The primary transcriptome of the major human pathogen Helicobacter pylori

By C. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, Sven Findeiss, A. Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, R. Reinhardt and 2 more. Nature, 2010

1,168 citations recorded by the source corpus.

Subfields: Molecular Biology, Small Animals, Surgery

View Paper: https://www.semanticscholar.org/paper/4fa53352df209a4b5a3135a8848d666a2ac22227

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In Molecular Biology

Citations in the corpus

Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa (2013, background): “…transcripts in diverse bacteria including Bacillus subtilis (Irnov et al., 2010), Chlamydia trachomatis (Albrecht et al., 2010), Helicobacter pylori (Sharma et al., 2010), Legionella pneumophila (Weissenmayer et al., 2011), Listeria monocytogenes (Oliver et al., 2009; Mraheil et al., 2011),…”
RNA-Seq methods for transcriptome analysis (2016, methodology): “Selective degradation has also been achieved by using the enzyme terminator 50-phosphate-dependent exonuclease (TEX), which recognizes RNA molecules with 50-monophosphate, as with rRNAs and tRNAs.(19) In summary, the selection of an approach for enriching RNA transcripts of interest for sequencing d”
Regulation by Small RNAs in Bacteria: Expanding Frontiers (2011, positive): “The advent of deep sequencing has turned the discovery of regulatory RNAs on its head, revealing literally hundreds of previously undetected transcripts, as illustrated by studies in Helicobacter pylori (Sharma et al., 2010) and Synechocystis (Mitschke et al.”
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis (2012, background): “Bacterial transcriptomes are surprisingly complex (1, 2, 3, 4, 5) and include diverse and abundant small RNAs and antisense RNAs (asRNAs).”
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021 (2013, positive): “These approaches revealed an unexpected abundance of cis -encoded antisense RNAs (asRNA) and trans -encoded sRNAs (sRNA), and thereby illuminated a previously unknown dimension of prokaryotic transcriptional activity [4-7].”
Single-cell RNA-seq: advances and future challenges (2014, positive): “Likewise, RNA-seq has facilitated the annotation of prokaryotic genomes by defining 5 and 3 untranslated regions of mRNAs and discovered many previously unrecognized RNA molecules including an unexpected degree of genome-wide antisense transcription (21).”
Pseudomonas genomes: diverse and adaptable. (2011, methodology): “For example, analysis of the transcriptome of Helicobacter pylori using a differential RNA-seq approach revealed considerable antisense transcription, hundreds of candidate small RNA genes and several genes for which the 5 0 end was misannotated (Sharma et al., 2010).”
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more (2012, methodology): “Mainly, the TEX exoribonuclease enzyme, which has a preference for 50-monophosphate (50-MP) ends (27), and ligation of synthetic RNA adapters to the whole RNA pool for 50-MP elimination (1) have been used.”
Bacterial small RNA regulators: versatile roles and rapidly evolving variations. (2011, background): “For example, there are reports of tens or hundreds of antisense RNAs encoded opposite annotated protein-coding genes, based on detection by microarray analysis or deep sequencing (Georg et al. 2009; Guell et al. 2009; Toledo-Arana et al. 2009; Sharma et al. 2010).”