Structural and functional studies of chromatin modifiers

染色质修饰剂的结构和功能研究

• 批准号: 10541158
• 负责人: Mario Halic
• 金额: $ 37.7万
• 依托单位: ST. JUDE CHILDREN'S RESEARCH HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-01-01 至 2024-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10541158
• 关键词: Active Sites; Acute leukemia; Address; Aging; Binding; Binding Proteins; Biochemical; Biochemistry; Cell Proliferation; Cell physiology; Cells; Centromere; Chromatin; Chromatin Modeling; Chromatin Remodeling Factor; Chromatin Structure; Chromosome Segregation; Clear cell renal cell carcinoma; Complex; Congenital Abnormality; Cryoelectron Microscopy; DNA Repair; DNA-Binding Proteins; Data; Deposition; Development; Disease; Enzymes; Epigenetic Process; Gene Expression; Genes; Genetic; Genetic Transcription; Genome; Genome Stability; Genomic Instability; Genomics; Glioblastoma; Goals; HMGN Proteins; Heterochromatin; Histone H3; Histone-Lysine N-Methyltransferase; Histones; Human; In Vitro; Infertility; Kinetochores; Knowledge; Lead; Lysine; Malignant Neoplasms; Malignant neoplasm of brain; Malignant neoplasm of lung; Malignant neoplasm of ovary; Malignant neoplasm of urinary bladder; Messenger RNA; Methylation; Microtubules; Mutate; Mutation; Nucleosomes; Outcome; Peptides; Pharmaceutical Preparations; Physical condensation; Positioning Attribute; Proteins; RNA Splicing; Reader; Regulation; Research; Specificity; Structural Protein; Structure; Ubiquitin; Ubiquitination; Variant; Visualization; Work; biophysical analysis; cancer cell; cancer genome; centromere autoantigen 80K; centromere protein A; centromere protein C; chromatin modification; chromatin protein; experimental study; histone methylation; histone modification; in vitro activity; in vivo; malignant breast neoplasm; overexpression; prevent; protein complex; recruit; small molecule; therapeutic target; tumorigenesis

Summary Regulation of genome expression is essential for cells to maintain their identity and loss of cell identity leads to tumorigenesis. Cancer Genome Project has revealed that chromatin modifiers and remodelers are highly mutated in human cancers, however, despite the importance of these factors, we know little about their mechanisms of activity. To address this knowledge gap, we will combine cryo-EM, biochemistry and genetics to determine how enzymes and structural proteins modify nucleosome and chromatin structure. Among the key players in the control of genome expression are histone modifications that, through specific reader domains, recruit various protein complexes to chromatin. Histone lysine methylation is a stable chromatin mark that is deposited by histone lysine methyltransferases (KMTs) and methylation of different lysine residues has different outcomes on gene expression; H3K36 methylation is deposited over actively transcribed genes, whereas H3K9 methylation is a hallmark of silent heterochromatin. Perturbations in KMT levels lead to aberrant genome expression and formation of cancers cells, however, we do not understand how KMTs bind and modify nucleosome. H3K9 methylation and heterochromatin are required for deposition of centromere specific histone H3 variant CENP-A to chromatin, an epigenetic mark of centromeres. The centromere is the specialized chromatin region on which kinetochores assemble to segregate chromosomes. Despite the importance, structure of centromeric chromatin assembled on CENP-A nucleosome is still largely unknown. Guided by the strong preliminary data, we propose to pursue three Specific Aims to understand how KMTs bind and modify nucleosomes and to characterize centromeric chromatin. We will combine cryo-EM with biochemistry and genetics to determine mechanisms of H3K36 (Aim 1) and H3K9 (Aim 2) methylation. Moreover, we will use cryo-EM to visualize centromeric chromatin assembled on CENP-A nucleosome (Aim 3). Together, our proposed studies will have broad impact in chromatin field by showing how chromatin proteins bind the nucleosome and how this interaction provides specificity for their activity. Our long-term goals are to understand the regulation of genome expression by chromatin and discover why mutations in chromatin proteins lead to the formation of cancer cells.

