Using Single-Cell Data to Decipher Mechanisms of NF-kB-chromatin-mediated HIV Transcriptional Regulation

使用单细胞数据破译 NF-kB 染色质介导的 HIV 转录调控机制

• 批准号: 1264246
• 负责人: Kathryn Miller-Jensen
• 金额: $ 31.18万
• 依托单位: Yale University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-08-01 至 2016-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1264246&HistoricalAwards=false
• 关键词: Using; Single; Cell; Data; Decipher

1264246Miller-Jensen, Kathryn Genetically identical cells can display significant phenotypic heterogeneity as a result of random fluctuations (noise) in gene expression, which is modulated by transcription factor binding and chromatin modifications at each gene promoter. The interaction of chromatin and transcription factors is especially evident among mammalian retroviruses, such as the human immunodeficiency virus-1 (HIV), which integrate semi-randomly into the genome of their host's DNA and depend on host regulatory factors to initiate viral gene expression and complete replication. In the case of HIV, noisy viral gene expression results in transcriptional delays that may be a precursor for latent infections. Latent HIV currently prevents complete eradication of the virus in a patient, and reversing viral latency via activation of the latent HIV reservoir is a promising therapeutic strategy. However, an incomplete understanding of the complex mechanisms underlying chromatin- and transcription factor-mediated regulation of HIV hinders progress. To address this knowledge gap, the proposed project integrates experimental and computational approaches to study how the canonical transcription factor NF-kB and the local chromatin environment at the viral integration site together regulate activation of the latent HIV LTR promoter. The inability to target and purge latent (i.e., silent) HIV-infected cells is currently the biggest obstacle to a cure, and this proposal seeks to address this significant public health problem. By integrating single-cell experiments and computational modeling, this research will improve understanding of how protein-DNA interactions called chromatin regulate HIV-1 transcription, and will further progress towards eradication of the latent viral reservoir. This work may also advance knowledge of mechanisms of chromatin-mediated transcriptional regulation more broadly, with the potential to impact immunology, development, and cancer. In addition, two educational initiatives are proposed to broaden participation of under-represented minority engineering students in interdisciplinary research through summer research fellowships; and to contribute to transformative teaching approaches at the interface of the biological and physical sciences through design of a new discussion session for an interdisciplinary graduate course.

1264246Miller-Jensen，Kathryn基因相同的细胞可以由于基因表达的随机波动(噪声)而表现出显著的表型异质性，这是由每个基因启动子上的转录因子结合和染色质修饰调节的。染色质和转录因子的相互作用在哺乳动物逆转录病毒中尤其明显，例如人类免疫缺陷病毒-1(HIV)，它们半随机地整合到宿主DNA的基因组中，依赖宿主调节因子启动病毒基因表达和完成复制。就艾滋病毒而言，嘈杂的病毒基因表达会导致转录延迟，这可能是潜在感染的前兆。潜伏的艾滋病毒目前阻止了患者体内病毒的完全根除，通过激活潜伏的艾滋病毒储存库来逆转病毒潜伏是一种很有前途的治疗策略。然而，对染色质和转录因子介导的HIV调控的复杂机制的不完全理解阻碍了进展。为了解决这一知识差距，拟议的项目结合了实验和计算方法，以研究规范转录因子NF-kB和病毒整合部位的局部染色质环境如何共同调节潜在HIV LTR启动子的激活。无法瞄准和清除潜伏的(即沉默的)艾滋病毒感染细胞是目前治愈艾滋病毒的最大障碍，这项提议旨在解决这一重大的公共卫生问题。通过结合单细胞实验和计算模型，这项研究将提高对称为染色质的蛋白质-DNA相互作用如何调控HIV-1转录的理解，并将进一步朝着根除潜在的病毒库迈进。这项工作还可能在更广泛的范围内促进对染色质介导的转录调控机制的了解，并有可能影响免疫学、发育和癌症。此外，还提出了两项教育举措，通过暑期研究奖学金扩大未占名额的少数族裔工程专业学生对跨学科研究的参与；通过为跨学科研究生课程设计新的讨论会，促进生物和物理科学相结合的变革性教学方法。