Chromatin regulation of epithelial stem cell function

摘要 干细胞是一种功能性细胞属性，由多能性（产生所有细胞的能力）的性质定义。 组织中分化的细胞类型）和自我更新（产生新干细胞的能力）。在成人上皮 在组织中，干细胞可以存在于：（1）占据特定生态位的专用干细胞，以及（2）分化的细胞 这些细胞具有可塑性，可以在受伤后驱动再生。干细胞必须平衡自我更新与 分化，分化的细胞必须平衡谱系特异性身份与可塑性，以参与 再生反应我的实验室有兴趣了解染色质修饰及其相关的 酶与位点特异性转录因子（TF）相互作用以建立细胞身份，同时 促进细胞命运的改变。我们专注于肠道干细胞（ISCs），它驱动肠道的更新， 在整个成年期，大约每周一次，作为模型系统。在接下来的五年里，我 一项研究计划将探索转座子和染色质修饰酶如何有助于退出 干细胞状态为ISC分化。目前的模型提出，快速分化和可塑性，在 肠上皮细胞受染色质景观的调节，这些染色质景观在所有肠上皮细胞中高度相似。 细胞类型，无论分化阶段。我的实验室最近的研究使用了一种 Sox 9 EGFP小鼠模型，允许我们用单个报告基因分离ISC、祖细胞和分化细胞 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， 与增强子一致的基因组位点的显著染色质动力学。我们的分析发现， 候选TF-染色质相互作用，并提出了令人兴奋的问题，染色质调控的重要性 在成人上皮干细胞中。我们未来的研究将建立在这一进展的基础上，以了解：（1）干细胞- 相关染色质在分化中被TF退役，（2）谱系特异性调控程序如何 是“启动”在ISCs，和（3）如何染色质修饰酶桥梁调节自我更新， 分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， 扩展到可塑性/去分化的研究，染色质调节上皮细胞对环境的反应， 挑战和发展。我们的目标是追求一个基本的机械理解染色质调控 对人类健康和疾病具有基础相关性，包括上皮反应 炎症、感染、损伤、衰老和肿瘤发生。

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.