摘要 对基因组表达的调节对于细胞维持其身份和丧失细胞身份是必不可少的 会导致肿瘤的发生。癌症基因组计划揭示了染色质修饰物和 然而，重构体在人类癌症中高度突变，尽管这些因素很重要， 我们对它们的活动机制知之甚少。为了解决这一知识差距，我们将结合 冷冻-EM、生物化学和遗传学，以确定酶和结构蛋白如何修饰 核小体和染色质结构。 在基因组表达控制中的关键角色是组蛋白修饰，通过 特定的阅读器结构域，招募各种蛋白质复合体到染色质。组蛋白赖氨酸甲基化是 稳定的染色质标记，由组蛋白赖氨酸甲基转移酶(KMTs)和 不同赖氨酸残基的甲基化对基因表达的影响不同；H3K36 甲基化沉积在活跃转录的基因上，而H3K9甲基化是 沉默的异染色质。KMT水平的扰动导致基因组表达和形成的异常 然而，对于癌细胞，我们不了解KMT是如何结合和修饰核小体的。H3K9 着丝粒特异性组蛋白H3的沉积需要甲基化和异染色质 CENP-A变异为染色质，这是着丝粒的表观遗传标记。着丝粒是专门化的 染色质区域，动粒聚集在该区域上以分离染色体。尽管 CENP-A核小体上组装着丝粒染色质的重要性和结构仍在很大程度上 未知。在强劲的初步数据指引下，我们建议追求三个具体目标： 了解KMT如何结合和修饰核小体，并确定着丝粒染色质的特征。我们 将冷冻-EM与生物化学和遗传学相结合以确定H3K36的机制(目标1) 和H3K9(目标2)甲基化。此外，我们将使用冷冻-EM来显示着丝粒染色质 组装在CENP-A核小体上(目标3)。 总之，我们提出的研究将通过展示染色质如何 蛋白质与核小体结合，以及这种相互作用如何为它们的活动提供特异性。我们的 长期目标是了解染色质对基因组表达的调节，并发现 为什么染色质蛋白的突变会导致癌细胞的形成。

项目成果

Bridging of DNA breaks activates PARP2-HPF1 to modify chromatin.

• DOI: 10.1038/s41586-020-2725-7
• 发表时间: 2020-09
• 期刊: Nature
• 影响因子: 64.8
• 作者: Bilokapic S;Suskiewicz MJ;Ahel I;Halic M
• 通讯作者: Halic M

Histone modifications regulate pioneer transcription factor cooperativity.

组蛋白修饰调节先锋转录因子的合作。

• DOI: 10.1038/s41586-023-06112-6
• 发表时间: 2023-07
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Sinha, Kalyan K. K.;Bilokapic, Silvija;Du, Yongming;Malik, Deepshikha;Halic, Mario
• 通讯作者: Halic, Mario

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome.

• DOI: 10.7554/elife.71420
• 发表时间: 2021-09-06
• 期刊: eLife
• 影响因子: 7.7
• 作者: Bacic L;Gaullier G;Sabantsev A;Lehmann LC;Brackmann K;Dimakou D;Halic M;Hewitt G;Boulton SJ;Deindl S
• 通讯作者: Deindl S

CENP-A and CENP-B collaborate to create an open centromeric chromatin state.

• DOI: 10.1038/s41467-023-43739-5
• 发表时间: 2023-12-12
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Nagpal, Harsh;Ali-Ahmad, Ahmad;Hirano, Yasuhiro;Cai, Wei;Halic, Mario;Fukagawa, Tatsuo;Sekulic, Nikolina;Fierz, Beat
• 通讯作者: Fierz, Beat

Increased fidelity of protein synthesis extends lifespan.

• DOI: 10.1016/j.cmet.2021.08.017
• 发表时间: 2021-11-02
• 期刊: Cell metabolism
• 影响因子: 29
• 作者: Martinez-Miguel VE;Lujan C;Espie-Caullet T;Martinez-Martinez D;Moore S;Backes C;Gonzalez S;Galimov ER;Brown AEX;Halic M;Tomita K;Rallis C;von der Haar T;Cabreiro F;Bjedov I
• 通讯作者: Bjedov I