High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons

Using 62 probe-level datasets obtained with a custom-designed Caulobacter crescentus microarray chip, we identify transcriptional start sites of 769 genes, 53 of which are transcribed from multiple start sites. Transcriptional start sites are identified by analyzing probe signal cross-correlation matrices created from probe pairs tiled every 5 bp upstream of the genes. Signals from probes binding the same message are correlated. The contribution of each promoter for genes transcribed from multiple promoters is identified. Knowing the transcription start site enables targeted searching for regulatory-protein binding motifs in the promoter regions of genes with similar expression patterns. We identified 27 motifs, 17 of which share no similarity to the characterized motifs of other C. crescentus transcriptional regulators. Using these motifs, we predict coregulated genes. We verified novel promoter motifs that regulate stress-response genes, including those responding to uranium challenge, a stress-response sigma factor and a stress-response noncoding RNA.

[1]  A. Newton,et al.  Ntr-like promoters and upstream regulatory sequence ftr are required for transcription of a developmentally regulated Caulobacter crescentus flagellar gene , 1989, Journal of bacteriology.

[2]  L. Shapiro,et al.  Expression of the Caulobacter heat shock gene dnaK is developmentally controlled during growth at normal temperatures , 1990, Journal of bacteriology.

[3]  L. Shapiro,et al.  A developmentally regulated Caulobacter flagellar promoter is activated by 3' enhancer and IHF binding elements. , 1992, Molecular biology of the cell.

[4]  L. Shapiro,et al.  A temporally controlled sigma-factor is required for polar morphogenesis and normal cell division in Caulobacter. , 1992, Genes & development.

[5]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[6]  B Ely,et al.  A consensus promoter sequence for Caulobacter crescentus genes involved in biosynthetic and housekeeping functions , 1995, Journal of bacteriology.

[7]  L. Shapiro,et al.  Regulation of a heat shock sigma32 homolog in Caulobacter crescentus , 1996, Journal of bacteriology.

[8]  L. Shapiro,et al.  Transcription of genes encoding DNA replication proteins is coincident with cell cycle control of DNA replication in Caulobacter crescentus , 1997, Journal of bacteriology.

[9]  Michael Gribskov,et al.  Combining evidence using p-values: application to sequence homology searches , 1998, Bioinform..

[10]  Y. Brun,et al.  Cell cycle-dependent transcriptional and proteolytic regulation of FtsZ in Caulobacter. , 1998, Genes & development.

[11]  L. Shapiro,et al.  Negative control of bacterial DNA replication by a cell cycle regulatory protein that binds at the chromosome origin. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[12]  G. Church,et al.  Systematic determination of genetic network architecture , 1999, Nature Genetics.

[13]  M. Østerås,et al.  Identification and Transcriptional Control of the Genes Encoding the Caulobacter crescentus ClpXP Protease , 1999, Journal of bacteriology.

[14]  David Page,et al.  A Probabilistic Learning Approach to Whole-Genome Operon Prediction , 2000, ISMB.

[15]  H. McAdams,et al.  Global analysis of the genetic network controlling a bacterial cell cycle. , 2000, Science.

[16]  Douglas L. Brutlag,et al.  BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes , 2000, Pacific Symposium on Biocomputing.

[17]  J. Helmann.  The extracytoplasmic function (ECF) sigma factors. , 2002, Advances in microbial physiology.

[18]  David R. Haynor,et al.  Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis , 2002, ISMB.

[19]  Lucy Shapiro,et al.  Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Lucy Shapiro,et al.  A Bacterial Cell-Cycle Regulatory Network Operating in Time and Space , 2003, Science.

[21]  C. Jacobs-Wagner,et al.  Spatial and temporal control of differentiation and cell cycle progression in Caulobacter crescentus. , 2003, Annual review of microbiology.

[22]  Lucy Shapiro,et al.  Oscillating Global Regulators Control the Genetic Circuit Driving a Bacterial Cell Cycle , 2004, Science.

[23]  Michael T. Laub,et al.  Cell-cycle progression and the generation of asymmetry in Caulobacter crescentus , 2004, Nature Reviews Microbiology.

[24]  L. Shapiro,et al.  Spatial complexity of mechanisms controlling a bacterial cell cycle. , 2004, Current opinion in microbiology.

[25]  Alison K. Hottes,et al.  DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus , 2005, Molecular microbiology.

[26]  Eoin L. Brodie,et al.  Whole-Genome Transcriptional Analysis of Heavy Metal Stresses in Caulobacter crescentus , 2005, Journal of bacteriology.

[27]  Bernhard Ø. Palsson,et al.  Immobilization of Escherichia coli RNA Polymerase and Location of Binding Sites by Use of Chromatin Immunoprecipitation and Microarrays , 2005, Journal of bacteriology.

[28]  Craig Stephens,et al.  Conserved modular design of an oxygen sensory/signaling network with species-specific output , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Harley H. McAdams,et al.  A Dynamically Localized Protease Complex and a Polar Specificity Factor Control a Cell Cycle Master Regulator , 2006, Cell.

[30]  Lucy Shapiro,et al.  DnaA couples DNA replication and the expression of two cell cycle master regulators , 2006, The EMBO journal.