Genome-Wide Detection of Expressed sRNAs in Yersinia pestis with RNA-seq

  • Yanping Han
Part of the Springer Protocols Handbooks book series (SPH)


The RNA sequencing (RNA-seq) technology has been used to identify small regulatory RNAs (sRNAs) in bacteria. The well-characterized sRNAs usually play critical roles in modulating the translation and/or stability of the target mRNAs by partial complementary base pairing. Most known sRNAs require the RNA-binding protein Hfq to facilitate their base-pairing interactions. Previous studies have shown that Hfq is required for the pathogenesis and physiology of Yersinia. To date, more than 100 sRNAs have been detected on Y. pestis chromosome and plasmids, and the majority was identified on a global scale with RNA-seq. Here, we provide the RNA-seq protocol used to discover Y. pestis sRNAs expressed in vitro and in vivo, including the associated RNA isolation, size fractionation, and cDNA library construction, and the principles of their bioinformatic analysis.

Key words

RNA-seq sRNA Hfq Yersinia pestis 


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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Yanping Han
    • 1
  1. 1.Beijing Institute of Microbiology and EpidemiologyBeijingChina

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