Transcriptional regulation in mammalian cells

项目摘要/摘要： 转录是一个基本的细胞过程，其适当的调控对建立和 维持健康的细胞状态。就像细胞中的许多调节过程一样，转录现在是 被理解为涉及蛋白质和RNA的大集合的动态形成和溶解 被称为生物分子凝聚体的分子。我们的研究计划集中在三个目标上 转录和浓缩的交集，我们相信这将为基因提供重要的新见解 并填补我们对凝析油及其监管的理解中的重要空白。目标1)我们将 测试许多长非编码RNA(LncRNAs)调节转录缩合物的假设 附近的基因。凝析油是由一系列低亲和力的分子相互作用形成的，而RNA可以 成为凝析油动态的有力调节器。数以千计的lncRNA物种在任何一个物种中都有表达 细胞类型，但这些RNA分子中的绝大多数功能尚不清楚。大多数lncRNA是 在10kb的蛋白质编码基因内转录，并似乎在这些位置积累，这表明 其中许多RNA的功能是通过影响局部蛋白质编码基因的表达来调节 局部凝析油形成和溶解的动力学目标2)我们将检验以下假设 凝析液不混溶有助于有效分离活性染色质和静默染色质。核电 细胞的结构包括转录活跃和不活跃的隔间，以及目前的证据 表示这两个隔室形成单独的冷凝物。我们观察到凝析油 由活跃基因和沉默基因的调节器形成的基因是不相容的，并假设这一特性有助于 涉及哺乳动物细胞核中活性和非活性隔间的功能分离。目标3) 我们将探索核凝析的物理化学环境，目标是确定 区分不同凝析油的化学成分类型。凝析油生物学中的一个主要问题是 不同凝析油的化学环境使生物专一性得以实现的程度。我们的 证据表明，小分子可以用来探测内部化学环境， 控制凝析油的行为，从而教会我们不同种类的 可实现生物特异性的缩合物。这些信息还可能提供对 在特定的凝析油中选择性地浓缩小分子的化学特征，这可能使 针对特定凝析油中靶点的药物设计的未来进展。在进行这些操作时 在研究中，我们将继续鉴定常染色质和异染色质的蛋白质和RNA成分 并投资于凝析油动态和转录产量的分析。我们还将 继续在促进合作的环境中培训和指导各种年轻科学家 生物化学、化学和物理领域的顶尖专家。

Project Summary/Abstract  Transcription is a fundamental cellular process whose proper regulation is essential to establishment and maintenance of healthy cell states. As with many regulatory processes in the cell, transcription is now understood to involve the dynamic formation and dissolution of large assemblies of protein and RNA molecules called biomolecular condensates. Our research program is focused on three goals at the intersection of transcription and condensates that we believe will provide important new insights into gene regulation and fill important gaps in our understanding of condensates and their regulation. Goal 1) We will test the hypothesis that many long noncoding RNAs (lncRNAs) regulate transcriptional condensates at nearby genes. Condensates are formed by an ensemble of low-affinity molecular interactions and RNA can be a powerful regulator of condensate dynamics. Thousands of lncRNA species are expressed in any one cell type, but the functions of the vast majority of these RNA molecules are not known. Most lncRNAs are transcribed within 10kb of protein coding genes and appear to accumulate at those loci, suggesting that many of these RNAs function to tune the expression of local protein coding genes by affecting the dynamics of local condensate formation and dissolution. Goal 2) We will test the hypothesis that condensate immiscibility contributes to the functional separation of active and silent chromatin. The nuclear architecture of a cell involves transcriptionally active and inactive compartments, and current evidence indicates that the two compartments form separate condensates. We have observed that condensates formed by regulators of active and silent genes are immiscible and postulate that this property contributes to the functional separation of active and inactive compartments in the nucleus of mammalian cells. Goal 3) We will explore the physicochemical environments of nuclear condensates with the goal of determining the types of chemistries that distinguish diverse condensates. A major issue in condensate biology is the extent to which the chemical environments of diverse condensates enable biological specificity. Our evidence indicates that small molecules can be used to probe the internal chemical environment that governs the behavior of condensates and thus teach us about the internal chemistry of diverse condensates that may enable biological specificity. This information may also provide insights into the chemical features that selectively concentrate small molecules in specific condensates, which may enable future advances in drug design for targets that reside in specific condensates. While conducting these studies, we will continue to identify protein and RNA components of euchromatic and heterochromatin condensates and to invest in assays of condensate dynamics and transcriptional output. We will also continue to train and mentor diverse young scientists in an environment that facilitates collaboration with leading experts in biochemistry, chemistry and physics.