Deciphering the role of the MOF complex and H4K16ac in the regulation of neuronal enhancers

解读 MOF 复合物和 H4K16ac 在神经元增强子调节中的作用

• 批准号: MR/T000783/1
• 负责人: Pradeepa Madapura-Marulasiddappa
• 金额: $ 104.61万
• 依托单位: Queen Mary University of London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FT000783%2F1
• 关键词: Deciphering; role; MOF; complex; H4K16ac

Histone proteins package DNA into a compact DNA-protein structure termed chromatin. Accessibility of compacted DNA for transcription is regulated by enzymatic complexes that add covalent modifications like acetyl and methyl groups to histones. Covalent modifications on the histones including acetylation play essential roles in many aspects of cellular function, including normal development of complex organs including the brain. Genes encoding histone-modifying protein complexes are frequently mutated in developmental disorders. Severe neurodevelopmental disorders are most commonly caused by new mutations in genes important for normal development of the central nervous system, with a wide range of phenotypes such as global developmental delay, severe intellectual disability and autism. It is estimated that about 1 in 220 children in the UK have severe neurodevelopmental impairments as a result of new mutations. Clear and early diagnosis and a better understanding of disease mechanism will improve the stratification of neurodevelopmental disorder patients for personalized therapy and support. Genes encoding epigenetic modifiers are frequently mutated in patients with developmental disorders. Male specific lethal 3 (MSL3) gene encoding a component of histone acetyltransferase complex (MSL/MOF) is mutated in a neurodevelopmental disorder called MSL3 syndrome. The MSL/MOF protein complex is responsible for acetylation of histone H4 at lysine 16 (H4K16ac), which is known to increase gene expression. However, a specific role of MSL/MOF complex in the development of the nervous system and how mutations in MSL3 contribute to a specific neurodevelopmental phenotype is not known.Only about 42% of patients with severe developmental disorders have detectable mutations that affect the protein coding regions of genes. Sequence variants found in non-coding distal regulatory elements called enhancers points contribution of enhancer dysfunction in developmental disorders. Enhancers are scattered around 98% of the genome that is non-coding and can regulate genes from large distances, hence it is challenging to delineate disease mechanism due to sequence variation in the enhancer DNA. Genome-wide profiling of acetylation of histone H3 at lysine 27 (H3K27ac) is widely method to identify active enhancers in the genome. We have previously discovered a new class of active enhancers based on the presence of H4K16ac that lack H3K27ac. In this project, we will identify genes and enhancers regulated by MOF and H4K16ac, then compare the activity of enhancers identified based on histone acetylation. Furthermore, we will investigate the mechanism through which histone acetyltransferase complex function to regulate gene expression. We will also investigate how mutations in genes encoding proteins in histone acetylation pathway leads to a specific neuronal phenotype. Finally, we will test if we can rescue altered cellular and gene expression phenotype by treating with drugs that increases histone acetylation levels.Overall, we will use state-of-the-art functional genomics and genome editing methods to comprehensively understand the mechanism through which MSL/MOF and H4K16ac regulate genes. Importantly, this work will provide important insights into the disease mechanism which results from mutations that leads to altered level of histone acetylation. This work will improve our understanding of the mechanisms through which mutations in MSL3 and enhancers contribute to neurodevelopmental disorders and, in addition, provide afunctional criterion on which to stratify patients for therapeutic intervention.

