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

Human Genomics
Kyung-Chang KimByeong-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 selecte...Continue Reading

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Citations

Jul 31, 2018·AIDS Research and Human Retroviruses·Sergio Castro-GonzalezRuth Serra-Moreno
Oct 2, 2019·Frontiers in Genetics·Sigrid Le ClercJean-François Zagury
Apr 4, 2020·BMC Medical Genomics·Seyoun ByunYounghee Lee

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Methods Mentioned

BETA
acetylation
ChIP-seq
SeT
PCR
PMA
reverse transcription PCR

Software Mentioned

CEAS
SICER
Pathway Commons Network Visualizer
WebGestalt )
WebGestalt
GEne SeT AnaLysis Toolkit (
PCViz
7500
idiographica
Pathway Commons

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