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.

当激活基因表达时，将存储在DNA中的特定蛋白质的信息复制到RNA分子中。在真核生物中，该初始RNA分子的前体形式不起作用，需要通过三个前MRNA加工反应来修饰。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），可以将其从细胞核导出到细胞的细胞质中，并将其转化为蛋白质。这些修饰之一是裂解和聚腺苷酸化，将特定位点的前mRNA切割在poly（a）位点，并在新创建的末端添加150个腺苷核苷酸（a）。这形成具有特征性poly（a）尾巴的成熟mRNA。最近发现，大多数真核基因具有多个这样的poly（a）位点，而这些位点的替代用法会产生长度不同的mRNA。在特定前MRNA中使用不同的poly（a）位点来创建具有不同端点的成熟转录本的过程，称为替代性裂解和聚腺苷酸化或APA。大多数替代聚（a）位点都在mRNA上的区域中发现，称为3'untranslated区域（3'UTR），这些区域不包含用于制造蛋白质的信息。取而代之的是，3'UTRS藏有可以调节mRNA用于翻译机械的信息，因此会影响可以从中产生的蛋白质的量。如果此类调节信息位于前MRNA中不同的（a）位点之间，则替代裂解和聚腺苷酸化可以产生MRNA分子，这些mRNA分子既存在或缺乏这种调节信息，从而影响由基因制成的最终蛋白质。以这种方式，APA被认为是调节基因表达的关键过程，并参与了真核细胞中一些最基本的过程，包括将干细胞分化为组织特异性细胞，调节细胞分裂和致癌。尽管其关键功能以及APA影响了所有基因的一半以上的事实，但我们仍然对调节如何选择不同的poly（a）位点的过程以及控制不同mRNA同工型的命运的机制知之甚少。这里提出的提案旨在解决我们所知的这些基本差距。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，我们确定了一种名为dicer的众所周知的蛋白质，是poly（a）位点选择的调节剂。现在，我们旨在表征DICER选择一个聚（A）位点而不是另一个分子机制。此外，我们的方法使我们能够从细胞核和细胞质中提取裂解和聚腺苷酸化的mRNA同工型。这种方法首次揭示了许多经历APA的mRNA，尤其是那些长3'UTR的mRNA，并未导出到细胞质中，但似乎被困在细胞核中。 mRNA同工型的核保留是一种有趣的方法，可以调节特定的mRNA同工型用于细胞质中的蛋白质产生。该建议旨在阐明控制特定的mRNA同工型的机制，这些特定mRNA同工型在细胞核中长3'UTR。该过程的重要性是通过发现其中几个保留的转录本起源于与癌症相关的基因的基础，这些基因的产生APA mRNA同工型具有短3'UTR，缺乏调节序列的基因。因此，该提案的结果不仅将进一步了解我们对真核生物中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避免特定的调节过程。

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.