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

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

1st Edition

Serial Volume Editors: Agamemnon Carpousis
Hardcover ISBN: 9780128159934
Imprint: Academic Press
Published Date: 1st December 2018
Page Count: 412
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Table of Contents

1. Characterizing the role of exoribonucleases in the control of microbial gene expression: Differential RNA seq.
Cecilia Arraiano
2. Conformational studies of bacterial chromosomes by high-throughput sequencing methods
Frederic Boccard
3. Measuring mRNA degradation: delay or not delay
Muriel Cocaign-Bousquet
4. Toxin-antitoxin systems in Helicobacter pylori
Fabien Darfeuille
5. The challenges of genome-wide analyses in a eukaryotic microorganism with two nuclear genomes
Sandra Duharcourt
6. Global recognition patterns of bacterial RNA-binding proteins
Erik Holmqvist
7. High-resolution profiling of NMD targets
Allan Jacobson
8. Generation of a metagenomic 3C/Hi-C library of human gut microbiota
Romain Koszul
9. Genome-wide mapping of yeast retrotransposons integration target sites
Pascale Lesage
10. Measuring protein synthesis rates
Gene-Wei Li
11. Finding unsuspected partners of small RNAs with new screening approaches
Eric Masse
12. Use of multiplexed transcriptomics to define the relationship between promoter sequence and transcription output
Bryce Nikels
13. RNA-based control of quorum sensing in Vibrio cholerae
Kai Papenfort
14. The role of membrane tethering in the initiation of mRNA decay in Bacillus subtilis
Harald Putzer
15. RNA 5’ end mapping and phosphorylation state in Staphylococcus aureus
Peter Redder
16. Identification of RNA targets of Staphylococcus aureus RNase III combining catalytically inactive mutant enzyme and RNA sequencing
Pascale Romby
17. Non-coding RNAs in Archaea: What do we know today?
Ruth Schmitz
18. Ribosome profiling of the Caulobacter cell cycle
Jared Schrader
19. High-throughput analysis of protein-RNA and RNA-RNA interactions in pathogenic bacteria
Jai Tree
20. Profiling RNA polymerase II modifications genome-wide in fission yeast
Lidia Vasiljeva
21. Multi-organism RNA-seq approaches to bacterial infections
Alexander J. Westermann
22. Sort-Seq in the analysis of genetic regulatory sequences
Wade C. Winkler
23. Genomic analysis of DNA double-strand break repair in Escherichia coli
David Leach


High-density sequencing of DNA and cDNA libraries has 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. Microorganisms are ideal for developing innovative applications of high-density sequencing because of the relative ease with which they can be manipulated in the laboratory.

Key Features

  • Many of the chapters detail methods used in research articles that were recently published in leading journals


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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© Academic Press 2018
Academic Press
Hardcover ISBN:

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About the Serial Volume Editors

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