The difficult interpretation of transcriptome data: the case of the GATC regulatory network

Genomic analyses on part of Escherichia coli's chromosome had suggested the existence of a GATC regulated network. This has recently been confirmed through a transcriptome analysis. Two hypotheses about the molecular control mechanism have been proposed--(i) the GATC network regulation is caused by the presence of GATC clusters within the coding sequences; the regulation is the direct consequence of the clusters' hemi-methylation and therefore their elevated melting temperature, (ii) the regulation is caused by the presence of GATCs in the non-coding 500 bp upstream regions of the affected genes; it is the consequence of an interaction with a regulatory protein like Fnr or CAP. An analysis of the transcriptome data has not allowed us to decide between the two hypotheses. We have therefore taken a classic genomic approach, analyzing the statistical distribution of GATC along the chromosome, using a realistic model of the chromosome as theoretical reference. We observe no part...

• Type: Journal
• Year: 2004
• Where: CANDC
• Authors: Alessandra Riva, Marie-Odile Delorme, Tony Chevalier, Nicolas Guilhot, Corinne Hénaut, Alain Hénaut
• Keywords: CANDC 2004, Emerging Technology, GATC, Gatc Cluster, GATC Network Regulation