High-Density Sequencing Applications in Microbial Molecular Genetics - 1st Edition - ISBN: 9780128159934, 9780128159941

High-Density Sequencing Applications in Microbial Molecular Genetics, Volume 612

1st Edition

Serial Volume Editors: Agamemnon Carpousis
eBook ISBN: 9780128159941
Hardcover ISBN: 9780128159934
Imprint: Academic Press
Published Date: 6th December 2018
Page Count: 574
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Table of Contents

    1. Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-Seq
    2. Vânia Pobre and Cecília M. Arraiano

    3. Conformational Studies of Bacterial Chromosomes by High-Throughput Sequencing Methods
    4. Virginia S. Lioy and Frédéric Boccard

    5. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay
    6. Sandrine Laguerre, Ignacio González, Sébastien Nouaille, Annick Moisan, Nathalie Villa-Vialaneix, Christine Gaspin, Marie Bouvier, Agamemnon J. Carpousis, Muriel Cocaign-Bousquet and Laurence Girbal

    7. FASTBAC-Seq: Functional AnalysiS of Toxin–Antitoxin Systems in BACteria by Deep Sequencing
    8. Sara Masachis, Nicolas J. Tourasse, Sandrine Chabas, Olivier Bouchez and Fabien Darfeuille

    9. The Challenges of Genome-Wide Studies in a Unicellular Eukaryote With Two Nuclear Genomes
    10. Sandra Duharcourt and Linda Sperling

    11. CLIP-Seq in Bacteria: Global Recognition Patterns of Bacterial RNA-Binding Proteins
    12. Liis Andresen and Erik Holmqvist

    13. High-Resolution Profiling of NMD Targets in Yeast
    14. Feng He, Alper Celik, Richard Baker and Allan Jacobson

    15. Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota
    16. Théo Foutel-Rodier, Agnès Thierry, Romain Koszul and Martial Marbouty

    17. Genome-Wide Mapping of Yeast Retrotransposon Integration Target Sites
    18. Anastasia Barkova, Amna Asif-Laidin and Pascale Lesage

    19. Genome-Wide Quantitation of Protein Synthesis Rates in Bacteria
    20. Grace E. Johnson and Gene-Wei Li

    21. On the Prowl: An In Vivo Method to Identify RNA Partners of a sRNA
    22. Marie-Claude Carrier, Claire Morin and Eric Massé

    23. Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTER
    24. Irina O. Vvedenskaya, Seth R. Goldman and Bryce E. Nickels

    25. Transcriptomic Approaches for Studying Quorum Sensing in Vibrio cholerae
    26. Roman Herzog and Kai Papenfort

    27. In Vitro Study of the Major Bacillus subtilis Ribonucleases Y and J
    28. Liliana Mora, Saravuth Ngo, Soumaya Laalami and Harald Putzer

    29. Mapping 5′-Ends and Their Phosphorylation State With EMOTE, TSS-EMOTE, and nEMOTE
    30. Peter Redder

    31. MS2-Affinity Purification Coupled With RNA Sequencing Approach in the Human Pathogen Staphylococcus aureus
    32. David Lalaouna, Emma Desgranges, Isabelle Caldelari and Stefano Marzi

    33. Noncoding RNAs in Archaea: Genome-Wide Identification and Functional Classification
    34. Anne Buddeweg, Michael Daume, Lennart Randau and Ruth A. Schmitz

    35. Methodology for Ribosome Profiling of Key Stages of the Caulobacter crescentus Cell Cycle
    36. James R. Aretakis, Nadra Al-Husini and Jared M. Schrader

    37. Transcriptome-Wide Analysis of Protein–RNA and RNA–RNA Interactions in Pathogenic Bacteria
    38. Jai J. Tree, Kenn Gerdes and David Tollervey

    39. Profiling RNA Polymerase II Phosphorylation Genome-Wide in Fission Yeast
    40. Tea Kecman, Dong-Hyuk Heo and Lidia Vasiljeva

    41. Toward Cell Type-Specific In Vivo Dual RNA-Seq
    42. Lutz Frönicke, Denise N. Bronner, Mariana X. Byndloss, Bridget McLaughlin, Andreas J. Bäumler and Alexander J. Westermann

    43. Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli

A.M. Mahedi Hasan, Benura Azeroglu and David R.F. Leach


High-Density Sequencing Applications in Microbial Molecular Genetics, Volume 612 in the Methods of Enzymology series provides the latest on the high-density sequencing of DNA and cDNA libraries and how they have revolutionized contemporary research in biology. Methods permitting tens of millions of sequence reads in a single experiment have paved the way to genome-wide studies that are contributing to our understanding of the complexity of living systems. Chapters in this updated volume include Characterizing the role of exoribonucleases in the control of microbial gene expression: Differential RNA seq., Conformational studies of bacterial chromosomes by high-throughput sequencing methods, Measuring mRNA degradation, and more.

Addition sections cover Global recognition patterns of bacterial RNA-binding proteins, High-resolution profiling of NMD targets, and the Generation of a metagenomic 3C/Hi-C library of human gut microbiota, Genome-wide mapping of yeast retrotransposons integration target sites, Measuring protein synthesis rates, Finding unsuspected partners of small RNAs with new screening approaches, Use of multiplexed transcriptomics to define the relationship between promoter sequence and transcription output, RNA-based control of quorum sensing in Vibrio cholerae, amongst other highly regarded topics.

Key Features

  • Detail methods used in research articles that were recently published in leading journals
  • Provides the latest on the high-density sequencing of DNA and cDNA libraries and how they have revolutionized contemporary research in biology


Students and researchers interested in using high-density sequencing methods as a tool for exploring the complexity of living systems. In addition to detailing protocols for a variety of applications in microbial molecular genetics, this volume will help a new generation of researchers to innovate by applying this technology to their research projects


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About the Serial Volume Editors

Agamemnon Carpousis

Agamemnon Carpousis Serial Volume Editor

Agamemnon James (A.J.) Carpousis is a Research Director in the CNRS. He graduated with honors in Biochemistry from the University of Pennsylvania and then did his doctoral studies in the Molecular Biology program at UCLA. His PhD work was on the mechanism of transcription initiation by Escherichia coli RNA polymerase. After postdoctoral research at UC Santa Barbara and the University of Geneva, A.J. Carpousis joined the LMGM, which is a CNRS Microbial Molecular Genetics Laboratory at the University of Toulouse. His research in Geneva contributed to the discovery that RNase E, which is an essential ribonuclease in E. coli, is a key enzyme in the initiation of mRNA degradation. In subsequent research, he purified RNase E and showed that it associates with other proteins involved in mRNA degradation forming a multienzyme complex, which is now known as the RNA degradosome. His group in Toulouse showed that RNase E has a composite structure consisting of a catalytic domain and a large non-catalytic region that serves as the scaffold for interactions with other components of the RNA degradosome. Other work includes studies on the role of RhlB, PNPase and poly(A) polymerase in mRNA degradation, and identification and characterization of beta-CASP ribonucleases in the Archaea. More recently, A.J. Carpousis and his colleagues showed that the RNA degradosome is localized to the inner cytoplasmic membrane of E. coli. They characterized a conserved element in the non-catalytic region of RNase E that directly anchors the RNA degradosome to the phospholipid bilayer of the inner membrane. RNA degradosomes on the inner membrane are highly dynamic forming short-lived clusters that are hypothesized to be centers of mRNA degradation. His group currently uses molecular genetics, biochemistry, high-density sequencing methods and super-resolution microscopy to address the question of the composition and supramolecular structure of the RNA degradosome clusters.

Affiliations and Expertise

CNRS, France