Regulation of mRNA processing: Mechanisms and Consequences

mRNA 加工的调控：机制和后果

基本信息

批准号：
10621295
负责人：
James L. Manley
金额：
$ 79.43万
依托单位：
COLUMBIA UNIV NEW YORK MORNINGSIDE
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-06-08 至 2026-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10621295
关键词：
Affect Amyotrophic Lateral Sclerosis Anemia Antiviral Response Area Brain Complex Coupled Cytoplasm Development Disease Event GATA1 gene Genes Genetic Transcription Goals Homeostasis Human Lead MAP3K7 gene Malignant Neoplasms Membrane Proteins Messenger RNA Motor Cortex Mutation NF-kappa B Neoplasms Neurodegenerative Disorders Nuclear Nuclear Inner Membrane Nuclear Pore Complex Nuclear Pore Complex Proteins Open Reading Frames Pathway interactions Patients Physiological Poly A Polyadenylation Pre-mRNA Polyadenylation Factor Process Protein Isoforms Proteins RNA RNA Helicase RNA Splicing Reaction Regulation SARS-CoV-2 infection Sampling Specificity Suggestion Translating Work cell type cofactor design exosome experimental study frontotemporal lobar dementia amyotrophic lateral sclerosis human embryonic stem cell insight mRNA Precursor p38 Mitogen Activated Protein Kinase permissiveness sporadic amyotrophic lateral sclerosis

项目摘要

Synthesis of eukaryotic mRNAs is a complex process, and includes splicing and 3’ end formation of mRNA precursors. My lab has studied these processes for many years, including recently how they function in differentiation and disease. This proposal continues our studies on these topics, and can be divided into the following areas. mRNA processing in cancer. Work investigating how mutations in genes encoding splicing factors lead to MDS and other neoplasms will be continued, with an emphasis on SF3B1. Studies to elucidate both the mechanism(s) by which SF3B1 mutations affect splicing as well as the pathways that are dysregulated and lead to disease will be pursued. With respect to mechanism, an immediate goal will be to continue characterizing the SF3B1-interacting region of SUGP1. Another goal is to identify the SUGP1- interacting RNA helicase and determine its function in normal BP recognition, which will then allow determination of the detailed mechanism by which SF3B1 mutations disrupt splicing. With respect to pathways, experiments to elucidate the details of the recently described MAP3K7/p38/GATA1 pathway that underlies anemia in MDS will be performed. Missplicing events that affect other relevant pathways, such as aberrant activation of NF-kB, will be studied. FUS and other RBPs in ALS/FTD. With respect to FUS, experiments to analyze FUS nucleocytoplasmic homeostasis, a process important for formation of toxic cytoplasmic FUS aggregates, will be continued. Evidence supporting a gating mechanism involving the NPC and interactions with specific nucleoporins, themselves implicated in amyotrophic lateral sclerosis (ALS), will be pursued. Suggestions that this process may involve cell-type specificity, with MNs perhaps being more permissive, will be investigated. Experiments pursing the observation that RBP aggregates and consequent missplicing occur in a large fraction of sporadic ALS/FTD patient brains in the absence of known mutations will be continued. Aggregates will be isolated from motor cortex samples and protein/RNA composition determined to investigate what might nucleate their formation. Regulation of PA factor activity by AS. Experiments investigating the functions of isoforms of the polyadenylation (PA) factor WDR33 will be pursued. Two short isoforms, v2 and v3, are produced by intronic PA), and v2 but not v3 is an inner nuclear membrane protein not directly involved in PA. Interacting proteins of both will be identified, and results suggesting they are upregulated by an NF-kB pathway will be pursued. Evidence that the two isoforms function in the antiviral response, including to SARS-CoV-2 infection, will be further investigated. The finding that 45 isoforms of the PA factor Fip1 are produced in humans will be explored. eRNAs as mRNAs. Results suggesting that certain nuclear unstable lncRNAs, including eRNAs, are stabilized, exported to the cytoplasm and in some case translated, will be pursued. Observations that up to 5% of eRNAs contain significant ORFs and may be translated when the exosome cofactor Mtr4 is depleted will be further investigated. The possible physiological significance of eRNA “activation” will be studied in differentiated hESCs, which were shown to have sharply reduced levels of Mtr4.

