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The primary transcriptome of the major human pathogen Helicobacter pylori


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 60 small RNAs including the ε-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.

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Figure 1: H. pylori TSS revealed by dRNA-seq.
Figure 2: TSS annotation and 5′ mRNA structure.
Figure 3: Discovery of H. pylori sRNAs including 6S RNA.
Figure 4: Trans and cis regulatory sRNAs.

Accession codes

Data deposits

Raw data are available from the NCBI Short Read Archive ( under accession number SRA010186.


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We thank F. Seifert; H. Hamoutene and B. Timmermann for technical support; M. Schmid for mass spectrometry analysis; H. De Reuse, A. van Vliet and M. K. Waldor for discussions; F. Thümmler for library preparation; M. Droege for pyrosequencing support. J.V. and R.R. are supported by NGFN+ grants (BMBF, Germany), and J.V. and P.F.S. by DFG Priority Program SPP1258 Sensory and Regulatory RNAs in Prokaryotes (Grants VO8751/2, VO8751/4; STA850/7-1). S.H. was supported by a formel.1 grant of the University of Leipzig, the Freistaat Sachsen (LIFE project), the German Research Foundation IZBI (BIZ6/1-4) and Volkswagen Stiftung (I/82 720). F.D. is supported by the French Agence Nationale de la Recherche (ANR-07-JCJC-0104-01), the French Association de la Recherche contre le Cancer (ARC) and La Ligue Nationale contre le Cancer (LNCC). We thank D. Rose for his supporting work and S. Washietl for a pre-release of the RNAcode software.

Author Contributions C.M.S., F.D., P.F.S. and J.V. designed the research; C.M.S., F.D., A.S., J.R., J.V. and S.C. performed all wet lab work. C.M.S., S.H., S.F., K.R., J.H. and P.F.S. conducted biocomputational analyses; R.R. carried out sequencing. J.V. wrote the manuscript, which all authors commented on, and supervised the project. Author information and raw data are available from C.M.S, P.F.S. and J.V.

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Correspondence to Jörg Vogel.

Supplementary information

Supplementary Methods

This file contains Supplementary Methods and Supplementary References. (PDF 288 kb)

Supplementary Figures

This file contains Supplementary Figures 1-23 with Legends and Supplementary References. (PDF 4224 kb)

Supplementary Tables

This file contains Supplementary Tables 1-3, 6 -11, 14, and 17-18 and Supplementary References. See separate files for Tables 4, 5, 12, 13, 15 and 16. (PDF 439 kb)

Supplementary Table 4

This file contains a TSS table. (XLS 582 kb)

Supplementary Table 5

This file contains an operon map of H. pylori. (XLS 102 kb)

Supplementary Table 12

This file contains a reannotation of genes. (XLS 34 kb)

Supplementary Table 13

This file contains the putative sRNA and antisense RNA TSS. (XLS 383 kb)

Supplementary Table 15

This file contains the predicted small ORFs in Helicobacter pylori 26695. (XLS 45 kb)

Supplementary Table 16

This file contains the expression differences at primary TSS. (XLS 136 kb)

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Sharma, C., Hoffmann, S., Darfeuille, F. et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464, 250–255 (2010).

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