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

High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Research Abstract Details 

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High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Abstract Text:

Patrick T McGrath,Honglak Lee,Li Zhang,Antonio A Iniesta,Alison K Hottes,Meng How Tan,Nathan J Hillson,Ping Hu,Lucy Shapiro,Harley H McAdams,

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.

High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Publishing Authors By Initials

PT McGrath,H Lee,L Zhang,AA Iniesta,AK Hottes,MH Tan,NJ Hillson,P Hu,L Shapiro,HH McAdams,

For similar genetic processes: gene expression: transcription, genetic research abstracts see: genetic processes: gene expression: transcription, genetic research

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High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Journal Published:

PUBLICATION TYPE: Research Support, U.S. Gov't,

Journal: Nature biotechnology

VOLUME: 25

Page Numbers: 584-92

Journal Abbreviation:

ISSN: 1087-0156

DAY: 1

MONTH: 04

YEAR: 2007

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

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LANGUAGE: eng

NlmUniqueID: 9604648

High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Keywords Mesh Terms:

KEYWORDS: Transcription, Genetic

MESH TERMS: genetics

Chemical & Substance for Abstract: High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Information

Substance Name: DNA, Bacterial

Registry Number: 0

Grant and Affiliation Information for High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons.

AFFILIATION: Department of Physics, Stanford University, Varian Physics, 382 Via Pueblo Mall, Stanford, California 94305, USA.

Country: United States

AGENCY: United States NHGRI

GRANT: T32 HG00044

ACRONYM: HG

MEDLINETA: Nat Biotechnol

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