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 广泛接受的是，细胞类型特异性基因表达主要通过细胞类型特异性表达来实现。 存在与同源DNA序列结合的转录因子（TF）。TF然后启动更改， 高级染色质结构通过招募染色质修饰剂，包括组蛋白修饰酶。 与TF不同，染色质修饰剂倾向于普遍表达。在众多的染色质中 修饰，组蛋白甲基化的调节因子在神经发育障碍中更频繁地突变， （NDD），如智力残疾（ID）和自闭症。为什么大脑对神经系统的失调如此敏感 组蛋白甲基化？神经元中甲基组蛋白的调节是独特的吗？有限数量细胞的研究 类型、癌细胞系和胚胎干细胞的研究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 调节是正常和病理性脑功能的基础。我们的重点是LSD 1-PHF 21 A组蛋白- 去甲基化复合物，其涉及神经元特异性选择性剪接。LSD 1是一种组蛋白脱甲基酶， 组蛋白H3赖氨酸4（H3 K4 me）。PHF 21 A是第一个发现的“零阅读器”，它识别未甲基化的 H3 K4（H3 K4 me 0），典型LSD 1（LSD 1-c）的反应产物。LSD 1和PHF 21 A haploinflammencies导致NDD，这表明它们在大脑发育中的重要性。神经元LSD 1 在其催化结构域中携带选择性外显子的同种型（LSD 1-n），据报道具有明显的 底物特异性然而，LSD 1-n靶向的特异性赖氨酸仍然存在争议。这个目标 该研究旨在确定神经元LSD 1-PHF 21 A复合物的作用。我们的初步研究表明， PHF 21 A还携带H3 K4 me 0识别PHD指上游的选择性外显子。这一地区 的PHF 21 A包含一个AT钩基序，它直接结合到DNA;我们发现，选择性外显子破坏了 AT-钩，因此DNA结合，但不H3 K4 me 0结合。这些观察提出了一个令人兴奋的 神经元PHF 21 A亚型（PHF 21 A-n）以不同方式识别核小体的可能性 与典型的PHF 21 A（PHF 21 A-c）相比，从而与LSD 1-n合作产生神经元 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测试这一假设， 生物化学和结构生物学。该研究计划的制定提供了两个机制的见解 组蛋白修饰的调节和更好地理解的发病机制， 神经发育障碍，这可能导致大脑特异性治疗靶点的新方法。

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