Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana.
Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana.
复制标题
PAPS1依赖性聚腺苷酸化的全基因组分析确定了拟南芥功能专业的聚（A）聚合酶的新作用。
DOI：
10.1371/journal.pgen.1005474
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发表时间：
2015-08
期刊：
影响因子：
4.5
通讯作者：
Lenhard M
中科院分区：
文献类型：
--
作者：
Kappel C;Trost G;Czesnick H;Ramming A;Kolbe B;Vi SL;Bispo C;Becker JD;de Moor C;Lenhard M
真核生物mRNA 3'端的poly（A）尾促进其核输出、稳定性和翻译效率，其长度的变化可强烈影响基因表达。拟南芥基因组编码三种典型的核聚腺苷酸聚合酶，PAPS 1、PAPS 2和PAPS 4。正如它们不同的突变体表型所示，这三种亚型在功能上是特化的，其中PAPS 1修饰器官生长并抑制组成性免疫应答。然而，这种特化的分子基础在很大程度上是未知的。在这里，我们在野生型和paps 1突变体中在整个转录组范围内估计了poly（A）尾长度。这确定了在paps 1突变体中受到特别强烈影响的基因类别，包括编码核糖体蛋白、细胞分裂因子和主要碳水化合物代谢蛋白的基因。我们实验验证了两个新的功能，PAPS 1在核糖体生物合成和氧化还原稳态，预测的基础上分析的poly（A）-尾长度的变化在PAPS 1突变体。当覆盖PAPS 1依赖性的影响，在这里观察到的与基于独立的微阵列数据的共表达分析，最密切的共表达与PAPS 1的两个集群的转录本显示出最强的变化，在我们的分析中，在聚（A）尾长度和转录丰度的paps 1突变体。这表明，它们的共表达至少部分反映了这些转录物的优先聚腺苷酸化的PAPS 1相对于其他两个聚（A）-聚合酶亚型。因此，对poly（A）-尾长度的全转录组分析鉴定了新的生物学功能和可能的PAPS 1多聚腺苷酸化的靶转录物。与大规模共表达数据的数据整合表明，异构体的相对活性的变化被用作协调调节植物基因表达的内源性机制。真核生物mRNA的poly（A）尾促进mRNA从细胞核的输出、在细胞质中的翻译和mRNA的稳定性，并且poly（A）尾长度的变化可以强烈地影响基因表达。拟南芥基因组编码三种核典型的poly（A）聚合酶（PAPS 1、PAPS 2、PAPS 4），它们实现不同的功能，推测是通过优先聚腺苷酸化前mRNA的某些亚群。在这里，我们使用一种基于分馏的技术来评估PAPS 1活性降低对整个转录组的影响，并确定对PAPS 1活性降低特别敏感的转录本的功能类别。这些成绩单的分析确定了两个新的生物功能PAPS 1在核糖体生物合成和氧化还原稳态，我们证实实验。通过将我们的结果与全基因组共表达的信息叠加，我们证明了与PAPS 1共表达的基因在PAPS 1突变体中的poly（A）-尾长和总丰度变化方面受到最强烈的影响。这提供了强有力的证据表明，在数千个微阵列中看到的这些基因与PAPS 1的共表达至少部分是由PAPS 1同种型的活性改变引起的，表明植物确实使用同种型活性平衡的调节来协调调节基因组的表达。
The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression. The poly(A) tail of eukaryotic mRNAs promotes export from the nucleus, translation in the cytoplasm and stability of the mRNA, and changes in poly(A)-tail length can strongly impact on gene expression. The Arabidopsis thaliana genome encodes three nuclear canonical poly(A) polymerases (PAPS1, PAPS2, PAPS4) that fulfill different functions, presumably by preferentially polyadenylating certain subpopulations of pre-mRNAs. Here, we use a fractionation-based technique to assess the transcriptome-wide impact of reduced PAPS1 activity and identify functional classes of transcripts that are particularly sensitive to reduced PAPS1 activity. Analysis of these transcripts identifies two novel biological functions for PAPS1 in ribosome biogenesis and in redox homeostasis that we confirm experimentally. By overlaying our results with information about genome-wide co-expression, we demonstrate that genes co-expressed with PAPS1 are the most strongly affected in terms of poly(A)-tail length and total-abundance changes in the paps1 mutants. This provides strong evidence that the co-expression of these genes with PAPS1 that is seen across thousands of microarrays is at least partly caused by altered activity of the PAPS1 isoform, suggesting that the plant indeed uses modulation of the balance of isoform activities to coordinately regulate the expression of groups of genes.