Chromatin regulation of epithelial stem cell function

摘要 茎是一种功能性细胞属性，由多能性(产生所有 组织中分化的细胞类型)和自我更新(产生新干细胞的能力)。在成体上皮中 在组织中，干细胞可以存在于：(1)专用干细胞占据特定的生态位，和(2)分化的细胞 表现出可塑性，以推动受伤后的再生。干细胞必须在自我更新和 分化，分化的细胞必须在谱系特异性和可塑性之间取得平衡才能参与 再生反应。我的实验室感兴趣的是了解染色质修饰及其相关的 酶与位点特异性转录因子(TF)相互作用，同时建立细胞身份 促进了细胞命运的更替。我们专注于肠道干细胞(ISCs)，它驱动肠道的更新 在整个成年生活中，大约每周一次上皮细胞，作为一个模型系统。在接下来的五年里，我 研究计划将探索转录因子和染色质修饰酶如何有助于退出 干细胞在ISC分化过程中的状态。目前的模型认为，细胞的快速分化和可塑性 肠上皮受染色质景观的调节，这些染色质景观在所有肠上皮中都高度相似 细胞类型，不分分化阶段。我的实验室最近的研究使用一种 Sox9EGFP小鼠模型，允许我们使用单个报告程序分离ISCs、祖细胞和已分化细胞 转基因。我们量化了染色质可及性和5-羟甲基胞嘧啶的变化，并确定了 基因组座位上与增强子一致的显着染色质动态。我们的分析确定了一部小说 候选转录因子与染色质的相互作用，并提出关于染色质调节重要性的令人兴奋的问题 在成人上皮干细胞中。我们未来的研究将以这一进展为基础，以了解：(1)干细胞如何- 相关的染色质在分化中被转录因子退役，(2)特定谱系的调控程序 以及(3)染色质修饰酶如何连接自我更新和 差异化。这里提出的方法将建立一个长期的研究计划，具有广泛的潜力 深入研究上皮细胞对环境反应的可塑性/去分化、染色质调控 挑战和发展。我们的目标是寻求对染色质调节的基本机械理解。 对人类健康和疾病，包括上皮性反应具有基础性意义的干细胞 炎症、感染、损伤、衰老和肿瘤形成。

ABSTRACT Stemness is a functional cellular attribute defined by properties of multipotency (the ability to produce all differentiated cell types in a tissue) and self-renewal (the ability to produce new stem cells). In adult epithelial tissues, stemness can exist in: (1) dedicated stem cells occupying a defined niche, and (2) differentiated cells that exhibit plasticity to drive regeneration following injury. Stem cells must balance self-renewal with differentiation, and differentiated cells must balance lineage specific identity with plasticity to participate in regenerative responses. My lab is interested in understanding how chromatin modifications and their associated enzymes interact with site-specific transcription factors (TFs) to establish cell identities while simultaneously facilitating alternative cell fates. We focus on intestinal stem cells (ISCs), which drive the renewal of the intestinal epithelium approximately once a week throughout adult life, as a model system. Over the next five years, my research program will explore how TFs and chromatin modifying enzymes contribute to an exit from the stem cell state as ISC differentiate. Current models propose that rapid differentiation and plasticity in the intestinal epithelium is regulated by chromatin landscapes that are highly similar across all intestinal epithelial cell types, regardless of differentiation stage. Recent studies in my lab have challenged this model using a Sox9EGFP mouse model that allows us to isolate ISCs, progenitors, and differentiated cells with a single reporter transgene. We quantified changes in chromatin accessibility and 5-hydroxymethylcytosine and identified significant chromatin dynamics at genomic loci consistent with enhancers. Our analyses identified novel candidate TF-chromatin interactions and raise exciting questions about the importance of chromatin regulation in adult epithelial stem cells. Our future research will build on this progress to understand: (1) how stem cell- associated chromatin is decommissioned by TFs in differentiation, (2) how lineage-specific regulatory programs are “primed” in ISCs, and (3) how chromatin modifying enzymes bridge regulation of self-renewal and differentiation. The approach proposed here will establish a long-term research program, with broad potential to expand into studies of plasticity/de-differentiation, chromatin regulation of epithelial responses to environmental challenges, and development. Our goal is to pursue a basic mechanistic understanding of chromatin regulation in stemness that will have foundational relevance to human health and disease, including epithelial responses to inflammation, infection, injury, aging, and tumorigenesis.