Enhancer regulation by H3K4 methyltransferase MLL4/KMT2D and associated factors

H3K4 甲基转移酶 MLL4/KMT2D 和相关因子的增强子调节

• 批准号: 10919468
• 负责人: Kai Ge
• 金额: $ 233.1万
• 依托单位: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10919468
• 关键词: Acetylation; Acetyltransferase; Binding; Cell Differentiation process; Cell Fate Control; Cells; Chromatin Remodeling Factor; Complex; Data; Development; EP300 gene; Embryonic Development; Enhancers; Feedback; Gene Expression; Genes; Genetic Transcription; Genets; Histones; ISWI; Kabuki Make-Up Syndrome; Malignant Neoplasms; Mammalian Cell; Mediating; Mediator; Methyltransferase; Modeling; Mus; Mutate; Nuclear Protein; PPAR gamma; Pathogenesis; Play; Proteins; RNA Polymerase II; Reader; Regulation; Role; Tissues; Transcriptional Regulation; Tumor Suppression; cancer type; cell type; cofactor; congenital heart disorder; developmental disease; embryonic stem cell; epigenomics; gene induction; lipid biosynthesis; mouse development; muscle regeneration; myogenesis; novel; protein complex; recruit; stem cells; transcription factor

PPARgamma is a lineage-determining transcription factor (LDTF) essential for adipogenesis. In search for novel PPARgamma cofactors, we identified a nuclear protein complex that contains MLL3/4 and the H3K27 demethylase UTX (KDM6A) (JBC 2007, PNAS 2007). MLL3/4 and UTX are highly mutated in many types of cancers as well as Kabuki syndrome and congenital heart disease. We have shown: 1) MLL3/4 colocalize with LDTFs on active enhancers and are generally required for enhancer activation, cell-type-specific gene expression, cell differentiation, tissue development and tumor suppression (eLife 2013, Development 2016, NAR 2019, Development 2020, Nat Cell Biol 2023, reviewed in Gene 2017, MCB 2020a). MLL3/4 control cell fate transition by orchestrating H3K27 acetyltransferases CBP/p300-mediated enhancer activation (PNAS 2016, NAR 2017). 2) MLL3/4 proteins, rather than H3K4me1, controls p300 recruitment to enhancers during ES cell differentiation (PNAS 2016). Consistently, MLL3/4 enzymatic activities and H3K4me1 are largely dispensable for enhancer activation during ES cell differentiation. By inactivating MLL3/4 enzymatic activities in mice and ES cells, we show that MLL3/4 methyltransferase activities are redundant and are essential for early embryonic development. MLL3/4 enzymatic activities control early embryonic development and ES cell differentiation in a lineage-selective manner (Nat Genet 2023). 3) The epigenomic reader Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis. Our data suggest a model of sequential actions of epigenomic regulators on enhancers: i) LDTFs recruit MLL3/4 to prime enhancers, ii) MLL3/4 facilitate the binding of CBP/p300, which activate enhancers, iii) Brd4 recognizes active enhancers and recruits Mediator and RNA Polymerase II to activate cell-type-specific gene expression (Nat Commun 2017). 4) Positive feedback between MLL4 and the SWI/SNF chromatin remodeling complex BAF in promoting LDTF-dependent activation of cell type-specific enhancers (Nat Commun 2021). 5) UTX protein, but not its H3K27 demethylase activity, is required for ES cell differentiation and mouse development (PNAS 2012). Interestingly, UTX demethylase activity is required for stem cell-mediated muscle regeneration (JCI 2016). 6) While the MED1 subunit of the Mediator coactivator complex marks active enhancers, it plays a cell- and gene-specific regulatory role and is not generally required for transcription (Genes Dev 2021).

