Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021:2314:513-531.
doi: 10.1007/978-1-0716-1460-0_22.

RNA Sequencing for Transcript 5'-End Mapping in Mycobacteria

M Carla Martini  1 , Huaming Sun  1   2 , Scarlet S Shell  3   4
Affiliations

RNA Sequencing for Transcript 5'-End Mapping in Mycobacteria

M Carla Martini et al. Methods Mol Biol. 2021.

Abstract

Next-generation sequencing technologies facilitate the analysis of multiple important properties of transcriptomes in addition to gene expression levels. Here, we describe a method for mapping RNA 5' ends in Mycobacterium tuberculosis and Mycobacterium smegmatis, which allows the determination of transcription start sites (TSSs), comparative analysis of promoter usage under different conditions, and mapping of endoribonucleolytic cleavage sites. We describe in detail the procedures for constructing RNA sequencing libraries appropriate for RNA 5' end mapping using an Illumina sequencing platform, as well as bioinformatic procedures for data analysis.

Keywords: Endoribonuclease; Mycobacterium smegmatis; Mycobacterium tuberculosis; RNA 5′ ends; RNA processing; RNA sequencing; RNA-seq; RNase; RNase cleavage; Transcription start site.

PubMed Disclaimer

References

    1. Shell SS, Wang J, Lapierre P, Mir M, Chase MR, Pyle MM, Gawande R, Ahmad R, Sarracino DA, Ioerger TR, Fortune SM, Derbyshire KM, Wade JT, Gray TA (2015) Leaderless transcripts and small proteins are common features of the mycobacterial translational landscape. PLoS Genet 11(11):e1005641. https://doi.org/10.1371/journal.pgen.1005641 - DOI - PubMed - PMC
    1. Martini MC, Zhou Y, Sun H, Shell SS (2019) Defining the transcriptional and post-transcriptional landscapes of mycobacterium smegmatis in aerobic growth and hypoxia. Front Microbiol 10:591. https://doi.org/10.3389/fmicb.2019.00591 - DOI - PubMed - PMC
    1. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 7(9):709–715. https://doi.org/10.1038/nmeth.1491 - DOI - PubMed - PMC
    1. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37(18):e123. https://doi.org/10.1093/nar/gkp596 - DOI - PubMed - PMC
    1. Vargas-Blanco DA, Zhou Y, Zamalloa LG, Antonelli T, Shell SS (2019) mRNA degradation rates are coupled to metabolic status in mycobacterium smegmatis. MBio 10(4):e00957–e00919. https://doi.org/10.1128/mBio.00957-19 - DOI - PubMed - PMC

MeSH terms

LinkOut - more resources