Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase

Julie Wells, Pearlly S. Yan, Meredith Cechvala, Hui-ming Huang, Peggy J. Farnham

Research output: Contribution to journalArticle

104 Citations (Scopus)

Abstract

The retinoblastoma (Rb) tumor suppressor protein is an important regulator of cell proliferation and differentiation. Many studies have shown that pRb can negatively regulate the activity of the E2F family of transcription factors during G0 and G1 phases of the cell cycle, perhaps by serving as a bridge between the E2Fs and transcriptional repressors such as histone deacetylases and methylases. However, pRb has also been shown to localize to discrete DNA foci during S phase, a time at which pRb is thought to be dissociated from E2F. Numerous other DNA binding proteins have been shown to interact with pRb, suggesting that pRb may control progression through S phase by binding to sites in the genome distinct from E2F target gene promoters. To test this hypothesis, we have identified novel pRb binding sites within the human genome using an unbiased approach which relies upon a combination of chromatin immunoprecipitation and CpG microarray analysis. To provide the greatest opportunity of finding distinct sets of pRb binding sites, we examined pRb binding in chromatin obtained from human Raji cells synchronized in either G0/G1 phase or S phase. These experiments have allowed us to identify a large set of new genomic binding sites for the pRb protein. We found that some sites are occupied by pRb only during G0/G1 phase, as would be predicted from previous models of pRb function. We also identified sites to which pRb bound only during S phase and other sites which were bound constitutively by pRb. Surprisingly, we found that E2F1 was present at most of the CpG islands bound by pRb, independent of the phase of the cell cycle. Thus, although pRb has the potential to interact with numerous transcription factors, our data suggest that the majority of DNA-bound pRb is recruited to E2F target promoters during both G0/G1 and S phases.

Original languageEnglish (US)
Pages (from-to)1445-1460
Number of pages16
JournalOncogene
Volume22
Issue number10
DOIs
StatePublished - Mar 13 2003
Externally publishedYes

Fingerprint

Cell Cycle Resting Phase
S Phase
G1 Phase
Binding Sites
Cell Cycle
E2F Transcription Factors
Tumor Suppressor Proteins
Retinoblastoma Protein
CpG Islands
Histone Deacetylases
Chromatin Immunoprecipitation
DNA
DNA-Binding Proteins
Human Genome
Microarray Analysis
Chromatin
Cell Differentiation
Transcription Factors
Cell Proliferation
Genome

Keywords

  • Chromatin immunoprecipitation
  • CpG island
  • E2F1
  • pRb

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research
  • Genetics

Cite this

Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. / Wells, Julie; Yan, Pearlly S.; Cechvala, Meredith; Huang, Hui-ming; Farnham, Peggy J.

In: Oncogene, Vol. 22, No. 10, 13.03.2003, p. 1445-1460.

Research output: Contribution to journalArticle

Wells, Julie ; Yan, Pearlly S. ; Cechvala, Meredith ; Huang, Hui-ming ; Farnham, Peggy J. / Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. In: Oncogene. 2003 ; Vol. 22, No. 10. pp. 1445-1460.
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abstract = "The retinoblastoma (Rb) tumor suppressor protein is an important regulator of cell proliferation and differentiation. Many studies have shown that pRb can negatively regulate the activity of the E2F family of transcription factors during G0 and G1 phases of the cell cycle, perhaps by serving as a bridge between the E2Fs and transcriptional repressors such as histone deacetylases and methylases. However, pRb has also been shown to localize to discrete DNA foci during S phase, a time at which pRb is thought to be dissociated from E2F. Numerous other DNA binding proteins have been shown to interact with pRb, suggesting that pRb may control progression through S phase by binding to sites in the genome distinct from E2F target gene promoters. To test this hypothesis, we have identified novel pRb binding sites within the human genome using an unbiased approach which relies upon a combination of chromatin immunoprecipitation and CpG microarray analysis. To provide the greatest opportunity of finding distinct sets of pRb binding sites, we examined pRb binding in chromatin obtained from human Raji cells synchronized in either G0/G1 phase or S phase. These experiments have allowed us to identify a large set of new genomic binding sites for the pRb protein. We found that some sites are occupied by pRb only during G0/G1 phase, as would be predicted from previous models of pRb function. We also identified sites to which pRb bound only during S phase and other sites which were bound constitutively by pRb. Surprisingly, we found that E2F1 was present at most of the CpG islands bound by pRb, independent of the phase of the cell cycle. Thus, although pRb has the potential to interact with numerous transcription factors, our data suggest that the majority of DNA-bound pRb is recruited to E2F target promoters during both G0/G1 and S phases.",
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