Archaeal genomes are densely packed; thus, correct transcription termination is an important factor for orchestrated gene expression. A systematic analysis of RNA 3´ termini, to identify transcription termination sites (TTS) using RNAseq data has hitherto only been performed in two archaea, Methanosarcina mazei and Sulfolobus acidocaldarius. In this study, only regions directly downstream of annotated genes were analysed, and thus, only part of the genome had been investigated. Here, we developed a novel algorithm (Internal Enrichment-Peak Calling) that allows an unbiased, genome-wide identification of RNA 3´ termini independent of annotation. In an RNA fraction enriched for primary transcripts by terminator exonuclease (TEX) treatment we identified 1,543 RNA 3´ termini. Approximately half of these were located in intergenic regions, and the remainder were found in coding regions. A strong sequence signature consistent with known termination events at intergenic loci indicates a clear enrichment for native TTS among them. Using these data we determined distinct putative termination motifs for intergenic (a T stretch) and coding regions (AGATC). In vivo reporter gene tests of selected TTS confirmed termination at these sites, which exemplify the different motifs. For several genes, more than one termination site was detected, resulting in transcripts with different lengths of the 3´ untranslated region (3´ UTR).

中文翻译：

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鉴定Haloferax volcanii中RNA 3´末端和终止位点。

古细菌基因组密集。因此，正确的转录终止是协调基因表达的重要因素。迄今为止，仅在两个古细菌Methanosarcina mazei和Sulfolobus acidocaldarius中进行了对RNA 3'末端的系统分析，以利用RNAseq数据鉴定转录终止位点（TTS）。在这项研究中，仅分析了注释基因的直接下游区域，因此，仅对基因组的一部分进行了研究。在这里，我们开发了一种新颖的算法（内部富集峰调用），该算法可以无偏倚地，不依赖注释地对全基因组RNA 3'末端进行鉴定。在通过终止子核酸外切酶（TEX）处理富集了主要转录本的RNA片段中，我们鉴定出1,543个RNA 3'末端。其中大约一半位于基因间区域，其余的位于编码区域。与基因间基因座上已知终止事件一致的强序列签名表明其中天然TTS明显富集。利用这些数据，我们确定了基因间（T延伸）和编码区（AGATC）的独特推定终止基序。选定的TTS的体内报道基因测试证实了这些位点的终止，这例证了不同的基序。对于多个基因，检测到多个终止位点，从而导致转录本的3´非翻译区（3´UTR）长度不同。利用这些数据，我们确定了基因间（T延伸）和编码区（AGATC）的独特推定终止基序。选定的TTS的体内报道基因测试证实了这些位点的终止，这例证了不同的基序。对于多个基因，检测到多个终止位点，从而导致转录本的3´非翻译区（3´UTR）长度不同。利用这些数据，我们确定了基因间（T延伸）和编码区（AGATC）的独特推定终止基序。选定的TTS的体内报道基因测试证实了这些位点的终止，这例证了不同的基序。对于多个基因，检测到多个终止位点，从而导致转录本的3´非翻译区（3´UTR）长度不同。