title: Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements.
abstract: Of all known transposable elements, phage Mu exhibits the highest transposition efficiency and the lowest target specificity. In vitro, MuB protein is responsible for target choice. In this work, we provide a comprehensive assessment of the genome-wide distribution of MuB and its relationship to Mu target selection using high-resolution Escherichia coli tiling DNA arrays. We have also assessed how MuB binding and Mu transposition are influenced by chromosome-organizing elements such as AT-rich DNA signatures, or the binding of the nucleoid-associated protein Fis, or processes such as transcription. The results confirm and extend previous biochemical and lower resolution in vivo data. Despite the generally random nature of Mu transposition and MuB binding, there were hot and cold insertion sites and MuB binding sites in the genome, and differences between the hottest and coldest sites were large. The new data also suggest that MuB distribution and subsequent Mu integration is responsive to DNA sequences that contribute to the structural organization of the chromosome.
authors.affiliation: Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Ge
authors.forename: Zheng
authors.initials: Z
authors.lastname: Lou
authors.forename: Hong
authors.initials: H
authors.lastname: Cui
authors.forename: Lei
authors.initials: L
authors.lastname: Shang
authors.forename: Rasika M
authors.initials: RM
authors.lastname: Harshey
mesh_terms: D010583:Bacteriophage mu / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping; D002875:Chromosomes / Q000737:chemistry / Q000235:genetics*; D004247:DNA / Q000737:chemistry / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics; D035021:Factor For Inversion Stimulation Protein / Q000172:deficiency / Q000235:genetics; D056656:Lab-On-A-Chip Devices; D016254:Mutagenesis, Insertional; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D010957:Plasmids; D011485:Protein Binding / Q000235:genetics; D017384:Sequence Deletion
chemical_list: D004251:DNA Transposable Elements; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; D004247:DNA