CTCF-dependent mechanisms of ATRX in neuronal differentiation

ATRX 在神经元分化中的 CTCF 依赖性机制

• 批准号: 10625522
• 负责人: Kavitha Sarma
• 金额: $ 53.06万
• 依托单位: WISTAR INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10625522
• 关键词: 3-Dimensional; ATRX gene; Affect; Alleles; Architecture; Behavior; Binding; Binding Sites; Biochemical; Brain; CRISPR/Cas technology; Cell Differentiation process; Cells; Chromatin; Complex; DNA Methylation; Data; Defect; Deposition; Development; Disease; Engineering; Epigenetic Process; Exhibits; Gene Expression; Genes; Genital; Genitalia; Genome; Genomic Segment; Genomics; Genotype; Histones; Impairment; Lead; Link; Maintenance; Malignant Neoplasms; Masks; Mediating; Molecular; Mus; Mutate; Mutation; Neurodevelopmental Disorder; Neurologic; Neuronal Differentiation; Oncogene Deregulation; Outcome; PHD Finger; Patients; Pattern; Phenotype; Polycomb; Positioning Attribute; Process; Proteins; Psychomotor Impairments; Reagent; Regulation; Role; Severity of illness; Site; Syndrome; Testing; Variant; chromatin remodeling; embryonic stem cell; epigenetic silencing; genome wide methylation; genome-wide; helicase; imprint; knock-down; mutant; nerve stem cell; neural; novel; prevent; programs; severe intellectual disability

PROJECT SUMMARY ATRX is an epigenetic factor that is mutated in ATRX syndrome. ATRX is required for the maintenance of multipotent neuroprogenitor cells (NPCs), particularly as these cells initiate differentiation programs in the brain. Mutations that cause ATRX syndrome cluster within two domains: the ATRX PHD finger domain, and the helicase domain. These mediate interactions with histones, and remodel chromatin, respectively. Interestingly, mutations in the PHD finger are associated with severe intellectual disability and psychomotor impairment, while mutations in the helicase domain often manifest with milder neurodevelopmental delays but more severe genital abnormalities13. The basis for this genotype-phenotype correlation has never been investigated. ATRX has well- established roles in molecular processes that are crucial for normal brain development including histone variant H3.3 deposition and Polycomb repressive complex 2 targeting for epigenetic silencing. It also has a poorly understood role in regulating CTCF, a critical genome architectural protein that is essential for development. Our preliminary data indicate PHD finger and helicase mutations of ATRX differentially regulate CTCF localization and may underlie genotype-phenotype correlations. Our preliminary data has uncovered a genome-wide role for ATRX in CTCF localization. We found that ATRX knock down (KD) in mouse embryonic stem cells (mESCs) results in CTCF accumulation at many genomic sites, including both imprinted and non-imprinted loci. We also discovered that ATRX interacts with ADNP and DNMT3L, both of which can prevent CTCF binding. Using CRISPR/Cas9, we have generated isogenic ESCs where the endogenous Atrx allele has been replaced by point mutants found in ATRX syndrome patients. We show that mutations in the PHD finger cause significant impairment of NPC differentiation, while mutations in the helicase domain cause more subtle differentiation delays. Our preliminary findings and novel reagents uniquely position us to interrogate the consequence of ATRX mutations, both for genome organization through CTCF, and for the ability of ESCs to differentiate into NPCs. Based on our preliminary data, we propose to test the hypothesis that distinct ATRX domains regulate specific chromatin processes that impinge to different extents on the function of CTCF. In Aim 1, we will investigate the consequence of ATRX syndrome mutations to gene expression and genome organization during neuronal differentiation. In Aim 2, we will decipher the mechanisms by which ATRX regulates CTCF localization.

项目概要 ATRX 是一种在 ATRX 综合征中发生突变的表观遗传因子。需要 ATRX 来维护 多能神经祖细胞（NPC），特别是当这些细胞在大脑中启动分化程序时。 导致 ATRX 综合征的突变集中在两个域内：ATRX PHD 手指域和 解旋酶结构域。它们分别介导与组蛋白的相互作用并重塑染色质。有趣的是， PHD 手指的突变与严重的智力障碍和精神运动障碍有关，而 解旋酶结构域的突变通常表现为较轻微的神经发育迟缓，但更严重的生殖器发育迟缓 异常13.这种基因型-表型相关性的基础从未被研究过。 ATRX 拥有良好的 在对正常大脑发育至关重要的分子过程（包括组蛋白变异）中确立了作用 H3.3 沉积和 Polycomb 抑制复合物 2 靶向表观遗传沉默。它也有一个较差的 CTCF 是一种对发育至关重要的关键基因组结构蛋白。我们的 初步数据表明 ATRX 的 PHD 指和解旋酶突变差异调节 CTCF 定位 并且可能是基因型-表型相关性的基础。我们的初步数据揭示了全基因组的作用 CTCF 本地化中的 ATRX。我们发现小鼠胚胎干细胞 (mESC) 中 ATRX 敲低 (KD) 导致 CTCF 在许多基因组位点积累，包括印记和非印记位点。我们也 发现 ATRX 与 ADNP 和 DNMT3L 相互作用，两者都可以阻止 CTCF 结合。使用 CRISPR/Cas9，我们生成了等基因ESC，其中内源Atrx等位基因已被点取代 ATRX 综合征患者中发现的突变体。我们发现 PHD 手指的突变会导致显着的 NPC 分化受损，而解旋酶结构域的突变会导致更细微的分化 延误。我们的初步发现和新颖试剂使我们能够独特地质疑 ATRX 的结果 突变，既用于通过 CTCF 进行基因组组织，又用于 ESC 分化为 NPC 的能力。 根据我们的初步数据，我们建议检验以下假设：不同的 ATRX 域调节特定的 染色质过程对 CTCF 的功能有不同程度的影响。在目标 1 中，我们将调查 ATRX 综合征突变对神经元发育过程中基因表达和基因组组织的影响 差异化。在目标 2 中，我们将破译 ATRX 调节 CTCF 定位的机制。