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

基本信息

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
项目类别：
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

项目摘要

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.

项目摘要十个易位（TET）蛋白在调节DNA的甲基化状态中起关键作用氧化甲基霉素（5MC），产生5-羟基甲基胞嘧啶（5HMC），两者都可以用作稳定表观遗传标记并参与活跃的脱甲基化。与其他TET家庭成员不同，Tet2不包含一个DNA结合域，目前尚不清楚如何募集到染色质。在这里我们证明 TET2由RNA结合蛋白拼贴分量1（PSPC1）通过转录募集活跃的基因座，包括内源性逆转录病毒（ERV），其长时间重复序列（LTR）已被选中由哺乳动物基因组作为分期和组织特异性的转录调节模块。我们发现PSPC1 TET2通过两种转录抑制通过组蛋白脱乙酰基酶和通过5HMC修饰对ERV RNA的转录后不稳定。我们的调查结果为转录活性ERV作为RNA的特定对接位点的功能作用提供了证据表观遗传调节和基因调节。该项目的目标是研究TET2是否以及如何通过RNA和RNA结合蛋白针对染色质，导致RNA羟甲基介导 MERVL的调节及其相关的2C基因对ESC的多能性，而不是零星 ESCS中的全能2C种群。我们假设RNA依赖性染色质的靶向TET2至关重要用于直接RNA脱甲基化和MERVL转录物的降解，这可能导致操纵干细胞和发育效力的有效工具。以下三个目标将测试假设并通过TET，RBP和ERV之间的紧密相互作用来控制干细胞效力。 1）在RNA修饰中建立TET2的RBP依赖性功能； 2）探索RNA-的新型TET2功能通过调节RNA靶标的ESC的多能性来实现依赖性染色质靶向； 3）操纵茎细胞和发育效力，具有RNA靶向CRISPR/RCAS9的靶向MERVL RNA修饰的RNA效力 ESC和开发胚胎。第一个目标将在HM5C修改中建立TET2的新功能 Mervl转录本以PSPC1依赖性方式。第二个目标将剖析HM5C的后果 Mervl转录本的修饰和HM5C介导的Mervl的分子机制降解。第三个目标将探索直接Mervl RNA操纵干细胞和开发效力修改。综上 TET2的染色质靶向干细胞效力中MERVL控制后的转录机理。这项目非常重要，因为预计将建立一个新的范式来理解ERV监管，TET 在RNA修饰和全能中的功能。

项目成果

期刊论文数量（14）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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

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

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

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

Comparative functional genomics identifies unique molecular features of EPSCs.

DOI：
10.26508/lsa.202201608
发表时间：
2022-11
期刊：
LIFE SCIENCE ALLIANCE
影响因子：
4.4
作者：
Malik, Vikas;Zang, Ruge;Fuentes-Iglesias, Alejandro;Huang, Xin;Li, Dan;Fidalgo, Miguel;Zhou, Hongwei;Wang, Jianlong
通讯作者：
Wang, Jianlong