Cell context dependent p53 Genome-wide binding patterns and enrichment at repeats

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Botcheva, Krassimira ^a,b   McCorkle, Sean R ^a  

^a BROOKHAVEN NATIONAL LABORATORY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN P53; DNA; TP53 PROTEIN, HUMAN;

ARTICLE; BINDING AFFINITY; BINDING SITE; BIOACCUMULATION; CANCER CELL LINE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CPG ISLAND; EPIGENETICS; GENE MAPPING; GENETIC ASSOCIATION; GENOME ANALYSIS; HUMAN; HUMAN CELL; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; RNA SEQUENCE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TREND STUDY; ANTIBODY SPECIFICITY; CELL LINE; GENETIC EPIGENESIS; GENETICS; HCT116 CELL LINE; HUMAN GENOME; LONG INTERSPERSED REPEAT; METABOLISM;

BINDING SITES; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; DNA; EPIGENESIS, GENETIC; GENOME, HUMAN; HCT116 CELLS; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; ORGAN SPECIFICITY; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84911934843     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113492     Document Type: Article

References (24)

1. El-Deiry WS, Kern SE, Pietenpol JA, Kinzler KW, Vogelstein B (1992) Definition of a consensus binding site for p53. Nat Genet 1: 45-49.
2. Funk WD, Pak DT, Karas RH, Wright WE, Shay JW (1992) A transcriptionally active DNA-binding site for human p53 protein complexes. Mol Cell Biol 12: 2866-2871.
3. Levine AJ, Oren M (2009) The first 30 years of p53: growing ever more complex. Nat Rev Cancer 9: 749-758.
4. Riley T, Sontag E, Chen P, Levine A (2008) Transcriptional control of human p53-regulated genes. Nat Rev Mol Cell Biol 9: 402-412.
5. Wang B, Xiao Z, Ren EC (2009) Redefining the p53 response element. Proceedings of the National Academy of Sciences U S A 106: 14373-14378.
6. Horvath MM, Wang X, Resnick MA, Bell DA (2007) Divergent evolution of human p53 binding sites: cell cycle versus apoptosis. PLoS Genet 3: e127.
7. Hearnes JM, Mays DJ, Schavolt KL, Tang L, Jiang X, et al. (2005) Chromatin immunoprecipitationbased screen to identify functional genomic binding sites for sequence-specific transactivators. Mol Cell Biol 25: 10148-10158.
8. Wei C-L, Wu Q, Vega VB, Chiu KP, Ng P, et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell 124: 207-219.
9. Krieg AJ, Hammond EM, Giaccia AJ (2006) Functional analysis of p53 binding under differential stresses. Mol Cell Biol 26: 7030-7045.
10. Kaneshiro K, Tsutsumi S, Tsuji S, Shirahige K, Aburatani H (2007) An integrated map of p53-binding sites and histone modification in the human ENCODE regions. Genomics 89: 178-188.
11. Smeenk L, van Heeringen SJ, Koeppel M, van Driel MA, Bartels SJ, et al. (2008) Characterization of genome-wide p53-binding sites upon stress response. Nucleic Acids Res 36: 3639-3654.
12. Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, et al. (2011) Role of p53 serine 46 in p53 target gene regulation. PLoS One 6: e17574.
13. Zeron-Medina J, Wang X, Repapi E, Campbell MR, Su D, et al. (2013) A polymorphic p53 response element in KIT ligand influences cancer risk and has undergone natural selection. Cell 155: 410-422.
14. Menendez D, Nguyen TA, Freudenberg JM, Mathew VJ, Anderson CW, et al. (2013) Diverse stresses dramatically alter genome-wide p53 binding and transactivation landscape in human cancer cells. Nucleic Acids Res 41: 7286-7301.
15. Nikulenkov F, Spinnler C, Li H, Tonelli C, Shi Y, et al. (2012) Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis. Cell Death Differ 19: 1992-2002.
16. Botcheva K, McCorkle SR, McCombie WR, Dunn JJ, Anderson CW (2011) Distinct p53 genomic binding patterns in normal and cancer-derived human cells. Cell Cycle 10: 4237-4249.
17. Millau J-F, Mai S, Bastien N, Drouin R (2010) p53 functions and cell lines: have we learned the lessons from the past? Bioessays 32: 392-400.
18. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27: 66-75.
19. Nakano K, Vousden KH (2001) PUMA, a novel proapoptotic gene, is induced by p53. Mol Cell 7: 683-694.
20. Yu J, Zhang L, Hwang PM, Kinzler KW, Vogelstein B (2001) PUMA induces the rapid apoptosis of colorectal cancer cells. Mol Cell 7: 673-682.
21. Hoh J, Jin S, Parrado T, Edington J, Levine AJ, et al. (2002) The p53MH algorithm and its application in detecting p53-responsive genes. Proceedings of the National Academy of Sciences U S A 99: 8467-8472.
22. Akdemir KC, Jain AK, Allton K, Aronow B, Xu X, et al. (2014) Genome-wide profiling reveals stimulusspecific functions of p53 during differentiation and DNA damage of human embryonic stem cells. Nucleic Acids Res 42: 205-223.
23. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
24. de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 7: e1002384.