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Association between ALS and retroviruses: evidence from bioinformatics analysis
2019
BMC Bioinformatics
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Bioinformatics analysis provides evidence to support pathological links between ALS and retroviral activation. The neuroinflammation and apoptotic regulation pathways are specifically implicated. ...
We explore whether connections exist between ALS and retroviruses through protein interaction networks (PIN) and pathway analysis, and consider the potential roles in drug target discovery. ...
Associations between ALS, HIV, Polio and West Nile virus protein interaction networks As evidence has shown associations between HIV and ALS, we applied the same analytical approach to generate a PIN for ...
doi:10.1186/s12859-019-3249-8
pmid:31861978
pmcid:PMC6923964
fatcat:qj6mjod4bvdcnmgveapecdc7ha
Endogenous retroviruses
2008
Cellular and Molecular Life Sciences (CMLS)
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Data from a RetroTector (see the section on bioinformatics) analysis of the chicken, human, chimpanzee and dog genomes, and from the literature, as specified in [32]
This genomic quasispecies is not static ...
An almost intact HERVT-like sequence in the opossum genome (monDom4) on chromosome | [Blomberg et al. , unpublished]. From RetroTector (see the section on bioinformatics). ...
doi:10.1007/s00018-008-8495-2
pmid:18818874
fatcat:734t4hzrcnhhvhr2s6hxrz4f6a
Human-Specific Endogenous Retroviruses
2007
The Scientific World Journal
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This information is given here in the context of other major genomic changes underlining differences between human and chimpanzee DNAs. ...
Finally, a comprehensive database, is available for download, of human-specific and polymorphic endogenous retroviruses is presented, which encompasses the data on their genomic localization, primary structure ...
In this respect, the genome-wide bioinformatical recovery of lineage-specific TEs, recently performed by Devine and associates [11] , provides an instrument for both quantitative and qualitative analysis ...
doi:10.1100/tsw.2007.270
pmid:18060323
pmcid:PMC5901341
fatcat:jjcepaxilrfgvnqjbqmxcvua5a
Effects of Retroviruses on Host Genome Function
2008
Annual Review of Genetics
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A paradigm for virus-host coevolution:
sequential counter-adaptations between endogenous and exogenous retroviruses. ...
(64) and some cell lines derived from
cancers and various neurodegenerative disor- HTLV-associated tumors (20), activation of a
ders has been debated. ...
doi:10.1146/annurev.genet.42.110807.091501
pmid:18694346
fatcat:renm3eekhraafpbnsfnsnskppe
Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
2012
Genome Research
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Analysis of expression quantitative trait loci (eQTLs) in recombinant BxD mouse strains demonstrated very strong genetic associations between the polymorphic ERV in cis and disrupted transcript levels. ...
Premature polyadenylation is triggered at genomic distances up to >12.5 kb upstream of the ERV, both in cis and between alleles. ...
NCI-Frederick and OSU are accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International and follow the U.S. ...
doi:10.1101/gr.130740.111
pmid:22367191
pmcid:PMC3337433
fatcat:uy63utxwnbgknekibsyzcpnkgm
HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses
2013
Genome Research
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The following reagents were obtained through the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH: HIV-1 BAL, ADA, 89.6, NL4.3, and HIV Tat86. ...
We thank Martin Kircher for access to the Neanderthal and Denisovan sequence reads. This work was supported by a generous grant (05-5089) ...
Evidence from recombinant sequences (i.e., clones 1A6, 7A6, and 14A4) also suggests that interchromosomal recombination occurred between certain chromosomes. ...
doi:10.1101/gr.144303.112
pmid:23657884
pmcid:PMC3759726
fatcat:6jnlmkjm75fq3avpi5ffcp4ncy
Activation of endogenous retroviruses during brain development causes neuroinflammation
[article]
2020
bioRxiv
pre-print
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Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. ...
This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results ...
Acknowledgements We would like to thank Molly Gale Hammell, Magdalena Götz, Sten Linnarsson, Chris Douse, Florence Cammas and Bryan Cullen for providing valuable reagents and input on the manuscript. ...
doi:10.1101/2020.07.07.191668
fatcat:trzhbgbclfb3hg6ep6yj6kmdnm
Endogenous retroviruses drive species-specific germline transcriptomes in mammals
[article]
2020
bioRxiv
pre-print
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We show that the expression of endogenous retroviruses, particularly the evolutionarily young K family (ERVK), is associated with gene activation after the mitosis-to-meiosis transition in male mice. ...
We demonstrate that accessible chromatin and H3K27ac, a marker of active enhancers, are tightly associated with ERVK loci as well as with the activation of neighboring evolutionarily young germline genes ...
Figure 6 . 6 A subset of human ERVKs and ERV1s are associated with meiotic gene expression in humans.
), providing further evidence that ERVKs have enhancer-like features. ...
doi:10.1101/2020.03.11.987230
fatcat:zphg6jfnvrcjlfcef7zed4jl7q
Resurrection of human endogenous retroviruses during aging reinforces senescence
[article]
2021
bioRxiv
pre-print
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Moreover, endogenous retrovirus expression is increased in aged human tissues and serum from the elderly. ...
