Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements

doi:10.1073/pnas.0407069102

Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements

Jiguo Chen and
Ivan Sadowski*

Department of Biochemistry and Molecular Biology, University of British Columbia, 2146 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3

Edited by Mark T. Groudine, Fred Hutchinson Cancer Research Center, Seattle, WA, and approved February 22, 2005 (received for review September 23, 2004)

Abstract

The ability to determine the global location of transcription factor binding sites in vivo is important for a comprehensive understanding of gene regulation in human cells. We have developed a technology, called serial analysis of binding elements (SABE), involving subtractive hybridization of chromatin immunoprecipitation-enriched DNA fragments followed by the generation and analysis of concatamerized sequence tags. We applied the SABE technology to search for p53 target genes in the human genome, and have identified several previously described p53 targets in addition to numerous potentially novel targets, including the DNA mismatch repair genes MLH1 and PMS2. Both of these genes were determined to be responsive to DNA damage and p53 activation in normal human fibroblasts, and have p53-response elements within their first intron. These two genes may serve as a sensor in DNA repair mechanisms and a critical determinant for the decision between cell-cycle arrest and apoptosis. These results also demonstrate the potential for use of SABE as a broadly applicable means to globally identify regulatory elements for human transcription factors in vivo.

Footnotes

↵ * To whom correspondence should be addressed. E-mail: sadowski{at}interchange.ubc.ca.
Author contributions: J.C. and I.S. designed research; J.C. performed research; J.C. and I.S. analyzed data; and J.C. and I.S. wrote the paper.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: SABE, serial analysis of binding elements; IP, immunoprecipitation; ChIP, chromatin IP; SAGE, serial analysis of gene expression; MMR, mismatch repair; MLH1, mutL homolog 1; PMS2, yeast postmeiotic segregation increased 2.