Regulation of gene expression by mechanisms that target alternatively cleaved and polyadenylated mRNA isoforms

通过针对选择性切割和多腺苷酸化 mRNA 亚型的机制来调节基因表达

基本信息

批准号：
BB/N001184/1
负责人：
Andre Furger
金额：
$ 41.79万
依托单位：
University of Oxford
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2016
资助国家：
英国
起止时间：
2016 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FN001184%2F1
关键词：
Regulation gene expression mechanisms target

项目摘要

When gene expression is activated, the information to make a particular protein that is stored in the DNA is copied into an RNA molecule. In eukaryotes, this initial RNA molecule is made in a precursor form that is not functional and needs to be modified by three pre-mRNA processing reactions. The completion of these reactions converts this initial pre-mRNA, into a mature messenger RNA (mRNA) that can be exported from the nucleus into the cytoplasm of cells where it will be translated into a protein. One of these modifications, cleavage and polyadenylation, cleaves the pre-mRNA at specific sites, the poly(A) sites, and adds 150 adenosine nucleotides (A) to the newly created end. This forms a mature mRNA with a characteristic poly(A) tail. It has recently been discovered that most eukaryotic genes have more than one such poly(A) site and alternative usage of these sites creates mRNAs that differ in length. The process of using different poly(A) sites in a particular pre-mRNA to create mature transcripts with different end points, is named alternative cleavage and polyadenylation or APA. Most of the alternative poly(A) sites are found in a region on the mRNA, called 3'Untranslated Region (3'UTR), that does not contain information to make a protein. Instead, 3'UTRs harbour information that can regulate the availability of an mRNA for the translation machinery and so influence the amounts of proteins that can be made from it. If such regulatory information is located between different poly(A) sites in pre-mRNAs, then alternative cleavage and polyadenylation can create mRNA molecules that either present or lack such regulatory information and consequently influence the final amounts of protein that are made from a gene. In this way, APA is believed to be a critical process to regulate gene expression and is involved in the establishment of some of the most fundamental processes in eukaryotic cells including the differentiation of stem cells into tissue specific cells, the regulation of cell division and carcinogenesis. Despite its critical functions and the fact that APA affects over half of all genes, we still know very little about the processes that regulate how different poly(A) sites are chosen and the mechanisms that control the fate of the different mRNA isoforms are ill understood. The proposal presented here aims to address these fundamental gaps in our knowledge. We have recently developed a new experimental approach that enables us to investigate APA in greater detail than was previously possible. By employing this approach we identified a well-known protein called Dicer, as a regulator of poly(A) site choice. We now aim to characterise the molecular mechanisms by which Dicer selects one poly(A) site over the other. In addition, our approach enabled us to extract alternatively cleaved and polyadenylated mRNA isoforms from the nucleus and the cytoplasm. This approach revealed for the first time that many mRNAs that undergo APA and in particular those that have long 3'UTRs, are not exported into the cytoplasm but appear trapped in the nucleus. Nuclear retention of mRNA isoforms presents an intriguing way to regulate the availability of specific mRNA isoforms for protein production in the cytoplasm. This proposal aims to elucidate the mechanisms that control the retention of specific mRNA isoforms that have long 3'UTRs in the nucleus. The importance of this process is underpinned by finding that several of these retained transcripts originate from genes that are associated with cancer where the production of APA mRNA isoforms with short 3'UTRs, that lack regulatory sequences, is favoured. The outcomes of this proposal will thus not only further our understanding of a highly important process that regulates gene expression in eukaryotes but it will also help us to understand how particular regulatory processes are evaded during diseases such as cancer.

