVs) exist in mice as infectious viruses and endogenous retroviruses (ERVs) inserted into mouse chromosomes. All three MLV subgroups are linked to leukemogenesis, which involves generation of recombinants with polytropic host range. Although P-MLVs are deemed to be the proximal agents of disease induction, few biologically characterized infectious P-MLVs have been sequenced for comparative analysis. We analyzed the complete genomes of 16 naturally occurring infectious P-MLVs, 12 of which were typed for pathogenic potential. We sought to identify ERV progenitors, recombinational hot spots, and segments that are always replaced, never replaced, or linked to pathogenesis or host range. Each P-MLV has an E-MLV backbone with P- or X-ERV replacements that together cover 100% of the recombinant genomes, with different substitution patterns for X- and P-ERVs. Two segments are always replaced, both coding for envelope (Env) protein segments: the N terminus of the surface subunit and the cytoplasmic tail R peptide. Viral gene replacements are influenced by host restriction genes and Pathogenic potential maps to the transmembrane subunit segment encoding the N-heptad repeat (HR1). Molecular dynamics simulations identified three novel interdomain salt bridges in the lymphomagenic virus HR1 that could affect structural stability, entry or sensitivity to host immune responses. The long terminal repeats of lymphomagenic P-MLVs are differentially altered by recombinations, duplications, or mutations. This analysis of the naturally occurring, sometimes pathogenic P-MLV recombinants defines the limits and extent of intersubgroup recombination and identifies specific sequence changes linked to pathogenesis and host interactions. During virus-induced leukemogenesis, ecotropic mouse leukemia viruses (MLVs) recombine with nonecotropic endogenous retroviruses (ERVs) to produce polytropic MLVs (P-MLVs). Analysis of 16 P-MLV genomes identified two segments consistently replaced: one at the envelope N terminus that alters receptor choice and one in the R peptide at the envelope C terminus, which is removed during virus assembly. Genome-wide analysis shows that nonecotropic replacements in the progenitor ecotropic MLV genome are more extensive than previously appreciated, covering 100% of the genome; contributions from xenotropic and polytropic ERVs differentially alter the regions responsible for receptor determination or subject to APOBEC3 and Fv1 restriction. All pathogenic viruses had modifications in the regulatory elements in their long terminal repeats and differed in a helical segment of envelope involved in entry and targeted by the host immune system. Virus-induced leukemogenesis thus involves generation of complex recombinants, and specific replacements are linked to pathogenesis and host restrictions.
[Mh] Termos MeSH primário: Especificidade de Hospedeiro/genética
Vírus da Leucemia Murina/classificação
Vírus da Leucemia Murina/patogenicidade
Leucemia Experimental/virologia
Infecções por Retroviridae/virologia
Infecções Tumorais por Vírus/virologia
Proteínas Virais/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Sequência de Bases
Evolução Molecular
Genoma Viral
Vírus da Leucemia Murina/genética
Camundongos
Simulação de Dinâmica Molecular
Conformação Proteica
Receptores Virais/genética
Receptores Virais/metabolismo
Homologia de Sequência
Sequências Repetidas Terminais
Proteínas Virais/química
Proteínas Virais/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Receptors, Virus); 0 (Viral Proteins)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171109
[Lr] Data última revisão:
171109
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170811
[St] Status:MEDLINE


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[PMID]:28715472
[Au] Autor:Lock FE; Babaian A; Zhang Y; Gagnier L; Kuah S; Weberling A; Karimi MM; Mager DL
[Ad] Endereço:Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada.
[Ti] Título:A novel isoform of IL-33 revealed by screening for transposable element promoted genes in human colorectal cancer.
[So] Source:PLoS One;12(7):e0180659, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Remnants of ancient transposable elements (TEs) are abundant in mammalian genomes. These sequences contain multiple regulatory motifs and hence are capable of influencing expression of host genes. TEs are known to be released from epigenetic repression and can become transcriptionally active in cancer. Such activation could also lead to lineage-inappropriate activation of oncogenes, as previously described in lymphomas. However, there are few reports of this mechanism occurring in non-blood cancers. Here, we re-analyzed whole transcriptome data from a large cohort of patients with colon cancer, compared to matched normal colon control samples, to detect genes or transcripts ectopically expressed through activation of TE promoters. Among many such transcripts, we identified six where the affected gene has described role in cancer and where the TE-driven gene mRNA is expressed in primary colon cancer, but not normal matched tissue, and confirmed expression in colon cancer-derived cell lines. We further characterized a TE-gene chimeric transcript involving the Interleukin 33 (IL-33) gene (termed LTR-IL-33), that is ectopically expressed in a subset of colon cancer samples through the use of an endogenous retroviral long terminal repeat (LTR) promoter of the MSTD family. The LTR-IL-33 chimeric transcript encodes a novel shorter isoform of the protein, which is missing the initial N-terminus (including many conserved residues) of Native IL-33. In vitro studies showed that LTR-IL-33 expression is required for optimal CRC cell line growth as 3D colonospheres. Taken together, these data demonstrate the significance of TEs as regulators of aberrant gene expression in colon cancer.
[Mh] Termos MeSH primário: Neoplasias Colorretais/patologia
Elementos de DNA Transponíveis/genética
Interleucina-33/genética
[Mh] Termos MeSH secundário: Sequência de Aminoácidos
Animais
Linhagem Celular Tumoral
Proliferação Celular
Regulação Neoplásica da Expressão Gênica
Seres Humanos
Interleucina-33/química
Regiões Promotoras Genéticas/genética
Isoformas de Proteínas/química
Isoformas de Proteínas/genética
Sequências Repetidas Terminais/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA Transposable Elements); 0 (IL33 protein, human); 0 (Interleukin-33); 0 (Protein Isoforms)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170926
[Lr] Data última revisão:
170926
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170718
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0180659


