Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication
Ming Li, … , Michelle A. Lally, Bharat Ramratnam
Ming Li, … , Michelle A. Lally, Bharat Ramratnam
Published July 25, 2016
Citation Information: J Clin Invest. 2016;126(8):3117-3129. https://doi.org/10.1172/JCI82360.
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Research Article AIDS/HIV

Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication

Abstract

A rare subset of HIV-1–infected individuals is able to maintain plasma viral load (VL) at low levels without antiretroviral treatment. Identifying the mechanisms underlying this atypical response to infection may lead to therapeutic advances for treating HIV-1. Here, we developed a proteomic analysis to compare peripheral blood cell proteomes in 20 HIV-1–infected individuals who maintained either high or low VL with the aim of identifying host factors that impact HIV-1 replication. We determined that the levels of multiple histone proteins were markedly decreased in cohorts of individuals with high VL. This reduction was correlated with lower levels of stem-loop binding protein (SLBP), which is known to control histone metabolism. Depletion of cellular SLBP increased promoter engagement with the chromatin structures of the host gene high mobility group protein A1 (HMGA1) and viral long terminal repeat (LTR), which led to higher levels of HIV-1 genomic integration and proviral transcription. Further, we determined that TNF-α regulates expression of SLBP and observed that plasma TNF-α levels in HIV-1–infected individuals correlated directly with VL levels and inversely with cellular SLBP levels. Our findings identify SLBP as a potentially important cellular regulator of HIV-1, thereby establishing a link between histone metabolism, inflammation, and HIV-1 infection.

Authors

Ming Li, Lynne D. Tucker, John M. Asara, Collins K. Cheruiyot, Huafei Lu, Zhijin J. Wu, Michael C. Newstein, Mark S. Dooner, Jennifer Friedman, Michelle A. Lally, Bharat Ramratnam

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Figure 5

Impact of SLBP depletion on HMGA1 and HIV-1 promoter activity and transcription factor accessibility.

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Impact of SLBP depletion on HMGA1 and HIV-1 promoter activity and transc...
(A) ChIP assay revealed that the transcription factor SP1 had higher binding affinity to specific promoter regions of HMGA1 upon SLBP depletion with relative enrichment of binding in the region –358 to –213 (P < 0.01). This was in agreement with predicted (EpiTect ChIP; Qiagen) SP1 binding sites (–289 to –278). (B) ChIP assay showed that the transcription factor SP1 also had higher binding affinity to specific regions of the HIV-1 promoter (or LTR). SP1 binding was enriched in the region of –153 to –22 (P < 0.05). The bottom schematic diagram shows the known binding regions of SP1 to HIV-1 LTR (http://www.hiv.lanl.gov/). (C) SLBP depletion was associated with higher transcription factor accessibility of promoter regions of both HMGA1 and HIV-1 as defined by EpiQ assay in both HeLa-T4 cells (left panel) and CEM cells (right panel). Real-time PCR was carried out using EpiQ primers specifically designed for human HMGA1 and HIV-1, respectively, and promoter accessibility (%) was quantified. Each heat map was based on 3 independent accessibility values from both the nontarget control and the SLBP experimental arm. Green represents high accessibility, while red represents low accessibility. GAPDH (constitutively expressed, fully accessible) was used as the control. Student’s t test; *P < 0.05, **P < 0.01; error bars represent ± SD.