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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被复制到RNA分子中。在真核生物中，这种最初的RNA分子是以前体形式产生的，它没有功能，需要通过三个前mRNA加工反应进行修饰。这些反应的完成将该初始前mRNA转化为成熟的信使RNA（mRNA），其可以从细胞核输出到细胞的细胞质中，在那里它将被翻译成蛋白质。这些修饰之一，切割和聚腺苷酸化，在特定位点切割前体mRNA，即聚腺苷酸位点，并在新产生的末端添加150个腺苷核苷酸（A）。这形成具有特征性poly（A）尾的成熟mRNA。最近已经发现，大多数真核基因具有多于一个这样的poly（A）位点，并且这些位点的替代使用产生长度不同的mRNA。在特定的前体mRNA中使用不同的poly（A）位点来产生具有不同终点的成熟转录物的过程被称为交替切割和多聚腺苷酸化或阿帕。大多数替代的poly（A）位点位于mRNA上的一个区域，称为3'UTR，不包含蛋白质的信息。相反，3'UTR含有可以调节mRNA对翻译机器的可用性的信息，从而影响可以由其制备的蛋白质的量。如果这种调节信息位于前mRNA中不同的poly（A）位点之间，那么交替的切割和多聚腺苷酸化可以产生存在或缺乏这种调节信息的mRNA分子，从而影响蛋白质的最终量，是由基因组成的因此，阿帕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，调节细胞分裂和致癌。尽管它的关键功能和事实，阿帕影响超过一半的基因，我们仍然知道很少的过程，调节不同的poly（A）位点的选择和机制，控制不同的mRNA异构体的命运是不了解。这里提出的建议旨在填补我们知识中的这些根本空白。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阿帕。通过采用这种方法，我们确定了一个众所周知的蛋白质称为切，作为多聚（A）位点选择的调节剂。我们现在的目标是阐明Dicer选择一个poly（A）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交替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阿帕的mRNA，特别是那些具有长3'UTR的mRNA，没有被输出到细胞质中，而是被困在细胞核中。mRNA异构体的核保留提出了一种有趣的方式来调节细胞质中蛋白质产生的特定mRNA异构体的可用性。该提案旨在阐明控制细胞核中具有长3'UTR的特定mRNA同种型保留的机制。这一过程的重要性得到了以下发现的支持，即这些保留的转录物中有几种来自与癌症相关的基因，其中具有短3'UTR的阿帕mRNA同种型的产生是有利的，缺乏调控序列。因此，这一提议的结果不仅将进一步加深我们对真核生物中调节基因表达的一个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.