真核mRNA的合成是一个复杂的过程，包括mRNA的剪接和3’端形成我的实验室对这些过程进行了多年的研究，包括最近它们如何发挥作用。该提案继续我们对这些主题的研究，并且可以分为致力于研究癌症中的 mRNA 加工过程。将继续对导致 MDS 和其他肿瘤的因素进行研究，重点是阐明 SF3B1。 SF3B1 突变影响剪接的机制以及影响剪接的途径就机制而言，当前的目标是消除失调并导致疾病。继续表征 SUGP1 的 SF3B1 相互作用区域的另一个目标是识别 SUGP1-。相互作用的 RNA 解旋酶并确定其在正常 BP 识别中的功能，从而允许确定 SF3B1 突变破坏剪接的详细机制。阐明最近描述的 MAP3K7/p38/GATA1 通路细节的实验 MDS 中的贫血将进行影响其他相关途径的错误剪接事件，例如异常。 NF-kB 的激活，将研究 ALS/FTD 中的 FUS 和其他 RBP。分析 FUS 核细胞质稳态，这是形成有毒细胞质 FUS 的重要过程将继续提供支持涉及 NPC 和互动的门控机制的证据。与肌萎缩性脊髓侧索硬化症（ALS）相关的特定核孔蛋白，将继续进行这一过程。涉及细胞类型特异性，MN 可能更宽容，将进行实验。观察发现，RBP 聚集和随后的错误剪接发生在很大一部分零星的细胞中。不存在已知突变的 ALS/FTD 患者大脑将继续被分离。确定运动皮层样本和蛋白质/RNA 组成，以研究可能使它们成核的物质 AS 对 PA 因子活性的调节实验研究同种型的功能。多聚腺苷酸 (PA) 因子 WDR33 将由 intronic 产生，即 v2 和 v3。 PA)，v2 但不是 v3 是不直接参与 PA 相互作用蛋白的内核膜蛋白。两者都将被鉴定，并且将寻求表明它们被 NF-kB 通路上调的结果。这两种异构体在抗病毒反应（包括 SARS-CoV-2 感染）中发挥作用的证据将得到证实人类产生 45 种 PA 因子 Fip1 亚型的发现将得到进一步研究。研究结果表明某些核不稳定的 lncRNA，包括 eRNA。稳定、输出到细胞质并在某些情况下进行翻译，将追求高达 5% 的观察结果。的 eRNA 含有重要的 ORF，并且当外泌体辅因子 Mtr4 耗尽时可能会被翻译进一步研究 eRNA“激活”可能的生理意义。分化的 hESC 的 Mtr4 水平急剧降低。

项目成果

期刊论文数量（18）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

The E592K variant of SF3B1 creates unique RNA missplicing and associates with high-risk MDS without ring sideroblasts.

DOI：
10.21203/rs.3.rs-2802265/v1
发表时间：
2023-04-14
期刊：
Research square
影响因子：
0
作者：
Choi, In Young;Ling, Jonathan;Dalton, W Brian
通讯作者：
Dalton, W Brian

Nuclear RNA transcript levels modulate nucleocytoplasmic distribution of ALS/FTD-associated protein FUS.

DOI：
10.1038/s41598-022-12098-4
发表时间：
2022-05-17
期刊：
Scientific reports
影响因子：
4.6
作者：
通讯作者：

The RNA polymerase II CTD "orphan" residues: Emerging insights into the functions of Tyr-1, Thr-4, and Ser-7.

RNA 聚合酶 II CTD“孤儿”残基：对 Tyr-1、Thr-4 和 Ser-7 功能的新见解。

DOI：
10.1080/21541264.2017.1338176
发表时间：
2018
期刊：
Transcription
影响因子：
0
作者：
Yurko,NathanM;Manley,JamesL
通讯作者：
Manley,JamesL

Replication protein A associates with nucleolar R loops and regulates rRNA transcription and nucleolar morphology.

DOI：
10.1101/gad.348858.121
发表时间：
2021-12-01
期刊：
Genes & development
影响因子：
10.5
作者：
Feng S;Manley JL
通讯作者：
Manley JL

C9orf72 and triplet repeat disorder RNAs: G-quadruplex formation, binding to PRC2 and implications for disease mechanisms.

C9orf72 和三联体重复紊乱 RNA：G 四链体形成、与 PRC2 的结合以及对疾病机制的影响。

DOI：
10.1261/rna.071191.119
发表时间：
2019
期刊：
RNA (New York, N.Y.)
影响因子：
0
作者：
Wang,Xueyin;Goodrich,KarenJ;Conlon,ErinG;Gao,Jianchao;Erbse,AnnetteH;Manley,JamesL;Cech,ThomasR
通讯作者：
Cech,ThomasR