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Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.

Publication ,  Journal Article
Ohler, U
Published in: Nucleic Acids Res
2006

The reliable recognition of eukaryotic RNA polymerase II core promoters, and the associated transcription start sites (TSSs) of genes, has been an ongoing challenge for computational biology. High throughput experimental methods such as tiling arrays or 5' SAGE/EST sequencing have recently lead to much larger datasets of core promoters, and to the assessment that the well-known core promoter sequence elements such as the TATA box appear to be much less frequent than thought. Here, we address the co-occurrence of several previously identified core promoter sequence motifs in Drosophila melanogaster to determine frequently occurring core promoter modules. We then use this in a new strategy to model core promoters as a set of alternative submodels for different core promoter architectures reflecting these different motif modules. We show that this system improves greatly on computational promoter recognition and leads to highly accurate in silico TSS prediction. Our results indicate that at least for the case of the fruit fly, we are getting closer to an understanding of how the beginning of a gene is defined in a eukaryotic genome.

Duke Scholars

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

2006

Volume

34

Issue

20

Start / End Page

5943 / 5950

Location

England

Related Subject Headings

  • Transcription Initiation Site
  • Sequence Analysis, DNA
  • Reproducibility of Results
  • Promoter Regions, Genetic
  • Models, Statistical
  • Markov Chains
  • Drosophila melanogaster
  • Developmental Biology
  • Computational Biology
  • Animals
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Journal cover image

Published In

Nucleic Acids Res

DOI

EISSN

1362-4962

Publication Date

2006

Volume

34

Issue

20

Start / End Page

5943 / 5950

Location

England

Related Subject Headings

  • Transcription Initiation Site
  • Sequence Analysis, DNA
  • Reproducibility of Results
  • Promoter Regions, Genetic
  • Models, Statistical
  • Markov Chains
  • Drosophila melanogaster
  • Developmental Biology
  • Computational Biology
  • Animals