TY  - JOUR
A1  - Westermann, Alexander J.
A1  - Barquist, Lars
A1  - Vogel, Jörg
T1  - Resolving host-pathogen interactions by dual RNA-seq
JF  - PLoS Pathogens
N2  - The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables “dual RNA-seq” studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host. In the five years since the concept of dual RNA-seq was introduced, the technique has been applied to a range of infection models. This has not only led to a better understanding of the physiological changes in pathogen and host during the course of an infection but has also revealed hidden molecular phenotypes of virulence-associated small noncoding RNAs that were not visible in standard infection assays. Here, we use the knowledge gained from these recent studies to suggest experimental and computational guidelines for the design of future dual RNA-seq studies. We conclude this review by discussing prospective applications of the technique.
KW  - Medicine
KW  - RNA sequencing
KW  - Salmonellosis
KW  - Transcriptome analysis
KW  - Gene expression
KW  - Bacterial pathogens
KW  - Salmonella
KW  - Host cells
KW  - Lysis (medicine)
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-171921
VL  - 13
IS  - 2
ER  - 
TY  - JOUR
A1  - Heidrich, Nadja
A1  - Bauriedl, Saskia
A1  - Barquist, Lars
A1  - Li, Lei
A1  - Schoen, Christoph
A1  - Vogel, Jörg
T1  - The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
JF  - Nucleic Acids Research
N2  - Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of −35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
KW  - RNA
KW  - Neisseria meningitidis
KW  - dRNA-seq
KW  - transcriptome
KW  - RNA chaperone Hfq
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170828
VL  - 45
IS  - 10
ER  -