Max Planck Institute for Infection Biology, RNA Biology Group, D-10117 Berlin, Germany.
Nature. 2010 Mar 11;464(7286):250-5. doi: 10.1038/nature08756. Epub 2010 Feb 17.
Genome sequencing of Helicobacter pylori has revealed the potential proteins and genetic diversity of this prevalent human pathogen, yet little is known about its transcriptional organization and noncoding RNA output. Massively parallel cDNA sequencing (RNA-seq) has been revolutionizing global transcriptomic analysis. Here, using a novel differential approach (dRNA-seq) selective for the 5' end of primary transcripts, we present a genome-wide map of H. pylori transcriptional start sites and operons. We discovered hundreds of transcriptional start sites within operons, and opposite to annotated genes, indicating that complexity of gene expression from the small H. pylori genome is increased by uncoupling of polycistrons and by genome-wide antisense transcription. We also discovered an unexpected number of approximately 60 small RNAs including the epsilon-subdivision counterpart of the regulatory 6S RNA and associated RNA products, and potential regulators of cis- and trans-encoded target messenger RNAs. Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species.
幽门螺杆菌的基因组测序揭示了这种普遍存在的人类病原体的潜在蛋白质和遗传多样性，但对其转录组织和非编码 RNA 产物知之甚少。大规模平行 cDNA 测序（RNA-seq）正在彻底改变全球转录组分析。在这里，我们使用一种新的差异方法（dRNA-seq），选择性地针对初级转录物的 5' 端，展示了幽门螺杆菌转录起始位点和操纵子的全基因组图谱。我们在操纵子内发现了数百个转录起始位点，与注释基因相对，这表明通过多顺反子的解偶联和全基因组反义转录，从小型幽门螺杆菌基因组中增加了基因表达的复杂性。我们还发现了数量惊人的大约 60 种小 RNA，包括调控 6S RNA 的ε亚群对应物和相关的 RNA 产物，以及顺式和反式编码靶信使 RNA 的潜在调节剂。我们的方法为许多生物的初级转录组图谱绘制和注释建立了范例。
