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Association between ALS and retroviruses: evidence from bioinformatics analysis

Jon P. Klein, Zhifu Sun, Nathan P. Staff
2019 BMC Bioinformatics  
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

V. Blikstad, F. Benachenhou, G. O. Sperber, J. Blomberg
2008 Cellular and Molecular Life Sciences (CMLS)  
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 , unpublished].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

Anton Buzdin
2007 The Scientific World Journal  
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

Patric Jern, John M. Coffin
2008 Annual Review of Genetics  
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

J. Li, K. Akagi, Y. Hu, A. L. Trivett, C. J. W. Hlynialuk, D. A. Swing, N. Volfovsky, T. C. Morgan, Y. Golubeva, R. M. Stephens, D. E. Smith, D. E. Symer
2012 Genome Research  
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

R. Contreras-Galindo, M. H. Kaplan, S. He, A. C. Contreras-Galindo, M. J. Gonzalez-Hernandez, F. Kappes, D. Dube, S. M. Chan, D. Robinson, F. Meng, M. Dai, S. D. Gitlin (+3 others)
2013 Genome Research  
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]

Marie E Jonsson, Raquel Garza, Yogita Sharma, Rebecca Petri, Erik Sodersten, Jenny G Johansson, Pia A Johansson, Diahann AM Atacho, Karolina Pircs, Sofia Madsen, David Yudovich, Ramprasad Ramakrishnan (+4 others)
2020 bioRxiv   pre-print
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]

Akihiko Sakashita, So Maezawa, Kris G Alavattam, Masashi Yukawa, Artem Barski, Mihaela Pavlicev, Satoshi H Namekawa
2020 bioRxiv   pre-print
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]

Xiaoqian Liu, Zunpeng Liu, Liang Sun, Jie Ren, Zeming Wu, Xiaoyu Jiang, Qianzhao Ji, Qianran Wang, Yanling Fan, Yusheng Cai, Si Wang, Wei Li (+6 others)
2021 bioRxiv   pre-print
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

Maria Tokuyama, Yong Kong, Eric Song, Teshika Jayewickreme, Insoo Kang, Akiko Iwasaki
2018 Proceedings of the National Academy of Sciences of the United States of America  
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

Rita Rebollo, Katharine Miceli-Royer, Ying Zhang, Sharareh Farivar, Liane Gagnier, Dixie L Mager
2012 Genome Biology  
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

Paul D. W. Kirk, Maxime Huvet, Anat Melamed, Goedele N. Maertens, Charles R. M. Bangham
2016 Nature Microbiology  
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

Batmagnai E, Erik Bongcam-Rudloff, Matthew Peter Kent, Göran Andersson
2018 Mongolian Journal of Agricultural Sciences  
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

Gkikas Magiorkinis, Daniel Blanco-Melo, Robert Belshaw
2015 Retrovirology  
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

Patricia K. Penton, Jason T. Blackard
2014 AIDS Research and Human Retroviruses  
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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