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RNA Sequencing for Transcript 5′-End Mapping in Mycobacteria

  • Scarlet S. Shell
  • Michael R. Chase
  • Thomas R. Ioerger
  • Sarah M. FortuneEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1285)

Abstract

Next-generation sequencing technologies facilitate the analysis of multiple important properties of the transcriptome in addition to gene expression levels. Here we describe a method for mapping RNA 5′ ends in Mycobacterium tuberculosis, which allows the determination of transcriptional start sites (TSSs), comparative analysis of promoter usage under different conditions, and mapping of endoribonucleolytic processing sites. We describe in detail the procedures for constructing RNA sequencing libraries appropriate for RNA 5′ end mapping using an Illumina sequencing platform. We also outline the major steps of data analysis.

Key words

RNA-seq RNA sequencing RNA processing Transcription start site Transcription start point Gene expression Illumina library Endoribonuclease RNase 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Scarlet S. Shell
    • 1
    • 2
  • Michael R. Chase
    • 1
  • Thomas R. Ioerger
    • 3
  • Sarah M. Fortune
    • 1
    Email author
  1. 1.Department of Immunology and Infectious DiseasesHarvard School of Public HealthBostonUSA
  2. 2.Department of Biology and BiotechnologyWorcester Polytechnic InstituteWorcesterUSA
  3. 3.Department of Computer ScienceTexas A&M UniversityCollege StationUSA

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