Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci.
Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci.
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DOI：
10.1261/rna.047324.114
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发表时间：
2015-03
期刊：
影响因子：
--
通讯作者：
Ponting CP
中科院分区：
文献类型：
--
作者：
Haerty W;Ponting CP
如果只能对基因组进行测序，而不能对 RNA 或蛋白质进行测序，那么功能性蛋白质编码外显子将可以通过其不寻常的核苷酸组成模式来识别，特别是整个外显子的高 GC 含量，以及靠近其边缘的不寻常的核苷酸含量。当然，RNA 和蛋白质可以进行测序，但基因间长非编码 RNA (lncRNA) 的功能程度由于其低核苷酸保守性而仍然受到质疑。受蛋白质编码外显子核苷酸组成模式的启发，我们寻找来自不同物种的 lncRNA 位点功能的证据。我们发现，跨多外显子 lncRNA 位点的这种模式反映了蛋白质编码基因的模式，尽管程度较小：具体而言，与内含子相比，lncRNA 外显子富含 GC。此外，我们报告了纯化选择作用的证据，以保留人类多外显子 lncRNA 中的外显子剪接增强子和果蝇 lncRNA 中的核苷酸组成。我们的研究结果为选择 lncRNA 位点内更有效的转录和剪接率提供了证据。尽管只有一小部分 RNA 碱基受到限制，但多外显子基因间 lncRNA 似乎需要其外显子的精确剪接才能发挥其功能。
If sequencing was possible only for genomes, and not for RNAs or proteins, then functional protein-coding exons would be recognizable by their unusual patterns of nucleotide composition, specifically a high GC content across the body of exons, and an unusual nucleotide content near their edges. RNAs and proteins can, of course, be sequenced but the extent of functionality of intergenic long noncoding RNAs (lncRNAs) remains under question owing to their low nucleotide conservation. Inspired by the nucleotide composition patterns of protein-coding exons, we sought evidence for functionality across lncRNA loci from diverse species. We found that such patterns across multiexonic lncRNA loci mirror those of protein-coding genes, although to a lesser degree: Specifically, compared with introns, lncRNA exons are GC rich. Additionally we report evidence for the action of purifying selection to preserve exonic splicing enhancers within human multiexonic lncRNAs and nucleotide composition in fruit fly lncRNAs. Our findings provide evidence for selection for more efficient rates of transcription and splicing within lncRNA loci. Despite only a minor proportion of their RNA bases being constrained, multiexonic intergenic lncRNAs appear to require accurate splicing of their exons to transact their function.
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