当基因表达被激活时，储存在 DNA 中的制造特定蛋白质的信息就会被复制到 RNA 分子中。在真核生物中，这种初始 RNA 分子以前体形式制成，没有功能，需要通过三个前 mRNA 加工反应进行修饰。这些反应的完成将这种初始的前 mRNA 转化为成熟的信使 RNA (mRNA)，可以从细胞核输出到细胞的细胞质中，并在细胞质中翻译成蛋白质。其中一种修饰（切割和聚腺苷酸化）会在特定位点（即 Poly(A) 位点）切割前 mRNA，并在新创建的末端添加 150 个腺苷核苷酸 (A)。这形成了具有特征性聚腺苷酸尾的成熟 mRNA。最近发现，大多数真核基因具有多个这样的聚腺苷酸位点，并且这些位点的替代使用会产生长度不同的 mRNA。在特定前体 mRNA 中使用不同的 Poly(A) 位点来创建具有不同终点的成熟转录本的过程称为选择性切割和聚腺苷酸化或 APA。大多数替代性 Poly(A) 位点位于 mRNA 上的一个区域，称为 3'非翻译区 (3'UTR)，该区域不包含制造蛋白质的信息。相反，3'UTR 包含的信息可以调节翻译机器中 mRNA 的可用性，从而影响从中产生的蛋白质的数量。如果此类调节信息位于前体 mRNA 中的不同 Poly(A) 位点之间，则选择性切割和聚腺苷酸化可以产生存在或缺乏此类调节信息的 mRNA 分子，从而影响由基因制成的蛋白质的最终量。这样，APA被认为是调节基因表达的关键过程，并参与真核细胞中一些最基本过程的建立，包括干细胞分化为组织特异性细胞、细胞分裂的调节和癌变。尽管 APA 具有重要的功能，而且 APA 影响超过一半的基因，但我们对调节不同 Poly(A) 位点选择的过程仍然知之甚少，对控制不同 mRNA 亚型命运的机制也知之甚少。。这里提出的提案旨在解决我们知识中的这些基本差距。我们最近开发了一种新的实验方法，使我们能够比以前更详细地研究 APA。通过采用这种方法，我们鉴定了一种名为 Dicer 的著名蛋白质，作为 Poly(A) 位点选择的调节剂。我们现在的目标是表征 Dicer 选择一个 Poly(A) 位点而不是另一个位点的分子机制。此外，我们的方法使我们能够从细胞核和细胞质中提取选择性切割和聚腺苷酸化的 mRNA 亚型。这种方法首次揭示了许多经历 APA 的 mRNA，特别是那些具有长 3'UTR 的 mRNA，不会被输出到细胞质中，而是被困在细胞核中。 mRNA 同工型的核保留提供了一种有趣的方法来调节细胞质中蛋白质生产的特定 mRNA 同工型的可用性。该提案旨在阐明控制细胞核中具有长 3'UTR 的特定 mRNA 亚型保留的机制。这一过程的重要性是基于以下发现：这些保留的转录物中的一些源自与癌症相关的基因，其中有利于产生具有短3'UTR且缺乏调节序列的APA mRNA亚型。因此，该提案的结果不仅将进一步加深我们对调节真核生物基因表达的非常重要的过程的理解，而且还将帮助我们了解在癌症等疾病期间如何逃避特定的调节过程。

项目成果

期刊论文数量（9）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Cold induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm

寒冷诱导的染色质压缩和时钟 mRNA 的核保留重置了昼夜节律

DOI：
10.1101/2020.06.05.127290
发表时间：
2020
期刊：
影响因子：
0
作者：
Fischl H
通讯作者：
Fischl H

Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)

DOI：
10.1101/2021.07.14.452379
发表时间：
2021-07
期刊：
bioRxiv
影响因子：
0
作者：
Philipp Lorenz;Anna Lamstaes;Harry Fischl;S. Xi;Aksel J Saukko-Paavola;S. Murray;Thomas Brown;Charlotte L. George;A. Furger;Andrew Angel;J. Mellor
通讯作者：
Philipp Lorenz;Anna Lamstaes;Harry Fischl;S. Xi;Aksel J Saukko-Paavola;S. Murray;Thomas Brown;Charlotte L. George;A. Furger;Andrew Angel;J. Mellor

Cold-induced chromatin compaction and nuclear retention of clock mRNAs resets the circadian rhythm.