Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
Genome Res. 2010 Dec;20(12):1639-50. doi: 10.1101/gr.112128.110. Epub 2010 Nov 2.
The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5' capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.
真核转录组的复杂性是由转录起始、终止、选择性剪接和其他形式的转录后修饰相互作用产生的。最近的研究表明，RNA 转录本也可能经历切割和二级 5'加帽。在这里，我们表明 RNA 的转录后切割通过生成一系列小 RNA 和长编码及非编码 RNA 来促进转录组的多样化。利用全基因组组蛋白修饰和 RNA 聚合酶 II 占据数据，我们证实了绝大多数内含子 CAGE 标签是来自转录后加工。通过将外显子 CAGE 标签与组织匹配的 PARE 数据进行比较，我们表明切割和随后的二级加帽是在发育阶段和组织特异性的方式下受到调控的。此外，我们在许多转录组数据集（包括 SAGE、cDNA、小 RNA 文库和深度测序的 RNA 分级分离池）中发现了普遍存在的 RNA 切割的证据。这些切割产物包括具有保留潜力的 mRNA 变体，可以翻译成缩短的功能性蛋白同工型。我们的结论是，转录后 RNA 切割是一个关键机制，它扩展了真核转录组的功能范围和调控控制的范围。
