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.

抽象的 人们普遍认为，细胞类型特异性基因表达主要是通过细胞类型特异性来实现的。 转录因子 (TF) 的存在，与同源 DNA 序列结合，然后引发变化。 通过招募染色质修饰剂（包括组蛋白修饰酶）来形成高阶染色质结构。 与 TF 不同，染色质修饰剂往往在众多染色质中普遍表达。 组蛋白甲基化的修饰和调节因子在神经发育障碍中更频繁地发生突变 （NDD），例如智力障碍（ID）和自闭症 为什么大脑对失调如此敏感。 组蛋白甲基化？神经元中的甲基组蛋白调节是否独特？ 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。 我的研究小组的总体目标是帮助理解甲基组蛋白如何 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。 去甲基化复合物，涉及神经元特异性选择性剪接，LSD1 是一种组蛋白去甲基化酶。 组蛋白 H3 赖氨酸 4 (H3K4me) 是第一个发现的“零读取器”，可识别非甲基化。 H3K4 (H3K4me0)，经典 LSD1 (LSD1-c) 的反应产物。 单倍体不足会导致 NDD，这表明它们在神经元 LSD1 中的重要性。 据报道，亚型（LSD1-n）在其催化结构域中携带替代外显子，具有独特的 然而，LSD1-n 的特定赖氨酸目标仍然存在争议。 我们的初步研究表明，我们的建议是确定神经元 LSD1-PHF21A 复合物的作用。 PHF21A 还在 H3K4me0 识别 PHD 手指的上游携带一个替代外显子。 PHF21A 包含一个 AT-hook 基序，它直接与 DNA 结合，我们发现替代外显子会破坏； AT-hook，因此是 DNA 结合，但不是 H3K4me0 结合。这些观察结果提出了令人兴奋的结果。 神经元 PHF21A 异构体 (PHF21A-n) 以独特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。 我们建议使用涵盖细胞生物学的多学科方法来检验该假设， 该研究计划的制定是为了提供机械见解。 深入了解组蛋白修饰的调节并更好地了解组蛋白修饰的发病机制 神经发育障碍，这可能会导致针对大脑特定治疗目标的新方法。

项目成果

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

用于冷冻电镜的高质量石墨烯网格的批量生产：荚膜甲基球菌可溶性甲烷单加氧酶羟化酶的冷冻电镜结构。

• 发表时间: 2023-03-28
• 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
• 通讯作者: Cho, Uhn

Modulation of chromatin architecture influences the neuronal nucleus through activity-regulated gene expression.

染色质结构的调节通过活性调节的基因表达影响神经元核。

• 发表时间: 2023-04-26
• 影响因子: 3.9
• 作者: Porter, Robert S;Iwase, Shigeki
• 通讯作者: Iwase, Shigeki

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。

• 发表时间: 2023-10-21
• 作者: Porter, Robert S;Nagai, Masayoshi;An, Sojin;Gavilan, Maria C;Murata;Bonefas, Katherine M;Zhou, Bo;Dionne, Olivier;Manuel, Jeru Manoj;St;Browning, Liam;Laurent, Benoit;Cho, Uhn;Iwase, Shigeki
• 通讯作者: Iwase, Shigeki

An atypical 12q24.31 microdeletion implicates six genes including a histone demethylase KDM2B and a histone methyltransferase SETD1B in syndromic intellectual disability.

非典型 12q24.31 微缺失涉及六个基因，包括组蛋白去甲基酶 KDM2B 和组蛋白甲基转移酶 SETD1B，与综合征性智力障碍有关。

• 发表时间: 2016-07
• 影响因子: 5.3
• 作者: Labonne, Jonathan D J;Lee, Kang;Iwase, Shigeki;Kong, Il;Diamond, Michael P;Layman, Lawrence C;Kim, Cheol;Kim, Hyung
• 通讯作者: Kim, Hyung

CRISPR-based Genome Editing of a Diurnal Rodent, Nile Grass Rat ( Arvicanthis niloticus).

基于 CRISPR 的日间啮齿动物尼罗河草鼠 (Arvicanthis niloticus) 基因组编辑。

• 发表时间: 2023-08-23
• 作者: Xie, Huirong;Linning;Demireva, Elena Y;Toh, Huishi;Abolibdeh, Bana;Shi, Jiaming;Zhou, Bo;Iwase, Shigeki;Yan, Lily
• 通讯作者: Yan, Lily