PPARgamma是脂肪形成所必需的谱系决定转录因子（LDTF）。在寻找新的PPARgamma辅因子时，我们鉴定了一种含有MLL 3/4和H3 K27脱甲基酶UTX（KDM 6A）的核蛋白复合物（JBC 2007，PNAS 2007）。MLL 3/4和UTX在许多类型的癌症以及歌舞伎综合征和先天性心脏病中高度突变。我们已经证明： 1)MLL 3/4与活性增强子上的LDTF共定位，通常是增强子激活、细胞类型特异性基因表达、细胞分化、组织发育和肿瘤抑制所需的（eLife 2013，Development 2016，NAR 2019，Development 2020，Nat Cell Biol 2023，综述于Gene 2017，MCB 2020 a）。MLL 3/4通过协调H3 K27乙酰转移酶CBP/p300介导的增强子激活来控制细胞命运转变（PNAS 2016，NAR 2017）。 2)MLL 3/4蛋白，而不是H3 K4 me 1，在ES细胞分化过程中控制p300向增强子的募集（PNAS 2016）。因此，MLL 3/4酶活性和H3 K4 me 1在很大程度上与ES细胞分化过程中增强子的激活有关。通过灭活小鼠和ES细胞中的MLL 3/4酶活性，我们表明MLL 3/4甲基转移酶活性是多余的，并且对早期胚胎发育至关重要。MLL 3/4酶活性以谱系选择性方式控制早期胚胎发育和ES细胞分化（Nat Genet 2023）。 3)表观基因组阅读器Brd 4与活性增强子结合以控制脂肪生成和肌生成中的细胞身份基因诱导。我们的数据表明表观基因组调节剂对增强子的顺序作用模型：i）LDTF招募MLL 3/4以引发增强子，ii）MLL 3/4促进CBP/p300的结合，从而激活增强子，iii）Brd 4识别活性增强子并招募介体和RNA聚合酶II以激活细胞类型特异性基因表达（Nat Commun 2017）。 4)MLL 4和SWI/SNF染色质重塑复合物BAF之间的正反馈促进细胞类型特异性增强子的LDTF依赖性激活（Nat Commun 2021）。 5)UTX蛋白，而不是其H3 K27脱甲基酶活性，是ES细胞分化和小鼠发育所必需的（PNAS 2012）。有趣的是，UTX脱甲基酶活性是干细胞介导的肌肉再生所必需的（JCI 2016）。 6)虽然介体共激活因子复合物的MED 1亚基标记活性增强子，但它发挥细胞和基因特异性调节作用，通常不是转录所需的（Genes Dev 2021）。

项目成果

Molecular basis for histone H3 "K4me3-K9me3/2" methylation pattern readout by Spindlin1.

Spindlin1 读出组蛋白 H3“K4me3-K9me3/2”甲基化模式的分子基础。

• DOI: 10.1074/jbc.ra120.013649
• 发表时间: 2020-12-04
• 期刊: The Journal of biological chemistry
• 作者: Zhao F;Liu Y;Su X;Lee JE;Song Y;Wang D;Ge K;Gao J;Zhang MQ;Li H
• 通讯作者: Li H

UTX inhibition as selective epigenetic therapy against TAL1-driven T-cell acute lymphoblastic leukemia.

• DOI: 10.1101/gad.276790.115
• 发表时间: 2016-03-01
• 期刊: Genes & development
• 影响因子: 10.5
• 作者: Benyoucef A;Palii CG;Wang C;Porter CJ;Chu A;Dai F;Tremblay V;Rakopoulos P;Singh K;Huang S;Pflumio F;Hébert J;Couture JF;Perkins TJ;Ge K;Dilworth FJ;Brand M
• 通讯作者: Brand M

Loss of Function of the Gene Encoding the Histone Methyltransferase KMT2D Leads to Deregulation of Mitochondrial Respiration.

编码组蛋白甲基转移酶 KMT2D 的基因功能丧失会导致线粒体呼吸失调。

• DOI: 10.3390/cells9071685
• 发表时间: 2020
• 期刊: Cells
• 影响因子: 6
• 作者: Pacelli,Consiglia;Adipietro,Iolanda;Malerba,Natascia;Squeo,GabriellaMaria;Piccoli,Claudia;Amoresano,Angela;Pinto,Gabriella;Pucci,Pietro;Lee,Ji-Eun;Ge,Kai;Capitanio,Nazzareno;Merla,Giuseppe
• 通讯作者: Merla,Giuseppe

Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers.

组蛋白 H3 赖氨酸 4 单甲基化调节增强子处的长程染色质相互作用。

• DOI: 10.1038/cr.2018.18
• 发表时间: 2018
• 期刊: Cell research
• 影响因子: 44.1
• 作者: Yan,Jian;Chen,Shi-AnA;Local,Andrea;Liu,Tristin;Qiu,Yunjiang;Dorighi,KristelM;Preissl,Sebastian;Rivera,ChloeM;Wang,Chaochen;Ye,Zhen;Ge,Kai;Hu,Ming;Wysocka,Joanna;Ren,Bing
• 通讯作者: Ren,Bing

Affinity purification of MLL3/MLL4 histone H3K4 methyltransferase complex.

• DOI: 10.1007/978-1-61779-376-9_30
• 发表时间: 2012
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Cho, Young-Wook;Hong, SunHwa;Ge, Kai
• 通讯作者: Ge, Kai