GC-compositional strand bias around transcription start sites in plants and fungi
GC-compositional strand bias around transcription start sites in plants and fungi
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DOI：
10.1186/1471-2164-6-26
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发表时间：
2005-02-28
期刊：
影响因子：
4.4
通讯作者：
Tomita, M
中科院分区：
文献类型：
--
作者：
Fujimori, S;Washio, T;Tomita, M
背景资料：最近报道了拟南芥基因转录起始位点（TSS）附近存在GC-组成链偏向或GC-偏斜（=（C-G）/（C+ G）），其中C和G表示胞嘧啶和鸟嘌呤残基的数目。然而，目前还不清楚其他真核生物是否也具有同样显著的GC-偏斜，这一性状的生物学意义仍然未知。结果：我们的研究证实了水稻TSS基因中存在显著的GC-偏斜（C > G）。利用统计分析比较拟南芥和水稻的全长cDNA和基因组序列。尽管两种植物TSS周围的G+ C含量存在显著差异，但偏倚程度几乎相同。尽管在人类和果蝇基因的TSS周围检测到轻微的GC-偏斜峰，包括相反的偏斜（C < G），但它们与在植物中鉴定的那些定性和定量不同。然而，在分析来自其他物种的表达序列标签和/或基因组序列后，在一些真菌中的翻译起始位点（TIS）上游区域中鉴定出植物样GC偏斜。根据我们的数据集，我们估计分别有> 70%和68%的拟南芥和水稻基因在100- bp窗口中具有较强的GC-偏斜（> 0.33）（即C残基的数量是G残基数量的两倍多）在TSS周围的+/- 100- bp窗口中）。拟南芥中高表达基因TSS的GC偏度值显著大于低表达基因。许多GC-偏斜峰优先位于TSS附近，因此我们研究了GC-偏斜作为TSS鉴定指标的潜在价值。结论：TSS附近的GC-偏斜（C> G）在单子叶植物和真双子叶植物中是严格保守的（即C > G），但在植物基因组中的TSS附近的GC-偏斜（C > G）在单子叶植物和真双子叶植物中是严格保守的（即C > G）。被子植物），在一些真菌中也观察到类似的偏斜。与低表达水平的基因相比，高表达的拟南芥基因在TSS中总体上具有更显著的GC-偏斜。因此，我们认为在某些植物和真菌中TSS周围的GC-偏斜与转录有关。它可能是由转录起始过程中的突变或频繁使用具有链偏好的转录因子结合位点引起的。此外，GC偏度是植物基因组中TSS预测的良好候选指标，其中CpG岛和基因之间缺乏相关性。
Background: A GC- compositional strand bias or GC- skew (=( C- G)/( C+ G)), where C and G denote the numbers of cytosine and guanine residues, was recently reported near the transcription start sites ( TSS) of Arabidopsis genes. However, it is unclear whether other eukaryotic species have equally prominent GC- skews, and the biological meaning of this trait remains unknown.Results: Our study confirmed a significant GC- skew ( C > G) in the TSS of Oryza sativa ( rice) genes. The full- length cDNAs and genomic sequences from Arabidopsis and rice were compared using statistical analyses. Despite marked differences in the G+ C content around the TSS in the two plants, the degrees of bias were almost identical. Although slight GC- skew peaks, including opposite skews ( C < G), were detected around the TSS of genes in human and Drosophila, they were qualitatively and quantitatively different from those identified in plants. However, plant- like GC-skew in regions upstream of the translation initiation sites ( TIS) in some fungi was identified following analyses of the expressed sequence tags and/ or genomic sequences from other species. On the basis of our dataset, we estimated that > 70 and 68% of Arabidopsis and rice genes, respectively, had a strong GC- skew (> 0.33) in a 100- bp window ( that is, the number of C residues was more than double the number of G residues in a +/- 100- bp window around the TSS). The mean GC- skew value in the TSS of highly- expressed genes in Arabidopsis was significantly greater than that of genes with low expression levels. Many of the GC- skew peaks were preferentially located near the TSS, so we examined the potential value of GC- skew as an index for TSS identification. Our results confirm that the GC- skew can be used to assist the TSS prediction in plant genomes.Conclusion: The GC- skew ( C > G) around the TSS is strictly conserved between monocot and eudicot plants ( ie. angiosperms in general), and a similar skew has been observed in some fungi. Highly- expressed Arabidopsis genes had overall a more marked GC- skew in the TSS compared to genes with low expression levels. We therefore propose that the GC- skew around the TSS in some plants and fungi is related to transcription. It might be caused by mutations during transcription initiation or the frequent use of transcription factor- biding sites having a strand preference. In addition, GC- skew is a good candidate index for TSS prediction in plant genomes, where there is a lack of correlation among CpG islands and genes.