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[PMID]:28700586
[Au] Autor:Ito J; Sugimoto R; Nakaoka H; Yamada S; Kimura T; Hayano T; Inoue I
[Ad] Endereço:Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, Japan.
[Ti] Título:Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses.
[So] Source:PLoS Genet;13(7):e1006883, 2017 Jul.
[Is] ISSN:1553-7404
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs). Overall, 794,972 HERV-TFBSs were identified. Subsequently, we identified "HERV/LTR-shared regulatory element (HSRE)," defined as a TF-binding motif in HERV-TFBSs, shared within a substantial fraction of a HERV/LTR type. HSREs could be an indication that the regulatory elements of HERV/LTRs are present before their insertions. We identified 2,201 HSREs, comprising specific associations of 354 HERV/LTRs and 84 TFs. Clustering analysis showed that HERV/LTRs can be grouped according to the TF binding patterns; HERV/LTR groups bounded to pluripotent TFs (e.g., SOX2, POU5F1, and NANOG), embryonic endoderm/mesendoderm TFs (e.g., GATA4/6, SOX17, and FOXA1/2), hematopoietic TFs (e.g., SPI1 (PU1), GATA1/2, and TAL1), and CTCF were identified. Regulatory elements of HERV/LTRs tended to locate nearby and/or interact three-dimensionally with the genes involved in immune responses, indicating that the regulatory elements play an important role in controlling the immune regulatory network. Further, we demonstrated subgroup-specific TF binding within LTR7, LTR5B, and LTR5_Hs, indicating that gains or losses of the regulatory elements occurred during genomic invasions of the HERV/LTRs. Finally, we constructed dbHERV-REs, an interactive database of HERV/LTR regulatory elements (http://herv-tfbs.com/). This study provides fundamental information in understanding the impact of HERV/LTRs on host transcription, and offers insights into the transcriptional modulation systems of HERV/LTRs and ancestral HERVs.
[Mh] Termos MeSH primário: Retrovirus Endógenos/genética
Elementos Reguladores de Transcrição/genética
Fatores de Transcrição/genética
Transcrição Genética
[Mh] Termos MeSH secundário: Seres Humanos
Sequências Reguladoras de Ácido Nucleico/genética
Sequências Repetidas Terminais/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Transcription Factors)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170808
[Lr] Data última revisão:
170808
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170713
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pgen.1006883


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[PMID]:28666125
[Au] Autor:Schorn AJ; Gutbrod MJ; LeBlanc C; Martienssen R
[Ad] Endereço:Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
[Ti] Título:LTR-Retrotransposon Control by tRNA-Derived Small RNAs.
[So] Source:Cell;170(1):61-71.e11, 2017 Jun 29.
[Is] ISSN:1097-4172
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Transposon reactivation is an inherent danger in cells that lose epigenetic silencing during developmental reprogramming. In the mouse, long terminal repeat (LTR)-retrotransposons, or endogenous retroviruses (ERV), account for most novel insertions and are expressed in the absence of histone H3 lysine 9 trimethylation in preimplantation stem cells. We found abundant 18 nt tRNA-derived small RNA (tRF) in these cells and ubiquitously expressed 22 nt tRFs that include the 3' terminal CCA of mature tRNAs and target the tRNA primer binding site (PBS) essential for ERV reverse transcription. We show that the two most active ERV families, IAP and MusD/ETn, are major targets and are strongly inhibited by tRFs in retrotransposition assays. 22 nt tRFs post-transcriptionally silence coding-competent ERVs, while 18 nt tRFs specifically interfere with reverse transcription and retrotransposon mobility. The PBS offers a unique target to specifically inhibit LTR-retrotransposons, and tRF-targeting is a potentially highly conserved mechanism of small RNA-mediated transposon control.
[Mh] Termos MeSH primário: Inativação Gênica
Pequeno RNA não Traduzido/metabolismo
RNA de Transferência/metabolismo
Retroviridae/genética
Células-Tronco/virologia
[Mh] Termos MeSH secundário: Animais
Células HeLa
Seres Humanos
Camundongos
Sequências Repetidas Terminais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Small Untranslated); 9014-25-9 (RNA, Transfer)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170922
[Lr] Data última revisão:
170922
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170701
[St] Status:MEDLINE


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[PMID]:28642606
[Au] Autor:Burns KH
[Ad] Endereço:Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
[Ti] Título:Transposable elements in cancer.
[So] Source:Nat Rev Cancer;17(7):415-424, 2017 Jul.
[Is] ISSN:1474-1768
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.
[Mh] Termos MeSH primário: Transformação Celular Neoplásica/genética
Elementos de DNA Transponíveis
Elementos Nucleotídeos Longos e Dispersos/genética
Neoplasias/genética
Fases de Leitura Aberta/genética
[Mh] Termos MeSH secundário: Seres Humanos
Repetições Minissatélites/genética
Regiões Promotoras Genéticas/genética
RNA/genética
Elementos Nucleotídeos Curtos e Dispersos/genética
Sequências Repetidas Terminais/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (DNA Transposable Elements); 63231-63-0 (RNA)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170823
[Lr] Data última revisão:
170823
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170624
[St] Status:MEDLINE
[do] DOI:10.1038/nrc.2017.35



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