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| Status |
Public on Dec 08, 2011 |
| Title |
Distinct p53 Genomic Binding Patterns in Normal and Cancer-derived Human Cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We report here genome-wide analysis of the tumor suppressor p53 binding sites in normal human cells. 743 high-confidence ChIP-seq peaks representing putative genomic binding sites were identified in normal IMR90 fibroblasts using a reference chromatin sample. More than 40 % were located within 2 kb of a transcription start site (TSS), a distribution similar to that documented for individually studied functional p53 binding sites and to date not observed by previous genome-wide studies. Nearly half of the high-confidence binding sites in the IMR90 cells reside in CpG islands, in marked contrast to sites reported in cancer-derived cells. The distinct genomic features of the IMR90 binding sites do not reflect a distinct preference for specific sequences, since the de novo developed p53 motif based on our study is similar to those reported by genome-wide studies of cancer cells. More likely the different chromatin landscape in normal compared to cancer-derived cells influences p53 binding via modulating availability of the sites. We compared the IMR90 ChIP-seq peaks to the recently published IMR90 methylome1, and demonstrated that they are enriched at hypomethylated DNA. Our study represents the first genome-wide, de novo mapping of p53 binding sites in normal human cells and reveals that p53 binding sites reside in distinct genomic landscapes in normal and cancer-derived human cells.
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| Overall design |
Identification of genomic p53 binding sites in normal human cells by ChIP-seq.
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| Contributor(s) |
Botcheva K, Anderson C |
| Citation(s) |
22127205 |
| |
| Submission date |
Aug 22, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Krassimira I Botcheva |
| E-mail(s) |
kalexiev@lbl.gov
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| Phone |
510 486 4368
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| Organization name |
Lawrence Berkeley National Laboratory
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| Department |
Cell and Molecular Biology
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| Street address |
One Cyclotron Rd MS977
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (2) |
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| Relations |
| SRA |
SRP007953 |
| BioProject |
PRJNA145681 |
