A Neuron-specific Methyl-histone Regulatory Complex

神经元特异性甲基组蛋白调节复合物

• 批准号: 10615745
• 负责人: Shigeki Iwase
• 金额: $ 48.22万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10615745
• 关键词: AT-Hook Motifs; Address; Adopted; Affect; Affinity; Alternative Splicing; Binding; Biochemistry; Brain; Cancer cell line; Catalytic Domain; Cells; Cellular biology; Chromatin; Chromatin Remodeling Factor; Chromatin Structure; Complement; Complex; Cryoelectron Microscopy; DNA; DNA Binding; DNA Sequence; Data; Defect; Development; Disease; Enzymes; Excitatory Synapse; Exons; Gene Expression; Genomic approach; Goals; Higher Order Chromatin Structure; Histone H3; Histones; Human; Human Genetics; Impairment; In Vitro; Intellectual functioning disability; Investigation; KDM1A gene; Knock-out; Knowledge; Lead; Lysine; Mediating; Mediator; Missense Mutation; Modeling; Mus; Mutate; Neurodevelopmental Disorder; Neurons; Nucleosomes; Nucleotides; Organ; PHD Finger; Pathogenesis; Pathologic; Patients; Pattern Recognition; Play; Protein Isoforms; Publishing; RNA Splicing; Reaction; Reader; Regulation; Reporting; Research; Role; Specificity; Substrate Specificity; Testing; autism spectrum disorder; cell type; chromatin modification; demethylation; design; embryonic stem cell; experimental study; functional genomics; histone demethylase; histone methylation; histone modification; in vivo; insight; interdisciplinary approach; mouse model; neurodevelopment; novel strategies; protein protein interaction; reconstitution; recruit; structural biology; synaptogenesis; therapeutic target; transcription factor; transcriptome

Abstract It is widely accepted that cell-type-specific gene expression is primarily achieved by cell-type-specific presence of transcription factors (TFs), which bind to cognate DNA sequences. TFs then initiate changes in higher-order chromatin structures by recruiting chromatin modifiers, including histone-modifying enzymes. Unlike TFs, chromatin modifiers tend to be ubiquitously expressed. Among the plethora of chromatin modifications, regulators of histone methylation are more frequently mutated in neurodevelopmental disorders (NDDs) such as intellectual disabilities (IDs) and autism. Why is the brain so sensitive to dysregulation of histone methylation? Is methyl-histone regulation in neurons unique? Investigation of a limited number of cell types, cancer-cell lines, and embryonic stem cells has hampered our ability to address these questions. The overarching goal of my research group is to contribute to the understanding of how methyl-histone regulations underlie normal and pathological brain functions. Our focus is on the LSD1-PHF21A histone- demethylation complex, which involves neuron-specific alternative splicing. LSD1 is a histone demethylase for histone H3 lysine 4 (H3K4me). PHF21A was the first-discovered “zero reader,” which recognizes unmethylated H3K4 (H3K4me0), the reaction product of canonical LSD1 (LSD1-c). Both LSD1 and PHF21A haploinsufficiencies lead to NDDs, suggesting their importance in brain development. The neuronal LSD1 isoform (LSD1-n), which carries an alternative exon in its catalytic domain, was reported to have distinct substrate specificity. However, the specific lysine(s) targeted by LSD1-n remains controversial. The goal of this proposal is to determine the roles of the neuronal LSD1-PHF21A complex. Our preliminary study showed that PHF21A also carries an alternative exon right upstream of the H3K4me0-recognizing PHD finger. This region of PHF21A contains an AT-hook motif, which directly binds to DNA; we found that the alternative exon disrupts the AT-hook, hence the DNA binding, but not H3K4me0 binding. These observations raise an exciting possibility that the neuronal PHF21A isoform (PHF21A-n) recognizes nucleosomes in a distinct manner compared to canonical PHF21A (PHF21A-c), thereby cooperating with LSD1-n to generate the neuronal transcriptome for normal brain development. We propose testing the hypothesis using multidisciplinary approaches encompassing cell biology, biochemistry, and structural biology. The research plan was developed to provide both mechanistic insights into the regulation of histone modifications and a better understanding of the pathogenesis of neurodevelopment disorders, which could lead to novel approaches for brain-specific therapeutic targets.

