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Identification of novel genes associated with HIV-1 latency by analysis of histone modifications

Overview of attention for article published in Human Genomics, May 2017
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Title
Identification of novel genes associated with HIV-1 latency by analysis of histone modifications
Published in
Human Genomics, May 2017
DOI 10.1186/s40246-017-0105-7
Pubmed ID
Authors

Kyung-Chang Kim, Sunyoung Lee, Junseock Son, Younghyun Shin, Cheol-Hee Yoon, Chun Kang, Byeong-Sun Choi

Abstract

A reservoir of HIV-1 is a major obstacle in eliminating HIV-1 in patients because it can reactivate in stopping antiretroviral therapy (ART). Histone modifications, such as acetylation and methylation, play a critical role in the organization of chromatin domains and the up- or downregulation of gene expression. Although many studies have reported that an epigenetic mechanism is strongly involved in the maintenance of HIV-1 transcriptional latency, neither the epigenetic control of viral replication nor how HIV-1 latency is maintained is not fully understood. We re-analyzed a high throughput parallel DNA sequencing (ChIP-seq) data from previous work to investigate the effect of histone modifications, H3K4me3 and H3K9ac, on HIV-1 latency in terms of chromosome distribution. The outputs of ChIP-seq from uninfected CD4+ T cell lines and HIV-1 latently infected cells were aligned to hg18 using bowtie and then analyzed using various software packages. Certain chromosomes (16, 17, 19, and 22) were significantly enriched for histone modifications in both decreased and increased islands. In the same chromosomes in HIV-1 latently infected cells, 38 decreased and 41 increased islands from common islands of H3K4me3 and H3K9ac were selected for functional annotation. In Gene Ontology analysis, the 38 genes associated with decreased islands were involved in the regulation of biological process, regulation of cellular process, biological regulation, and purinergic receptor signaling pathway, while the 41 genes associated with increased islands were involved in nucleic acid binding, calcium-activated cation channel activity, DNA binding, and zinc ion binding. In Pathway Commons analysis, the 38 genes were strongly involved in the p63 transcription factor network, while the 41 genes were involved in the RNA polymerase III transcription termination pathway. Several genes such as Nuclear factor I X (NFIX) and TNF receptor association factor 4 (TRAF4) were selected as candidate genes for HIV latency. Especially, NFIX was highly expressed in HIV-1 latently infected cell lines and showed a dramatic reduction in expression after phorbol-13-myristate-12-acetate (PMA) treatment. These results show that the unique enrichment of histone modifications and its linked genes in specific chromosomes might play a critical role in the establishment and maintenance of HIV-1 latency.

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Mendeley readers

The data shown below were compiled from readership statistics for 25 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 25 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 5 20%
Student > Ph. D. Student 4 16%
Student > Bachelor 4 16%
Student > Postgraduate 3 12%
Student > Doctoral Student 1 4%
Other 1 4%
Unknown 7 28%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 6 24%
Agricultural and Biological Sciences 5 20%
Immunology and Microbiology 2 8%
Pharmacology, Toxicology and Pharmaceutical Science 1 4%
Unspecified 1 4%
Other 1 4%
Unknown 9 36%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 May 2017.
All research outputs
#14,676,177
of 16,639,069 outputs
Outputs from Human Genomics
#300
of 327 outputs
Outputs of similar age
#229,986
of 270,667 outputs
Outputs of similar age from Human Genomics
#1
of 1 outputs
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