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Comparative analysis of alternative polyadenylation in S. cerevisiae and S. pombe
Genome Research ( IF 7 ) Pub Date : 2017-10-01 , DOI: 10.1101/gr.222331.117
Xiaochuan Liu , Mainul Hoque , Marc Larochelle , Jean-François Lemay , Nathan Yurko , James L. Manley , François Bachand , Bin Tian

Alternative polyadenylation (APA) is a widespread mechanism that generates mRNA isoforms with distinct properties. Here we have systematically mapped and compared cleavage and polyadenylation sites (PASs) in two yeast species, S. cerevisiae and S. pombe. Although >80% of the mRNA genes in each species were found to display APA, S. pombe showed greater 3′ UTR size differences among APA isoforms than did S. cerevisiae. PASs in different locations of gene are surrounded with distinct sequences in both species and are often associated with motifs involved in the Nrd1-Nab3-Sen1 termination pathway. In S. pombe, strong motifs surrounding distal PASs lead to higher abundances of long 3′ UTR isoforms than short ones, a feature that is opposite in S. cerevisiae. Differences in PAS placement between convergent genes lead to starkly different antisense transcript landscapes between budding and fission yeasts. In both species, short 3′ UTR isoforms are more likely to be expressed when cells are growing in nutrient-rich media, although different gene groups are affected in each species. Significantly, 3′ UTR shortening in S. pombe coordinates with up-regulation of expression for genes involved in translation during cell proliferation. Using S. pombe strains deficient for Pcf11 or Pab2, we show that reduced expression of 3′-end processing factors lengthens 3′ UTR, with Pcf11 having a more potent effect than Pab2. Taken together, our data indicate that APA mechanisms in S. pombe and S. cerevisiae are largely different: S. pombe has many of the APA features of higher species, and Pab2 in S. pombe has a different role in APA regulation than its mammalian homolog, PABPN1.



中文翻译:

酿酒酵母粟酒裂殖酵母交替多腺苷酸化的比较分析

替代性聚腺苷酸化(APA)是一种广泛的机制,可产生具有不同特性的mRNA同工型。在这里,我们已经系统地绘制和比较了两个酿酒酵母,酿酒酵母粟酒裂殖酵母中的切割和聚腺苷酸化位点(PAS)。尽管发现每个物种中> 80%的mRNA基因都显示APA,但与酿酒酵母相比,粟酒裂殖酵母在APA亚型之间显示出更大的3'UTR大小差异。在基因的不同位置的PAS在两个物种中都被不同的序列包围,并且通常与Nrd1-Nab3-Sen1终止途径中涉及的基序相关。在粟酒裂殖酵母中远端PAS周围的强烈基序导致长3'UTR亚型比短序列更高的丰度,这在酿酒酵母中是相反的。会聚基因之间的PAS位置差异会导致发芽和裂变酵母之间的反义转录本景观截然不同。在这两个物种中,当细胞在营养丰富的培养基中生长时,短3'UTR亚型更可能被表达,尽管每个物种都影响不同的基因组。重要的是,粟酒裂殖酵母中3'UTR的缩短与细胞增殖过程中参与翻译的基因的表达上调相协调。使用粟酒裂殖酵母缺乏Pcf11或Pab2的菌株,我们显示3'末端加工因子表达的减少延长了3'UTR,Pcf11比Pab2具有更强的作用。综上所述,我们的数据表明,粟酒裂殖酵母酿酒酵母中的APA机制存在很大差异:粟酒裂殖酵母具有许多较高物种的APA特征,而粟酒裂殖酵母中的Pab2在APA调控中的作用与其哺乳动物不同。同源物,PABPN1。

更新日期:2017-10-03
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