摘要 人们普遍认为，特定细胞类型的基因表达主要是通过特定细胞类型来实现的 存在转录因子(TF)，可与同源DNA序列结合。然后，TFS在 通过招募染色质修饰剂，包括组蛋白修饰酶，来构建更高级的染色质结构。 与转录因子不同的是，染色质修饰物往往是普遍表达的。在过多的染色质中 组蛋白甲基化的修饰和调节在神经发育障碍中更频繁地发生突变 智力障碍(IDs)和自闭症。为什么大脑对大脑的失调如此敏感？ 组蛋白甲基化？神经元中的甲基组蛋白调节是独一无二的吗？对有限数量的牢房进行调查 类型、癌细胞系和胚胎干细胞阻碍了我们解决这些问题的能力。 我的研究小组的首要目标是帮助理解甲基组蛋白是如何 调节是正常和病理性大脑功能的基础。我们的重点是LSD1-PHF21A组蛋白- 去甲基化复合体，它涉及神经元特异性的选择性剪接。LSD1是一种组蛋白去甲基酶 组蛋白H3赖氨酸4(H3K4me)。PHF21A是第一个被发现的“零阅读器”，它识别未甲基化的 H3K4(H3K4me0)，正则LSD1(LSD1-c)的反应产物。LSD1和PHF21A 单倍体不足导致NDD，这表明它们在大脑发育中的重要性。神经元LSD1 据报道，异构体(LSD1-n)在其催化结构域中携带一个替代外显子，具有不同的 底物专一性。然而，LSD1-n靶向的特定赖氨酸(S)仍然存在争议。这样做的目的是 建议确定神经元LSD1-PHF21A复合体的作用。我们的初步研究表明 PHF21A还在H3K4me0识别PHD手指的上游携带另一个外显子。这一地区 包含一个AT-挂钩基序，它直接与DNA结合；我们发现替代外显子破坏了 AT-挂钩，因此是DNA结合，但不是H3K4me0结合。这些观察引起了一个令人兴奋的问题 神经元PHF21A亚型(PHF21A-n)以一种独特的方式识别核小体的可能性 与典型的PHF21A(PHF21A-c)相比，从而与LSD1-n合作生成神经元 正常大脑发育的转录组。 我们建议使用包括细胞生物学在内的多学科方法来检验这一假设， 生物化学和结构生物学。研究计划的制定既提供了机械性的见解，也提供了 组蛋白修饰的调节和更好地理解组蛋白修饰的发病机制 神经发育障碍，这可能导致针对大脑特定治疗靶点的新方法。

项目成果

Batch Production of High-Quality Graphene Grids for Cryo-EM: Cryo-EM Structure of Methylococcus capsulatus Soluble Methane Monooxygenase Hydroxylase.

• DOI: 10.1021/acsnano.3c00463
• 发表时间: 2023-03-28
• 期刊: ACS NANO
• 影响因子: 17.1
• 作者: Ahn, Eungjin;Kim, Byungchul;Park, Soyoung;Erwin, Amanda L.;Sung, Suk Hyun;Hovden, Robert;Mosalaganti, Shyamal;Cho, Uhn-Soo
• 通讯作者: Cho, Uhn-Soo

A neuron-specific microexon ablates the novel DNA-binding function of a histone H3K4me0 reader PHF21A.

神经元特异性微外显子消除了组蛋白 H3K4me0 阅读器 PHF21A 的新型 DNA 结合功能。

• DOI: 10.1101/2023.10.20.563357
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 作者: Porter,RobertS;Nagai,Masayoshi;An,Sojin;Gavilan,MariaC;Murata-Nakamura,Yumie;Bonefas,KatherineM;Zhou,Bo;Dionne,Olivier;Manuel,JeruManoj;St-Germain,Joannie;Browning,Liam;Laurent,Benoit;Cho,Uhn-Soo;Iwase,Shigeki
• 通讯作者: Iwase,Shigeki