Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network.
Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network.
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酵母中非编码 RNA 的功能和转录分析揭示了背景依赖性表型以及对蛋白质调控网络的反式影响。
DOI：
10.1371/journal.pgen.1008761
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发表时间：
2021-01
期刊：
影响因子：
4.5
通讯作者：
Delneri D
中科院分区：
文献类型：
--
作者：
Balarezo-Cisneros LN;Parker S;Fraczek MG;Timouma S;Wang P;O'Keefe RT;Millar CB;Delneri D
非编码RNA（ncRNA），包括最近发现的稳定未注释转录本（SUTs）和隐藏不稳定转录本（CUT），越来越多地被证明在真核生物基因的转录和转录后调控中发挥关键作用。在此，我们对酿酒酵母中的ncRNA进行了大规模筛选，为SUT和CUT功能提供了证据。收集了372个ncRNA缺失菌株在23种不同生长条件下的表型数据，鉴定了负责显著细胞适应性变化的ncRNA。对18个单倍体ncRNA缺失突变体和2个必需的ncRNA杂合缺失体进行转录组图谱组装。在所得RNA-seq数据的指导下，我们分析了蛋白质编码基因和非编码转录物的全基因组失调。新的功能性ncRNA，SUT 125，SUT 126，SUT 035和SUT 532，通过调节转录因子的反式作用进行了鉴定。此外，我们描述了SUTs和CUT在调节编码基因表达以响应不同环境条件，调节重要的生物过程如呼吸（SUT 125，SUT 126，SUT 035，SUT 432），类固醇生物合成（CUT 494，SUT 053，SUT 468）或rRNA加工（SUT 075和snR 30）中的影响。总的来说，这些数据捕获并整合了ncRNA和蛋白质编码基因的调控和表型网络，为ncRNA对细胞稳态的影响提供了全基因组证据。酵母基因组的四分之一包含非编码RNA分子（ncRNA），其不翻译成蛋白质，但参与基因表达的调控。ncRNA可以通过物理干扰其转录来影响附近的基因（顺式作用模式），或者它们与DNA、蛋白质或其他RNA相互作用以调节远端基因的表达（反式作用模式）。顺式作用的ncRNA的例子已经被广泛描述，然而，全基因组范围内的研究，以确定功能的反式作用的ncRNA参与全球基因调控仍然缺乏。在这里，我们使用ncRNA酵母缺失收集来评分ncRNA在不同环境条件下对细胞功能的影响。选择了一组具有广泛适应度多样性的20个ncRNA缺失突变体，以研究ncRNA对蛋白质和ncRNA表达网络的影响。我们发现改变的表型和全球转录变化之间的高度相关性，在环境依赖的方式。我们证实了基因组中ncRNA的反式调节及其在改变转录因子表达中的作用。这些发现支持ncRNA通过调节转录因子参与微调细胞表达的概念，作为一种有利的RNA介导的机制，对细胞来说可以是快速和具有成本效益的。
Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT053, SUT468) or rRNA processing (SUT075 and snR30). Overall, these data capture and integrate the regulatory and phenotypic network of ncRNAs and protein-coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis. A quarter of the yeast genome comprises non-coding RNA molecules (ncRNAs), which do not translate into proteins but are involved in the regulation of gene expression. ncRNAs can affect nearby genes by physically interfering with their transcription (cis mode of action), or they interact with DNA, proteins or other RNAs to regulate the expression of distant genes (trans mode of action). Examples of cis-acting ncRNAs have been broadly described, however, genome-wide studies to identify functional trans-acting ncRNAs involved in global gene regulation are still lacking. Here, we used a ncRNA yeast deletion collection to score ncRNA impact on cellular function in different environmental conditions. A group of 20 ncRNA deletion mutants with broad fitness diversity were selected to investigate the ncRNA effect on the protein and ncRNA expression network. We showed a high correlation between altered phenotypes and global transcriptional changes, in an environmental dependent manner. We confirmed the trans acting regulation of ncRNAs in the genome and their role in altering the expression of transcription factors. These findings support the notion of the involvement of ncRNAs in fine tuning cellular expression via regulation of transcription factors, as an advantageous RNA-mediated mechanism that can be fast and cost-effective for the cells.
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