David C. Grainger

Footprint-seq: a simple method to quantitatively map in vitro protein-DNA interactions on a genome-wide scale at high spatial resolution

Footprint-seq quantitatively maps protein-DNA interactions in vitro with high resolution and sensitivity, demonstrating its effectiveness for bacterial systems.

Widespread coupling of promoters and terminators of transcription in bacteria

The paper shows that promoters and terminators in bacteria are often coupled, with termination sequences contributing to promoter function, leading to regulatory interference between adjacent transcription units.

Systematic chemical genomic screening of Vibrio cholerae maps gene-phenotype relationships

This study uses chemical genomics to identify gene-phenotype relationships in Vibrio cholerae by screening 104 stress conditions across 3,026 single-gene mutants, revealing 1,518 significant growth phenotypes including 88 unannotated genes.

A 3UTR-derived small RNA modulates the life-cycle of the cholera toxin-encoding filamentous phage, CTXphi

The paper identifies and characterizes CisR, a small RNA that inhibits CTXφ phage production by repressing cep mRNA through Hfq-dependent base-pairing, linking phage activation to cell density and nutrient availability in V. cholerae.

Genome-wide mapping of cyclic AMP receptor protein binding in Enteroaggregative Escherichia coli reveals targeting of virulence-associated genes

This study maps CRP binding sites in EAEC to reveal its role in regulating virulence genes linked to nutritional state.

H-NS is a bacterial transposon capture protein

This study identifies H-NS as a transposon capture protein that directs transposition to specific chromosomal regions, affecting phenotypic diversity and gene function in bacteria.

The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli

The paper provides in vivo evidence that NAP-mediated chromosome re-modelling regulates transcription of the osmoresponsive proVWX operon in E. coli by destabilizing and re-establishing H-NS bridges under hyperosmotic conditions.

Widespread divergent transcription from prokaryotic promoters

The paper shows that prokaryotic promoters often drive divergent transcription due to symmetric elements and reciprocal stimulation between transcription start sites.