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.

项目概要 10-11 易位 (TET) 蛋白通过以下方式在调节 DNA 甲基化状态中发挥关键作用：氧化甲基胞嘧啶 (5mC)，生成 5-羟甲基胞嘧啶 (5hmC)，两者均可作为稳定的表观遗传标记并参与主动去甲基化。与其他 TET 家族成员不同，TET2 不含有 DNA 结合结构域，但目前尚不清楚它是如何被招募到染色质上的。在这里我们表明 TET2 通过转录被 RNA 结合蛋白 Paraspeckle 成分 1 (PSPC1) 招募活性位点，包括长末端重复序列（LTR）已被增选的内源性逆转录病毒（ERV）由哺乳动物基因组作为阶段和组织特异性转录调节模块。我们发现PSPC1 TET2 通过转录抑制促进 ERV 和 ERV 相关基因调节通过 5hmC 修饰抑制组蛋白脱乙酰酶和 ERV RNA 转录后不稳定。我们的研究结果为转录活性 ERV 作为 RNA 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控。该项目的目标是研究 TET2 是否以及如何可能通过 RNA 和 RNA 结合蛋白靶向染色质，导致 RNA 羟甲基化介导 MERVL 及其相关 2C 基因对 ESC 多能性的调节，而不是零星的 ESC 中的全能 2C 群体。我们假设 TET2 的 RNA 依赖性染色质靶向至关重要用于直接 RNA 去甲基化和 MERVL 转录本的降解，这可能导致操纵干细胞和发育潜能的有效工具。以下三个目标将对此进行测试假设并探索通过 TET、RBP 和 ERV 之间的密切相互作用来控制干细胞效力。 1）建立 TET2 在 RNA 修饰中依赖 RBP 的功能； 2）探索RNA中新的TET2功能- 通过调节 RNA 靶点实现 ESC 多能性的依赖性染色质靶向； 3) 操纵阀杆利用 RNA 靶向 CRISPR/RCas9 进行靶向 MERVL RNA 修饰的细胞和发育效力 ESC 和发育中的胚胎。第一个目标是建立 TET2 在 hm5C 修饰中的新功能 MERVL 以 PSPC1 依赖性方式转录。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。第三个目标是探索通过直接 MERVL RNA 操纵干细胞和发育潜能修改。总而言之，这三个目标将为 RNA 依赖性提供相当新颖的见解。 TET2 染色质靶向用于 MERVL 控制干细胞效力的转录后机制。这该项目非常重要，因为它有望建立一个理解 ERV 监管、TET 的新范式在 RNA 修饰和全能性中发挥作用。

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.

Tet 介导的 RNA 羟甲基胞嘧啶在小鼠 ES 细胞和分化过程中的功能作用。

DOI：
发表时间：
2020
期刊：
影响因子：
16.6
作者：
Lan, Jie;Rajan, Nicholas;Bizet, Martin;Penning, Audrey;Singh, Nitesh K;Guallar, Diana;Calonne, Emilie;Li Greci, Andrea;Bonvin, Elise;Deplus, Rachel;Hsu, Phillip J;Nachtergaele, Sigrid;Ma, Chengjie;Song, Renhua;Fuentes;Ha
通讯作者：
Ha

ZFP281 coordinates DNMT3 and TET1 for transcriptional and epigenetic control in pluripotent state transitions.

ZFP281 协调 DNMT3 和 TET1，以实现多能状态转换中的转录和表观遗传控制。

DOI：
发表时间：
2023-03-25
期刊：
影响因子：
0
作者：
Huang, Xin;Balmer, Sophie;Lyu, Cong;Xiang, Yunlong;Malik, Vikas;Wang, Hailin;Zhang, Yu;Xie, Wei;Hadjantonakis, Anna;Zhou, Hongwei;Wang, Jianlong
通讯作者：
Wang, Jianlong

Ribosome heterogeneity in stem cells and development.

干细胞和发育中的核糖体异质性。

DOI：
发表时间：
2020
期刊：
影响因子：
0
作者：
Li, Dan;Wang, Jianlong
通讯作者：
Wang, Jianlong

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

TET1-PSPC1-Neat1 分子轴调节 PRC2 控制干细胞二价的功能。

DOI：
发表时间：
2022-06-07
期刊：
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

ZFP281 recruits polycomb repressive complex 2 to restrict extraembryonic endoderm potential in safeguarding embryonic stem cell pluripotency.

ZFP281 招募多梳抑制复合物 2 来限制胚胎外内胚层的潜力，从而保护胚胎干细胞的多能性。