title: Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR inE. coli.
abstract: The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism inEscherichia coli. Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions. Thus, our data indicate a broader regulatory role for GalR, and suggest that regulation by GalR is modulated by other factors. Surprisingly, we detect regulation of 158 transcripts by GalR, with few regulated genes being associated with a nearby GalR binding site. Based on our earlier observation of long-range interactions between distally bound GalR dimers, we propose that GalR indirectly regulates the transcription of many genes by inducing large-scale restructuring of the chromosome.
authors.affiliation: Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Qian
authors.affiliation: Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA.
authors.forename: Andrei
authors.initials: A
authors.lastname: Trostel
authors.affiliation: Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA.
authors.forename: Dale E A
authors.initials: DE
authors.lastname: Lewis
authors.affiliation: Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon, Korea.
authors.forename: Sang Jun
authors.initials: SJ
authors.lastname: Lee
authors.affiliation: Laboratory of Metabolism, National Institutes of Health, National Cancer Institute Bethesda, MD, USA.
authors.forename: Ximiao
authors.initials: X
authors.lastname: He
authors.affiliation: Wadsworth Center, New York State Department of Health Albany, NY, USA.
authors.forename: Anne M
authors.initials: AM
authors.lastname: Stringer
authors.affiliation: Wadsworth Center, New York State Department of HealthAlbany, NY, USA; Department of Biomedical Sciences, School of Public Health, University of AlbanyAlbany, NY, USA.
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Wade
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Institutes of Health, National Cancer Institute, Center for Cancer Research Frederick, MD, USA.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Schneider
authors.affiliation: DNASTAR, Inc. Madison, WI, USA.
authors.forename: Tim
authors.initials: T
authors.lastname: Durfee
authors.affiliation: Laboratory of Molecular Biology, National Institutes of Health, National Cancer Institute Bethesda, MD, USA.
authors.forename: Sankar
authors.initials: S
authors.lastname: Adhya
keywords: ChIP-chip; DNA superhelicity; GalR regulon; mega-loop; nucleoid