Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.
Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.
复制标题
DOI：
10.1261/rna.040675.113
复制
发表时间：
2013-12
期刊：
影响因子：
--
通讯作者：
Gullerova M
中科院分区：
文献类型：
--
作者：
Schlackow M;Marguerat S;Proudfoot NJ;Bähler J;Erban R;Gullerova M
裂殖酵母中多聚腺苷酸化信号的全基因组分析揭示了普遍存在的AATAAA基序的保守性。切割位点的杂合是常见的，因为是替代的多聚腺苷酸化。此外，不同的生理条件可以对聚（A）位点的使用产生深远的影响。这些数据可在用户友好的数据库Pomb（A）中查阅。前体mRNA的多聚腺苷酸化是真核基因表达的关键步骤，由统称为多聚腺苷酸化信号的顺式元件介导。这种多聚腺苷酸化信号的全基因组分析在裂变酵母中缺失，尽管它是一种重要的模式生物。我们证明，典型的AATAAA基序是最常见的和功能的多聚腺苷酸化信号裂殖酵母粟酒裂殖酵母。通过分析在各种生理条件下生长的细胞的RNA-Seq数据集，我们鉴定了近90%的酵母基因的3 ′ UTR。切割位点的异源化是常见的，因为在条件内和条件之间的交替聚腺苷酸化也是如此。我们通过qRT-PCR和3 ′ RACE分析等功能分析验证了可能促进多聚腺苷酸化的计算鉴定序列元件。通过对含有AATAAA基序的基因的功能分析，强调了AATAAA基序的生物学重要性。在这里，我们表明，收敛基因缺乏粘连蛋白（2号染色体上）通常与较长的重叠mRNA转录。我们的生物信息学和实验全基因组结果进行了总结，可以在用户友好的数据库Pomb（A）中访问和定制。
Genome-wide analysis of polyadenylation signals in Schizosaccharomyces pombe reveals conservation of the ubiquitous AATAAA motif. Heterogeneity of cleavage sites is common, as is alternative polyadenylation. Furthermore, different physiological conditions can have profound effects on poly(A) site usage. These data are accessible in a user-friendly database Pomb(A). Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3′ UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3′RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).
登录
查看更多内容
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
3.2
作者：
Bennett, CL;Brunkow, ME;Chance, PF
通讯作者：
Chance, PF
影响因子：
64.5
作者：
Lewis, BP;Shih, IH;Burge, CB
通讯作者：
Burge, CB
影响因子：
64.5
作者：
Mayr C;Bartel DP
通讯作者：
Bartel DP
影响因子：
11.4
作者：
GICK, O;KRAMER, A;BIRNSTIEL, ML
通讯作者：
BIRNSTIEL, ML