Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p
Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p
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DOI：
10.1038/srep15518
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发表时间：
2015-10-23
影响因子：
4.6
通讯作者：
Pavitt, Graham D.
中科院分区：
文献类型：
--
作者：
Kershaw, Christopher J.;Costello, Joseph L.;Pavitt, Graham D.
rna结合蛋白PUF家族通过转录后调控基因表达。酿酒酵母Puf3p的特点是结合核编码mrna指定线粒体蛋白。对其调控COX17的广泛研究表明其在mRNA衰变中的作用。使用集成的全基因组方法，我们定义了一组扩展的Puf3p靶mRNA，并使用mRNA和多体分析以及定量蛋白质组学定量评估了PUF3缺失对基因表达的全球影响。与先前的研究一致，我们对亲和纯化的Puf3-TAP相关mrna （RIP-seq）进行测序，鉴定出编码线粒体靶向蛋白的mrna。此外，我们还发现了720个新的mRNA靶点，这些靶点主要编码进入细胞核的蛋白质。比较野生型和puf3的转录本水平。细胞显示，只有一小部分mRNA水平改变，这表明Puf3p仅决定其靶mRNA的有限子集的mRNA稳定性。最后，蛋白质组学和翻译学研究表明，Puf3p的缺失对mRNA翻译有广泛但适度的影响。综合我们的综合多组学数据，我们发现Puf3p的多个靶点显示出一致的转录后调控特性，这表明Puf3p在基因表达的微调中发挥着广泛而微妙的作用。
The PUF family of RNA-binding proteins regulate gene expression post-transcriptionally. Saccharomyces cerevisiae Puf3p is characterised as binding nuclear-encoded mRNAs specifying mitochondrial proteins. Extensive studies of its regulation of COX17 demonstrate its role in mRNA decay. Using integrated genome-wide approaches we define an expanded set of Puf3p target mRNAs and quantitatively assessed the global impact of loss of PUF3 on gene expression using mRNA and polysome profiling and quantitative proteomics. In agreement with prior studies, our sequencing of affinity-purified Puf3-TAP associated mRNAs (RIP-seq) identified mRNAs encoding mitochondrially-targeted proteins. Additionally, we also found 720 new mRNA targets that predominantly encode proteins that enter the nucleus. Comparing transcript levels in wild-type and puf3. cells revealed that only a small fraction of mRNA levels alter, suggesting Puf3p determines mRNA stability for only a limited subset of its target mRNAs. Finally, proteomic and translatomic studies suggest that loss of Puf3p has widespread, but modest, impact on mRNA translation. Taken together our integrated multi-omics data point to multiple classes of Puf3p targets, which display coherent post-transcriptional regulatory properties and suggest Puf3p plays a broad, but nuanced, role in the fine-tuning of gene expression.