Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea
Widespread formation of alternative 3′ UTR isoforms via transcription termination in archaea
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DOI：
10.1038/nmicrobiol.2016.143
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发表时间：
2016-10-01
影响因子：
28.3
通讯作者：
Sorek, Rotem
中科院分区：
文献类型：
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作者：
Dar, Daniel;Prasse, Daniela;Sorek, Rotem
转录终止设定了RNA的3‘端边界，在基因调控中起着关键作用。尽管在细菌中对终止进行了很好的研究，但在古生菌中介导终止的信号仍然知之甚少。在这里，我们应用Term-seq以单碱基的精度全面地定位了两个在系统发育上相距遥远的古菌：甲烷链霉菌和Sulfolobus acidocaldarius的RNA3‘末端。对数百个基因的RNA3‘末端的比较揭示了每个生物体中转录终止子的序列组成，突出了不同古生物门之间的共同和不同特征。我们发现，与细菌相反，相当一部分古生菌基因由多个连续的终止子控制，为30%的基因产生了几个替代的3‘非翻译区亚型。这些可供选择的异构体经常呈现显著的长度差异，这意味着古生菌可以通过与真核生物类似的可供选择的3‘非翻译区来进行调控。虽然大多数终止子是基因间的，但我们发现许多情况下，一个基因的终止发生在下游基因的编码区，这意味着泄漏终止可能调节多基因操纵子中的转录间化学计量学。这些结果提供了古生菌转录终止子的第一个高通量图谱，并指出了一条连接细菌和真核生物非编码调控策略的进化路径。
Transcription termination sets the 3' end boundaries of RNAs and plays key roles in gene regulation. Although termination has been well studied in bacteria, the signals that mediate termination in archaea remain poorly understood. Here, we applied term-seq to comprehensively map RNA 3' termini, with single-base precision, in two phylogenetically distant archaea: Methanosarcina mazei and Sulfolobus acidocaldarius. Comparison of RNA 3' ends across hundreds of genes revealed the sequence composition of transcriptional terminators in each organism, highlighting both common and divergent characteristics between the different archaeal phyla. We find that, in contrast to bacteria, a considerable portion of archaeal genes are controlled by multiple consecutive terminators, generating several alternative 3' untranslated region isoforms for >30% of the genes. These alternative isoforms often present marked length differences, implying that archaea can employ regulation via alternative 3' untranslated regions, similar to eukaryotes. Although most of the terminators are intergenic, we discover numerous cases in which termination of one gene occurs within the coding region of a downstream gene, implying that leaky termination may tune inter-transcript stoichiometry in multi-gene operons. These results provide the first high-throughput maps of transcriptional terminators in archaea and point to an evolutionary path linking bacterial and eukaryal non-coding regulatory strategies.