Evidence map›Paper›PMID 24872592›Full record

ArticleJournal of virology2014

Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein.

Marta J Gonzalez-Hernandez, James D Cavalcoli, Maureen A Sartor, Rafael Contreras-Galindo, Fan Meng, Manhong Dai, Derek Dube, Anjan K Saha, Scott D Gitlin, Gilbert S Omenn and 2 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of virology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.

0numbers the graph read from it
0cells of the map it votes in
58citing papers in PubMed
10.7field-weighted citation impact, top 2% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

58 citing papers in PubMed, 71 citations in OpenAlex.

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  15. Human endogenous retroviruses and exogenous viral infections.Frontiers in cellular and infection microbiology · 2024
    Review
  16. Article
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  18. Article
  19. Retroviral Elements in Pathophysiology and as Therapeutic Targets for Amyotrophic Lateral Sclerosis.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2022
    Review
  20. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 1 institution in 1 country.

Marta J Gonzalez-HernandezDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA.
James D CavalcoliCenter for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
Maureen A SartorCenter for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA School of Public Health, University of Michigan, Ann Arbor, Michigan, USA.
Rafael Contreras-GalindoDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
Fan MengCenter for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, USA.
Manhong DaiCenter for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, USA.
Derek DubeDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
Anjan K SahaDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
Scott D GitlinDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Department of Veterans Affairs, University of Michigan, Ann Arbor, Michigan, USA.
Gilbert S OmennDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA School of Public Health, University of Michigan, Ann Arbor, Michigan, USA National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, Michigan, USA Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Mark H KaplanDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
David M MarkovitzDepartment of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan, USA Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, USA dmarkov@umich.edu.
University of Michigan–Ann Arbor · US

Funding

MICHIGAN INSTITUTE FOR CLINICAL AND HEALTH RESEARCH (MICHR) (UL1): (BPCA)UL1RR024986 · NCRR · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI SHANLEY, THOMAS P. · 2007 to 2011
$51.2M
MICHIGAN MEDICAL SCIENTIST TRAINING PROGRAMT32GM007863 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI COLLINS, KATHLEEN L. · 1985 to 2024
$38.3M
Strategic Vision & Impact on Environmental HealthP30ES017885 · NIEHS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Dana Dolinoy · 2011 to 2026
$21.3M
Nation Center- Integrative Biomedical Informatics(RMI)U54DA021519 · NIDA · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ATHEY, BRIAN DAVID · 2005 to 2010
$21.3M
Molecular Mechanisms of Microbial Pathogenesis Training ProgramT32AI007528 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI CARRUTHERS, VERNON BRUCE · 1998 to 2024
$6.8M
Replication of Human Endogenous Retroviruses in Modern HumansR01CA144043 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI MARKOVITZ, DAVID MICHAEL · 2009 to 2013
$6.4M
CXC Chemokines and HIV PathogenesisR01AI062248 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI MARKOVITZ, DAVID MICHAEL · 2005 to 2009
$1.6M
Role of HIV-1 Tat in the activation of HERV-K and development of HIV-1-lymphomaF31CA150523 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI GONZALEZ-HERNANDEZ, MARTA JEANNETTE · 2010 to 2011
$65k
NCI NIH HHS 1F31CA150523NCI NIH HHS 3R01CA144043-03S1NCI NIH HHS F31 CA150523NCI NIH HHS R01 CA144043NCI NIH HHS R01CA144043NCRR NIH HHS UL1 RR024986NCRR NIH HHS UL1RR24986NIAID NIH HHS 5T32AI007528NIAID NIH HHS R01 AI062248NIAID NIH HHS R01AI062248NIAID NIH HHS T32 AI007528NIDA NIH HHS U54 DA021519NIDA NIH HHS U54DA021519NIEHS NIH HHS P30 ES017885NIEHS NIH HHS P30U54ES017885NIGMS NIH HHS T32 GM007863RMOD NIH HHS RM-08-029
6 · The paper itself

Abstract

unlabelledApproximately 8% of the human genome is made up of endogenous retroviral sequences. As the HIV-1 Tat protein activates the overall expression of the human endogenous retrovirus type K (HERV-K) (HML-2), we used next-generation sequencing to determine which of the 91 currently annotated HERV-K (HML-2) proviruses are regulated by Tat. Transcriptome sequencing of total RNA isolated from Tat- and vehicle-treated peripheral blood lymphocytes from a healthy donor showed that Tat significantly activates expression of 26 unique HERV-K (HML-2) proviruses, silences 12, and does not significantly alter the expression of the remaining proviruses. Quantitative reverse transcription-PCR validation of the sequencing data was performed on Tat-treated PBLs of seven donors using provirus-specific primers and corroborated the results with a substantial degree of quantitative similarity. IMPORTANCE: The expression of HERV-K (HML-2) is tightly regulated but becomes markedly increased following infection with HIV-1, in part due to the HIV-1 Tat protein. The findings reported here demonstrate the complexity of the genome-wide regulation of HERV-K (HML-2) expression by Tat. This work also demonstrates that although HERV-K (HML-2) proviruses in the human genome are highly similar in terms of DNA sequence, modulation of the expression of specific proviruses in a given biological situation can be ascertained using next-generation sequencing and bioinformatics analysis.

Indexed as

Cells, CulturedEndogenous RetrovirusesGene Products, tatGenome, HumanHigh-Throughput Nucleotide SequencingHIV-1HIV InfectionsHumansLymphocytesProvirusesRNA, ViralTranscriptomeViral ProteinsGene Products, tatRNA, ViralViral Proteins

Identifiers

PMID24872592
PMCPMC4136263
OpenAlexW2110016010

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.