Bacterial Genomics: Genome Organization and Gene Expression Tools

Cover
Title
Copyright
Dedication
Contents
List of Figures
Acknowledgements
1 Introduction: Bacterial Genomes and Gene Expression
2 Comparative Genomics in the Era of Sanger Sequencing
	2.1 Introduction
	2.2 The process of assembling and annotating bacterial genomes
		2.2.1 Genome assembly and gap closure
		2.2.2 Genome-scale computational identification of features
		2.2.3 Annotating genes with functions
	2.3 Case studies
		2.3.1 The Escherichia coli complex and large-scale horizontal gene acquisition
		2.3.2 Genome reduction in intracellular pathogens, endosymbionts and marine a-proteobacteria
		2.3.3 The dynamic genomes of Helicobacter pylori and Campylobacter jejuni
	2.4 Some lessons learnt from studying 2,000 bacterial genomes
		2.4.1 Genome size
		2.4.2 Coding density
		2.4.3 Gene order conservation
		2.4.4 Comparative genomics of gene functions: Systematic annotation
		2.4.5 Comparative genomics of gene functions: Scaling laws
	Summary
3 Studying Bacterial Genome Variation with Microarrays
	3.1 Introduction
	3.2 DNA microarrays: The concept
	3.3 DNA microarrays: From fluorescence intensities to information
		3.3.1 Background correction
		3.3.2 Normalisation
		3.3.3 Differences in signal from the same probe between two samples
	3.4 Comparative genome hybridisation and bacterial phylogenomics
	3.5 Case studies
		3.5.1 Comparative genome hybridisation studies of Escherichia coli
		3.5.2 Comparative genome hybridisation studies of Staphylococcus aureus
		3.5.3 Comparative genome hybridisation studies of Helicobacter pylori
	Summary
4 Studying Bacterial Genomes using Next-Generation Sequencing
	4.1 Introduction
	4.2 Next-generation sequencing technologies
		4.2.1 Template preparation strategies
		4.2.2 Sequencing strategies
	4.3 Sequencing data processing for genome sequencing and re-sequencing
		4.3.1 Genome assembly
		4.3.2 Aligning short reads to long genomes
	4.4 Case studies
		4.4.1 Pyrosequencing-enabled complete genome sequence of Acinetobacter baumanii
		4.4.2 On the track of pandemics: The genome of the aetiological agent of Black Death
		4.4.3 From community genomes to complete genomes to single-cell genomes
		4.4.4 Bacteria evolving in the laboratory
		4.4.5 Bacteria evolving in their biotic hosts
	Summary
5 Genome-Scale Analysis of Gene Expression and its Regulation in Bacteria
	5.1 Introduction
	5.2 The process of transcription and the regulation of its initiation: An overview
	5.3 Measuring gene expression on a genomic scale: Technologies
	5.4 Next-generation sequencing for gene expression measurements: Data analysis
		5.4.1 Transcriptome assembly
		5.4.2 Measuring gene expression levels
	5.5 Gene expression at high temporal resolution using fluorescent reporters
	5.6 Constructing transcriptional regulatory networks: ChIP-chip and ChIP-seq
	5.7 Case studies
		5.7.1 Experimental annotation of bacterial genomes
		5.7.2 Bioinformatic analysis of bacterial promoters
		5.7.3 DNA topology and its interplay with gene expression
		5.7.4 RNA polymerase occupancy and the s-factors
		5.7.5 Transcription factors and transcriptional regulatory networks
		5.7.6 Transcriptional control by the small-molecule alarmone ppGpp
		5.7.7 RNA chaperones and their regulons
	Summary
6 DNA Methylation in Bacteria: A Case for Bacterial Epigenetics
	6.1 Introduction
	6.2 DNA methyltransferases in bacteria: From restriction–modification systems
	6.3 Identifying sites of DNA methylation on a genomic scale
		6.3.1 Methylated DNA immunoprecipitation
		6.3.2 Bisulphite sequencing
		6.3.3 DNA cytosine methylation in laboratory
	6.4 Detecting DNA methylation by single-molecule real-time sequencing
		6.4.1 DNA adenine methylation in pathogenic E. coli by SMRT sequencing
		6.4.2 Insight into the epigenetic control of Caulobacter crescentus cell cycle from SMRT sequencing
	Summary
Index