Studying transcription factors in E.coli with Chip2™ microarray

Tuesday 23 August 2011

Professor Steve Busby and Dr David Grainger of the University of Birmingham have been using OGT’s Chip2 ™ microarrays to study the global distribution of transcription factors in E. coli. The ChIP-chip technology has provided a direct method to identify binding targets, independently of their consequences on gene expression, avoiding the shortcomings of PCR-based transcriptomics approaches.

Their research has gone from strength to strength: “When we started using OGT’s Chip2 microarrays in 2004 we were just looking at transcription factors but now, we are using the technology to ask new questions,” said Prof Busby. “The ChIP-chip technology has a potentially huge range of applications, and we are now looking at the global distribution of RNA polymerase within the cell. A lot of the RNA polymerase appears to be stuck, paused or ‘poised’ on the DNA and, to progress, needs assistance from factors. This was an unexpected but exciting development for us.”

“A related development has led us to study the global organisation of DNA folding in E. coli,” continued Prof Busby. “Unlike eukaryotic DNA, which is folded by histones, nobody really knows how DNA is organised in bacterial cells. Now that we are moving on from looking at transcription factors that may bind at ten, or perhaps 100 targets, to looking at elongation factors and RNA polymerase which move through the genome, the benefits of the high density OGT arrays will really kick in. All in all, I guess we have moved on from merely collecting stamps!”

“The OGT arrays are a manageable cost, and can be applied to any bacterium, as long as you have its sequence. We have established proof of principle with E. coli as the model system and now, of course, people have applied the technology to other bacteria. The growth in this area of work will come from real bacteria in real situations, such as pathogenic bacteria. Lots of folk are going to be calling OGT and saying, ‘I have this bacteria here, I’d like you to take a look.”

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