组蛋白将DNA包装成紧凑的DNA-蛋白质结构，称为染色质。压缩的DNA转录的可及性由酶复合物调节，酶复合物向组蛋白添加共价修饰，如乙酰基和甲基。组蛋白上的共价修饰包括乙酰化在细胞功能的许多方面发挥重要作用，包括复杂器官（包括脑）的正常发育。编码组蛋白修饰蛋白复合物的基因在发育障碍中经常发生突变。严重神经发育障碍最常见的原因是对中枢神经系统正常发育重要的基因发生新突变，具有广泛的表型，如全面发育迟缓、严重智力残疾和自闭症。据估计，在英国，每220名儿童中就有1名因新的突变而患有严重的神经发育障碍。明确早期诊断和更好地了解疾病机制，将有助于提高神经发育障碍患者的分层，为患者提供个性化的治疗和支持。编码表观遗传修饰物的基因在发育障碍患者中经常发生突变。编码组蛋白乙酰转移酶复合物（MSL/MOF）组分的雄性特异性致死3（MSL 3）基因在称为MSL 3综合征的神经发育障碍中发生突变。MSL/MOF蛋白复合物负责组蛋白H4在赖氨酸16（H4 K16 ac）处的乙酰化，已知其增加基因表达。然而，MSL/MOF复合物在神经系统发育中的特定作用以及MSL 3突变如何促成特定的神经发育表型尚不清楚。只有约42%的严重发育障碍患者具有可检测到的影响基因蛋白编码区的突变。在称为增强子的非编码远端调控元件中发现的序列变体指出了发育障碍中增强子功能障碍的贡献。增强子散布在非编码基因组的98%周围，并且可以从大距离调节基因，因此由于增强子DNA中的序列变异，描绘疾病机制是具有挑战性的。组蛋白H3在赖氨酸27处的乙酰化（H3 K27 ac）的全基因组谱分析是鉴定基因组中的活性增强子的广泛方法。我们之前发现了一类新的活性增强子，其基于H4 K16 ac的存在而缺乏H3 K27 ac。本研究将通过组蛋白乙酰化鉴定受MOF和H4 K16 ac调控的基因和增强子，并比较两种增强子的活性。此外，我们还将研究组蛋白乙酰转移酶复合物调控基因表达的机制。我们还将研究组蛋白乙酰化途径中编码蛋白质的基因突变如何导致特定的神经元表型。最后，我们将测试是否可以通过增加组蛋白乙酰化水平的药物治疗来挽救改变的细胞和基因表达表型。总之，我们将使用最先进的功能基因组学和基因组编辑方法来全面了解MSL/MOF和H4 K16 ac调节基因的机制。重要的是，这项工作将提供重要的见解，疾病的机制，导致突变，导致组蛋白乙酰化水平的改变。这项工作将提高我们对MSL 3和增强子突变导致神经发育障碍的机制的理解，此外，还将提供一个功能性标准，用于对患者进行分层治疗干预。

项目成果

Additional file 1 of Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

小鼠和人类核糖体 DNA 的遗传变异影响相关表观遗传状态的附加文件 1

• DOI: 10.6084/m9.figshare.19174015
• 发表时间: 2022
• 作者: Rodriguez-Algarra F

PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity

PSIP1/LEDGF 减少转录位点的 R 环以维持基因组完整性

• DOI: 10.1101/2022.12.02.518862
• 发表时间: 2022
• 作者: Jayakumar S

H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function.

• DOI: 10.1038/s41594-023-01016-5
• 发表时间: 2023-07
• 期刊: NATURE STRUCTURAL & MOLECULAR BIOLOGY
• 影响因子: 16.8
• 作者: Pal, Debosree;Patel, Manthan;Boulet, Fanny;Sundarraj, Jayakumar;Grant, Olivia A.;Branco, Miguel R.;Basu, Srinjan;Santos, Silvia D. M.;Zabet, Nicolae Radu;Scaffidi, Paola;Pradeepa, Madapura M.
• 通讯作者: Pradeepa, Madapura M.

Additional file 3 of Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

小鼠和人类核糖体 DNA 的遗传变异影响相关表观遗传状态的附加文件 3

• DOI: 10.6084/m9.figshare.19174021
• 发表时间: 2022
• 作者: Rodriguez-Algarra F

Regulatory de novo mutations underlying intellectual disability.

• DOI: 10.26508/lsa.202201843
• 发表时间: 2023-05
• 期刊: Life science alliance
• 影响因子: 4.4