ABSTRACTHuman endogenous retroviruses (HERVs) are under strict control by the host surveillance system but can become awakened under pathological conditions. ...
Al-Abed, Endogenous retroviruses are associated with hippocampus-based memory impairment. ...
doi:10.1101/2021.02.22.432260
fatcat:jzsygcu54zh3hcsgmr7o2jlx5y
ERVmap analysis reveals genome-wide transcription of human endogenous retroviruses
2018
Proceedings of the National Academy of Sciences of the United States of America
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Endogenous retroviruses (ERVs) are integrated retroviral elements that make up 8% of the human genome. However, the impact of ERVs on human health and disease is not well understood. ...
Use of ERVmap across a range of diseases and experimental conditions has the potential to uncover novel disease-associated antigens and effectors involved in human health that is currently missed by focusing ...
This work was supported in part by grants provided by AbbVie (to A.I.); a Translation Accelerator grant from the Brigham and Women's Hospital (to A.I.); Roslyn and Jerome Meyer Pilot Awards for Research ...
doi:10.1073/pnas.1814589115
pmid:30455304
pmcid:PMC6294949
fatcat:l24evcbuezastk4q2wr2kbbeoq
Epigenetic interplay between mouse endogenous retroviruses and host genes
2012
Genome Biology
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To better understand the role of DNA methylation in the relationship between transposable elements and genes, we assessed the methylation state of mouse endogenous retroviruses (ERVs) located near genes ...
Spreading from methylated ERV copies to nearby genes was rarely observed, with the regions between the ERVs and genes apparently acting as a boundary, enriched in H3K4me3 and CTCF, which possibly protects ...
This work was supported by a grant from the Canadian Institutes of Health Research to DLM with core support provided by the BC Cancer Agency. ...
doi:10.1186/gb-2012-13-10-r89
pmid:23034137
pmcid:PMC3491417
fatcat:e2hgfkhdwjdf5pmg52gjdbzsyi
Retroviruses integrate into a shared, non-palindromic DNA motif
2016
Nature Microbiology
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Palindromic consensus 19 nucleotide sequences are also found at the genomic integration sites of retroviruses 2-6 and 20 other transposable elements 7-9 , and it has been suggested that this palindromic ...
These preferences are evident on at least three scales: 46 chromatin conformation and intranuclear location; proximity to specific genomic features such 47 as transcription start sites or transcription ...
Muller and Varmus 155 28 concluded that the bendability of DNA could explain the preferential integration of certain 156 retroviruses in DNA associated with nucleosomes. ...
doi:10.1038/nmicrobiol.2016.212
pmid:27841853
fatcat:fvvbgy6oivdpfo6aaffpcwybeu
The identification and classification of endogenous retroviruses in the horse genome
2018
Mongolian Journal of Agricultural Sciences
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Endogenous retroviruses (ervs) are sequences that derived from ancient retroviral infections of germ cells and integrated in humans, mammals and other vertebrates millions years ago. ...
endogenous retroviruses have been revealed using ltr_struc tool and double checked by retrotector online tool and ncbi-blast tool. ...
Many microsatellites are closely associated with and generated by retrotransposons like LINEs and SINEs (Arcot et al. 1995; Nadir et al. 1996; Wilder and Hollocher 2001; Yandava et al. 1997 ). ...
doi:10.5564/mjas.v23i01.1012
fatcat:6f3gvzxnrbdadlgp7mnngc2sc4
The decline of human endogenous retroviruses: extinction and survival
2015
Retrovirology
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Endogenous Retroviruses (ERVs) are retroviruses that over the course of evolution have integrated into germline cells and eventually become part of the host genome. ...
The human genome differs from that of related species both in maintaining up until at least recently a replicating old ERV lineage and in not having acquired any new lineages. ...
This work was supported by The Wellcome Trust (RB), and an MRC Clinician Scientist Fellowship (GM). ...
doi:10.1186/s12977-015-0136-x
pmid:25640971
pmcid:PMC4335370
fatcat:mkbhvve7g5c27nhch3bah7tuqq
Analysis of HIV Quasispecies Suggests Compartmentalization in the Liver
2014
AIDS Research and Human Retroviruses
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An increasing body of evidence suggests that HIV infection is associated with exacerbated liver fibrosis and that HIV has the ability to infect several hepatic cell types. ...
Statistical evidence of HIV compartmentalization in the liver was demonstrated in 85.4% of comparisons. Signature sequence analysis identified several liver-specific amino acids in all patients. ...
Eleanor Powell for her review of this manuscript and the University Honors Program for funding this summer undergraduate research project and for facilitating interactions between College of Medicine faculty ...
doi:10.1089/aid.2013.0146
pmid:24074301
pmcid:PMC5972776
fatcat:s4rsmlxwnfb5vce37i4tzyprpm
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