RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells

TET2 的 RNA 依赖性染色质靶向用于多能干细胞中的内源逆转录病毒控制

• 批准号: 10401429
• 负责人: Jianlong Wang
• 金额: $ 32.94万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-21 至 2024-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10401429
• 关键词: Affect; Cells; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Coupled; DNA; DNA Binding Domain; DNA Methylation; DNA Transposable Elements; Development; Docking; Embryo; Endogenous Retroviruses; Epigenetic Process; Family; Family member; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Goals; Health; Histone Deacetylase; Hydroxymethyltransferases; Immunoprecipitation; Individual; Knock-out; Knowledge; Lead; Light; Long Terminal Repeats; Malignant Neoplasms; Mammalian Cell; Massive Parallel Sequencing; Mediating; Methylation; Methyltransferase; Mission; Modification; Molecular; Mus; Outcome; Oxides; Pathologic; Play; Pluripotent Stem Cells; Population; Post-Transcriptional Regulation; Protein translocation; Proteins; Public Health; RNA; RNA Binding; RNA Degradation; RNA methylation; RNA-Binding Proteins; Regulation; Regulatory Element; Repression; Research; Role; Site; Stem Cell Development; Testing; Tetanus Helper Peptide; Tissues; Totipotency; Totipotent; Transcript; Transcriptional Regulation; United States National Institutes of Health; Work; base; crosslink; crosslinking and immunoprecipitation sequencing; demethylation; derepression; embryo cell; embryonic stem cell; epigenetic regulation; epitranscriptome; gene repression; histone methylation; human disease; insight; mammalian genome; member; novel; novel strategies; pluripotency; recruit; stem cell genes; stem cells; tool; transcriptome

PROJECT SUMMARY Ten-eleven translocation (TET) proteins play key roles in regulating the methylation status of DNA through oxidizing methylcytosines (5mC), generating 5-hydroxymethylcytosines (5hmC) that can both serve as stable epigenetic marks and participate in active demethylation. Unlike the other TET-family members, TET2 does not contain a DNA-binding domain, and it remains unclear how it is recruited to chromatin. Here we show that TET2 is recruited by the RNA-binding protein Paraspeckle component 1 (PSPC1) through transcriptionally active loci, including endogenous retroviruses (ERVs) whose long terminal repeats (LTRs) have been co-opted by mammalian genomes as stage- and tissue-specific transcriptional regulatory modules. We find that PSPC1 and TET2 contribute to ERV and ERV-associated gene regulation by both transcriptional repression via histone deacetylases and post-transcriptional destabilization of ERV RNAs through 5hmC modification. Our findings provide evidence for a functional role of transcriptionally active ERVs as specific docking sites for RNA epigenetic modulation and gene regulation. The goal of this project is to study whether and how TET2 may be targeted to chromatin via RNAs and RNA-binding proteins leading to RNA hydroxymethylation-mediated regulation of MERVL and their associated 2C genes for pluripotency of ESCs, as opposed to the sporadic totipotent 2C populations in ESCs. We hypothesize that RNA-dependent chromatin targeting of TET2 is critical for direct RNA demethylation and degradation of MERVL transcripts, which may lead to development of efficient tools in manipulating stem cell and developmental potency. The following three aims will test this hypothesis and explore stem cell potency control by an intimate interplay among TETs, RBPs, and ERVs. 1) Establish RBP-dependent functions of TET2 in RNA modification; 2) Explore novel TET2 functions in RNA- dependent chromatin targeting by regulating RNA targets for pluripotency of ESCs; and 3) Manipulate stem cell and developmental potency with RNA targeting CRISPR/RCas9 for targeted MERVL RNA modification in ESCs and developing embryos. The first aim will establish novel functions of TET2 in hm5C modification of MERVL transcripts in a PSPC1-dependent manner. The second aim will dissect the consequence of hm5C modification of MERVL transcripts and the molecular mechanism underlying hm5C-mediated MERVL degradation. The third aim will explore manipulating stem cell and development potency by direct MERVL RNA modification. Taken together, these three aims will provide considerable novel insight into RNA-dependent chromatin targeting of TET2 for the posttranscriptional mechanism of MERVL control in stem cell potency. The project is highly significant as it is expected to establish a new paradigm in understanding ERV regulation, TET functions in RNA modification, and totipotency.

项目总结

项目成果

Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation.

• DOI: 10.1038/s41467-020-18729-6
• 发表时间: 2020-10-02
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Lan J;Rajan N;Bizet M;Penning A;Singh NK;Guallar D;Calonne E;Li Greci A;Bonvin E;Deplus R;Hsu PJ;Nachtergaele S;Ma C;Song R;Fuentes-Iglesias A;Hassabi B;Putmans P;Mies F;Menschaert G;Wong JJL;Wang J;Fidalgo M;Yuan B;Fuks F
• 通讯作者: Fuks F

eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of stem cell pluripotency.

• DOI: 10.1126/sciadv.abm0478
• 发表时间: 2022-04
• 期刊: Science advances
• 影响因子: 13.6
• 作者: Li D;Yang J;Huang X;Zhou H;Wang J
• 通讯作者: Wang J

An RNAi screen of RNA helicases identifies eIF4A3 as a regulator of embryonic stem cell identity.

• DOI: 10.1093/nar/gkac1084
• 发表时间: 2022-11-28
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Li, Dan;Yang, Jihong;Malik, Vikas;Huang, Yuting;Huang, Xin;Zhou, Hongwei;Wang, Jianlong
• 通讯作者: Wang, Jianlong

Pursuing totipotency: authentic totipotent stem cells in culture.

• DOI: 10.1016/j.tig.2022.03.012
• 发表时间: 2022-07
• 期刊: TRENDS IN GENETICS
• 影响因子: 11.4
• 作者: Malik, Vikas;Wang, Jianlong
• 通讯作者: Wang, Jianlong

A TET1-PSPC1-Neat1 molecular axis modulates PRC2 functions in controlling stem cell bivalency.

• DOI: 10.1016/j.celrep.2022.110928
• 发表时间: 2022-06-07
• 期刊: CELL REPORTS
• 影响因子: 8.8
• 作者: Huang, Xin;Bashkenova, Nazym;Hong, Yantao;Lyu, Cong;Guallar, Diana;Hu, Zhe;Malik, Vikas;Li, Dan;Wang, Hailin;Shen, Xiaohua;Zhou, Hongwei;Wang, Jianlong
• 通讯作者: Wang, Jianlong