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The p53MH algorithm and its application in detecting p53-responsive genes.

J Hoh1, S Jin, T Parrado

  • 1Laboratories of Statistical Genetics and Cancer Biology of The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA. jhoh@linkage.rockefeller.edu

Proceedings of the National Academy of Sciences of the United States of America
|June 22, 2002
PubMed
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A new computer algorithm, p53MH, identifies potential p53 transcription factor binding sites across genomes. Experiments confirmed that 63% of newly identified potential target genes respond to p53.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • The p53 transcription factor plays a crucial role in cellular responses to stress.
  • Identifying p53 DNA-binding sites is essential for understanding gene regulation.

Purpose of the Study:

  • To develop a computational tool for large-scale identification of p53 DNA-binding sites.
  • To discover novel p53 target genes.

Main Methods:

  • Development of the p53MH computer algorithm for genomewide scanning.
  • Utilizing known p53 DNA-binding motif characteristics (10-bp palindrome with a spacer).
  • Scanning human and mouse genomes, including flanking regulatory regions.

Main Results:

Related Experiment Videos

  • The p53MH algorithm identified approximately 300 potential p53 target genes.
  • Experimental validation using semiquantitative reverse transcription-PCR on 16 candidate genes.
  • Functional validation confirmed p53 response in 10 out of 16 tested genes (63% concordance).

    • Conclusions:

    • The p53MH algorithm is a powerful and versatile tool for identifying p53 target genes.
    • The study successfully identified novel genes regulated by p53.
    • This approach aids in understanding p53-mediated transcriptional regulation.