Data_Sheet_3_Genome-Wide Characterization of Host Transcriptional and Epigenetic Alterations During HIV Infection of T Lymphocytes.pdf

Background and methods: Host genomic alterations are closely related to dysfunction of CD4+ T lymphocytes in the HIV–host interplay. However, the roles of aberrant DNA methylation and gene expression in the response to HIV infection are not fully understood. We investigated the genome-wide DNA methylation and transcriptomic profiles in two HIV-infected T lymphocyte cell lines using high-throughput sequencing.
Results: Based on DNA methylation data, we identified 3,060 hypomethylated differentially methylated regions (DMRs) and 2,659 hypermethylated DMRs in HIV-infected cells. Transcription-factor-binding motifs were significantly associated with methylation alterations, suggesting that DNA methylation modulates gene expression by affecting the binding to transcription factors during HIV infection. In support of this hypothesis, genes with promoters overlapping with DMRs were enriched in the biological function related to transcription factor activities. Furthermore, the analysis of gene expression data identified 1,633 upregulated genes and 2,142 downregulated genes on average in HIV-infected cells. These differentially expressed genes (DEGs) were significantly enriched in apoptosis-related pathways. Our results suggest alternative splicing as an additional mechanism that may contribute to T-cell apoptosis during HIV infection. We also demonstrated a genome-scale correlation between DNA methylation and gene expression in HIV-infected cells. We identified 831 genes with alterations in both DNA methylation and gene expression, which were enriched in apoptosis. Our results were validated using various experimental methods. In addition, consistent with our in silico results, a luciferase assay showed that the activity of the PDX1 and SMAD3 promoters was significantly decreased in the presence of HIV proteins, indicating the potential of these genes as genetic markers of HIV infection.
Conclusions: Our results suggest important roles for DNA methylation and gene expression regulation in T-cell apoptosis during HIV infection. We propose a list of novel genes related to these processes for further investigation. This study also provides a comprehensive characterization of changes occurring at the transcriptional and epigenetic levels in T cells in response to HIV infection.

研究背景与方法：宿主基因组改变与HIV-宿主相互作用过程中CD4+ T淋巴细胞（CD4+ T lymphocytes）的功能异常密切相关。然而，在HIV感染应答过程中，异常DNA甲基化与基因表达所发挥的作用尚未完全阐明。本研究采用高通量测序（high-throughput sequencing）技术，对两株HIV感染T淋巴细胞系的全基因组DNA甲基化与转录组谱进行了分析。
研究结果：基于DNA甲基化数据，本研究在HIV感染细胞中鉴定出3060个低甲基化差异甲基化区域（differentially methylated regions, DMRs）以及2659个高甲基化DMRs。转录因子结合基序（transcription-factor-binding motifs）与甲基化改变显著相关，这提示在HIV感染过程中，DNA甲基化可通过影响转录因子的结合来调控基因表达。为验证这一假说，启动子区域与DMRs重叠的基因显著富集于与转录因子活性相关的生物学功能通路中。此外，对基因表达数据的分析显示，HIV感染细胞中平均存在1633个上调基因与2142个下调基因。这些差异表达基因（differentially expressed genes, DEGs）显著富集于凋亡相关通路。本研究结果提示，可变剪接（alternative splicing）可能是HIV感染过程中介导T细胞凋亡的另一潜在机制。本研究还证实了HIV感染细胞中DNA甲基化与基因表达之间存在全基因组范围的相关性。本研究鉴定出831个同时存在DNA甲基化与基因表达改变的基因，这些基因显著富集于凋亡相关生物学过程。本研究结果通过多种实验方法得到了验证。此外，与本研究的计算机模拟分析（in silico）结果一致，萤光素酶实验（luciferase assay）显示，在HIV蛋白存在的情况下，PDX1与SMAD3的启动子活性显著降低，这表明这些基因可作为HIV感染的潜在遗传标志物。
研究结论：本研究结果表明，DNA甲基化与基因表达调控在HIV感染过程中的T细胞凋亡过程中发挥重要作用。本研究提出了一系列与上述过程相关的新基因，以供后续研究探索。本研究还全面刻画了T细胞在应对HIV感染时，转录组与表观基因组层面发生的一系列变化。