The role of natural antisense transcripts in plant gene regulation

天然反义转录本在植物基因调控中的作用

• 批准号: BB/D015774/1
• 负责人: Peter Meyer
• 金额: $ 38.21万
• 依托单位: University of Leeds
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2006
• 资助国家: 英国
• 起止时间: 2006 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FD015774%2F1
• 关键词: role; natural; antisense; transcripts; plant

In higher organisms, genetic information that is responsible for the production of a protein, is transcribed into an RNA molecule in the nucleus, which is then processed into a messenger RNA and exported into the cytoplasm for translation into an amino acid sequence. Protein-encoding genes only constitute a minority of the genomes of most organisms. In theory, there should therefore be sufficient space for individual genes to be separated from each other on the chromosomes, to ensure that transcription processes do not interfere with each other. When we analysed the distribution of protein-encoding genes in the model plant Arabidopsis thaliana, we found, to our surprise, that a considerable number of genes (a total of 956) partially overlap with other genes, in a sense-antisense arrangement. We named these loci Convergently Overlapping Gene pairs (COPs). This contrasts historical arguments that the convergent arrangement of overlapping genes is detrimental and has been preferentially removed during evolution. When we examined expression data from about 1,400 individual experiments, we found that both the sense and the overlapping antisense transcripts of the 956 COPs are often present in the same tissue types. This implies that the two transcripts could align to form double-stranded RNA (dsRNA) molecules. We know that dsRNA molecules can be recognised by a degradation mechanism, termed RNA interference (RNAi), which causes the destruction of both transcripts. Our analysis of the distribution of sense and antisense transcript, which we have recently published, shows, however, no indication for a specific degradation of COPs transcript. We know from animal systems that antisense transcripts can fulfil alternative roles than forming dsRNAs for the RNAi system. In plants, however, no such alternative pathways have been described. We therefore would like to find out, which alternative pathways plants have, for which antisense transcripts are required. Our analysis of the organisation and expression of the 956 COPs helped us to make an educated guess to postulate two alternative functions for antisense transcripts. (i) Among COPs, we find a much higher than expected proportion of genes that have more than one transcript, either because different regions are removed from the original RNA copy (alternative splice variants) or because the transcripts differ in length (alternative polyadenylation variants). This implies that antisense transcripts are required to modify sense transcript processing. (ii) We also frequently find that, while both the sense and antisense genes are transcribed, they often behave antagonistically: In many tissue types, one transcript type is high and the other low. For COPs where a particular stress treatment increases sense transcript levels, the antisense transcript level is reduced. Very soon, however, antisense transcript levels increase and sense transcript levels are reduced. A similar antagonistic pattern can be seen for COPs genes whose transcript levels change periodically during the day (circadian clock genes). These observations suggests a 'trancription interference' model, where transcription of one gene affects transcription of the other, which may be used to reset transcript levels after induction. We want to test if and how antisense transcripts can influence the production or composition of sense transcripts. For this we have selected individual COPs as potential model genes for each of the two mechanisms that we propose. We use Arabidopsis, because for each of our model COPs, there is a mutant line, with an insertion in the antisense gene. These lines allow us to assay if and how sense transcription or transcript processing is altered if the antisense gene in inactive. We think that our work will help to widen the current perception of gene expression, which focuses on transcription and transcript stability, but does not consider the regulatory effects from antisense transcripts.

在高等生物中，负责产生蛋白质的遗传信息在细胞核中转录成RNA分子，然后加工成信使RNA并输出到细胞质中翻译成氨基酸序列。蛋白质编码基因仅构成大多数生物体基因组的一小部分。因此，从理论上讲，染色体上的各个基因应该有足够的空间相互分离，以确保转录过程不会相互干扰。当我们分析模式植物拟南芥中蛋白质编码基因的分布时，我们惊讶地发现，相当多的基因（总共956个）与其他基因部分重叠，呈正义-反义排列。我们将这些位点命名为收敛重叠基因对（COP）。这与历史观点形成鲜明对比，历史观点认为重叠基因的趋同排列是有害的，并且在进化过程中已被优先去除。当我们检查来自约 1,400 个单独实验的表达数据时，我们发现 956 个 COP 的有义转录本和重叠的反义转录本通常存在于相同的组织类型中。这意味着两个转录本可以对齐形成双链 RNA (dsRNA) 分子。我们知道 dsRNA 分子可以通过称为 RNA 干扰 (RNAi) 的降解机制来识别，这会导致两个转录本被破坏。然而，我们最近发表的对有义和反义转录本分布的分析表明，没有迹象表明 COP 转录本有特定的降解。我们从动物系统中得知，反义转录本除了为 RNAi 系统形成 dsRNA 之外，还可以发挥其他作用。然而，在植物中，尚未描述过此类替代途径。因此，我们想知道植物有哪些替代途径，哪些需要反义转录本。我们对 956 个 COP 的组织和表达的分析帮助我们做出有根据的猜测，假设反义转录本有两种替代功能。 (i) 在 COP 中，我们发现具有多个转录本的基因比例远高于预期，这要么是因为从原始 RNA 拷贝中删除了不同区域（替代剪接变体），要么是因为转录本长度不同（替代多腺苷酸化变体）。这意味着需要反义转录本来修改有义转录本处理。 (ii)我们还经常发现，虽然有义基因和反义基因都被转录，但它们的行为常常是相反的：在许多组织类型中，一种转录类型高，另一种转录类型低。对于 COP，当特定应激处理增加有义转录物水平时，反义转录物水平会降低。然而，很快，反义转录物水平增加，正义转录物水平减少。对于转录水平在白天周期性变化的 COP 基因（生物钟基因），可以看到类似的拮抗模式。这些观察结果表明了一种“转录干扰”模型，其中一个基因的转录影响另一个基因的转录，这可用于在诱导后重置转录水平。我们想要测试反义转录本是否以及如何影响有义转录本的产生或组成。为此，我们选择了单独的 COP 作为我们提出的两种机制的潜在模型基因。我们使用拟南芥，因为对于我们的每个模型 COP，都有一个突变株系，其中插入了反义基因。这些线使我们能够测定反义基因失活时正义转录或转录处理是否以及如何改变。我们认为我们的工作将有助于扩大目前对基因表达的认识，其重点是转录和转录本稳定性，但不考虑反义转录本的调节作用。

项目成果

Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region.

• DOI: 10.1371/journal.pone.0016769
• 发表时间: 2011-02-02
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Zubko E;Kunova A;Meyer P
• 通讯作者: Meyer P

A pair of partially overlapping Arabidopsis genes with antagonistic circadian expression.

• DOI: 10.1155/2012/349527
• 发表时间: 2012
• 期刊: International journal of plant genomics
• 作者: Kunova A;Zubko E;Meyer P
• 通讯作者: Meyer P