Uncovering the regulatory logic of gene expression encoded by disordered regions

揭示无序区域编码的基因表达的调控逻辑

• 批准号: 10687601
• 负责人: Alex S Holehouse
• 金额: $ 139.95万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10687601
• 关键词: Automobile Driving; Binding; Binding Sites; Bioinformatics; Cell physiology; Cells; Complex; Consensus; DNA; DNA Binding; DNA Binding Domain; DNA Folding; Disease; Event; Gene Expression; Genes; Goals; Growth; Homeostasis; Immune response; In Vitro; Libraries; Logic; Malignant Neoplasms; Mediating; Molecular; Mutation; Nerve Degeneration; Pathologic; Play; Proteins; Regulation; Resolution; Role; Virus Diseases; cofactor; design; disease-causing mutation; human disease; in silico; interest; loss of function; novel; recruit; therapeutically effective; transcription factor

Cellular state, identity, and function are primarily determined by the genes expressed at a given moment. Many diseases are characterized by dysregulation of gene expression, leading to inappropriate gain/loss of function that can drive proliferative growth (cancer), impede homeostasis (neurodegeneration), or rewire the immune response (viral infection). Limitations in our understanding of the complex, pleiotropic, and inherently adaptive molecular mechanisms that underlie pathological changes in gene expression are a significant barrier to our ability to design effective therapeutic strategies to alleviate these conditions. Eukaryotic gene expression is a coordinated event driven by an array of cellular processes. Among the various molecular components, transcription factors are arguably the core determinant of expression. Transcription factors are modular proteins that possess DNA-specific binding domains and facilitate the recruitment of additional co-factors that drive (or occasionally suppress) gene expression. Our understanding of how the folded DNA binding domains recognize consensus DNA binding sites is relatively mature. In contrast, we lag behind in a high-resolution understanding of other domains' various roles. Of particular interest, transcription factors are enriched for intrinsically disordered regions. These regions are often considered to play a role in driving gene expression as “activation domains” - regions that determine the strength of gene expression. However, both numerous high-throughput studies and systematic bioinformatic analyses predict that, on average, only 15% of any given transcription factor is strictly required for robust gene expression. This raises a question: what is the remaining 85% of each transcription factor IDR doing? This proposal centers on the discovery that transcription factor IDRs play a second, previously unappreciated role in coordinating gene expression. We will dissect this new role to decode the underlying molecular logic. This will involve using rational sequence design to probe the sequence-determinants of gene expression through a novel library-based approach. This will be combined with in vitro and in silico analyses to disentangle the molecular basis for our observations. Our ultimate goal is to understand how the mutations that appear in transcription factors IDRs can alter gene expression in non-intuitive and pathological ways.

细胞的状态、身份和功能主要由在给定的转录水平上表达的基因决定。 时刻.许多疾病的特征在于基因表达的失调，导致 不适当的功能获得/丧失，可驱动增殖性生长（癌症），阻碍 体内平衡（神经变性）或重新连接免疫反应（病毒感染）。局限性 我们对复杂、多效性和内在适应性分子机制的理解 基因表达病理变化的基础是一个重要的障碍， 设计有效的治疗策略来缓解这些情况。 真核基因表达是一系列细胞过程驱动的协调事件。 在各种分子组成中，转录因子可以说是核心 表达的决定因素。转录因子是具有DNA特异性的模块化蛋白质， 结合结构域，并促进募集额外的辅因子， 抑制）基因表达。我们对折叠的DNA结合结构域 识别共有DNA结合位点的技术相对成熟。相比之下，我们在 对其他域的各种角色的高分辨率理解。特别令人感兴趣的是， 转录因子富含固有无序区域。这些地区往往 被认为在驱动基因表达中发挥作用的“激活结构域”-区域， 决定基因表达的强度。然而，大量的高通量研究 系统的生物信息学分析预测，平均而言， 转录因子是稳健基因表达的严格要求。这就提出了一个问题： 剩下的85%的每个转录因子IDR在做什么？ 这项提议的核心是发现转录因子IDRs在转录过程中起着第二个作用， 在协调基因表达中未被重视的作用。我们将剖析这个新角色， 潜在的分子逻辑这将涉及使用合理的序列设计来探测 序列决定因素的基因表达通过一种新的图书馆为基础的方法。这将是 结合体外和计算机分析，解开我们的分子基础， 意见。我们的最终目标是了解转录中出现的突变 IDRs可以以非直观和病理性的方式改变基因表达。