Recent genome-wide analyses and meta-analyses of genome-wide datasets of p53 DNA-binding and
gene
regulation show that p53 is a direct activator of a limited number of genes
compared to
the number of putative response-elements
identified genome-wide. They also provide evidence that p53 is not a direct repressor
of
genes.
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This study identified 350 genes that are confirmed direct p53 targets (see below) based on a meta-analysis of 15 genome-wide datasets and over 300 single-gene studies. These genes have roles in several cellular functions including apoptosis, cell-cycle arrest, autophagy, metabolism, DNA repair, translational control, feedback mechanisms.This study also summarizes several other studies that collectively show that p53 is not a direct repressor of genes but can indirectly repress genes through activation of the p21-DREAM/RB pathway. Most repressed genes through this p53-p21-DREAM/RB pathway are cell-cycle genes.
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This study provides a comprehensive annotation of canonical and non-canonical p53 REs in the human genome, ranked on predicted transactivation potential.
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This study shows that TP53 activates a genetically robust transcriptional program with highly distributed tumor suppressive functions acting in diverse cellular contexts.
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This study shows that TP53 enhancers represent a class of unsophisticated cell-autonomous enhancers containing a single TP53 binding site.
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This study used a common analysis pipeline to perform a meta-analysis of 41 datasets from genome-wide ChIP-seq studies, providing a platform to characterize p53 binding throughout the human genome.
Census p53 target genes by Fischer (2017)
CDKN1A | ABCA12 | NTPCR | PGPEP1 | RNF19B | LCE1E | EPN3 | SCN4B | ARVCF | FCHO2 | PANK2 | TMEM8B |
RRM2B | ANKRA2 | ORAI3 | PLCL2 | SAC3D1 | LIMK2 | FBXO32 | SCRIB | BHLHE40 | FCHSD2 | PAQR7 | TP53 |
MDM2 | CCNG1 | PRKAB1 | PMAIP1 | SYTL1 | LRP1 | FHL2 | SEMA3B | BMP7 | FLRT2 | PCBP4 | TP53I11 |
SUSD6 | CYFIP2 | PTP4A1 | PRDM1 | TNFRSF10A | MCC | HES2 | SLC25A45 | BORCS7 | GBE1 | PERP | TRAK1 |
GDF15 | DRAM1 | SESN2 | RAP2B | TNFRSF10D | NUPR1 | KCNN4 | SLC44A5 | BTBD10 | GPC1 | PLLP | TRIP6 |
BTG2 | FBXO22 | SLC30A1 | RRAD | TSPAN11 | PARD6G | KLHDC7A | SLC4A11 | BTG3 | HES1 | POU3F1 | TSGA10 |
DDB2 | ISCU | SPATA18 | ZNF219 | VWCE | PHPT1 | LMNA | SLC9A1 | C17orf89 | HRAS | PPFIBP1 | UNC5B |
GADD45A | PHLDA3 | TGFA | ZNF337 | DDIT4 | PIDD1 | MLF2 | STAT3 | CAPN2 | HSD17B3 | PPM1J | UQCC1 |
PLK3 | SERPINB5 | TLR3 | ACTA2 | RAD51C | PML | MR1 | STK17A | CASP6 | ICOSLG | PPP4R3A | VDR |
TIGAR | SERTAD1 | TM7SF3 | EDN2 | SERPINE1 | PTPRE | MYO6 | STX6 | CATSPERG | IGFBP7 | PTAFR | YPEL3 |
RPS27L | TRAF4 | TMEM68 | ALOX5 | TNFAIP8 | PVRL4 | NEFL | TP73 | CAV1 | IL1B | RALGDS | ZNF195 |
TNFRSF10B | TRIM22 | WDR63 | ARHGEF3 | TSKU | RETSAT | NKAIN4 | TRIM32 | CCNK | ISYNA1 | RBM38 | ZNF385A |
TRIAP1 | CES2 | ZNF561 | CERS5 | PCNA | REV3L | PCLO | TRIM38 | CFLAR | JAG1 | RGL1 | ZNF488 |
ZMAT3 | CMBL | ZNF79 | DDR1 | ACYP2 | RNASE7 | PDE4C | TRIM5 | CGB7 | KRT8 | RGS20 | |
BAX | FBXW7 | ASCC3 | DHRS3 | APAF1 | SFN | PGAP1 | TYMSOS | CHST14 | KSR1 | RHOC | |
PGF | HSPA4L | ACER2 | DUSP14 | APOBEC3H | TNFRSF10C | PLCXD2 | AKAP9 | COBLL1 | LACC1 | RPS19 | |
POLH | KITLG | ANXA4 | E2F7 | BCL2L1 | TRIML2 | PLEKHF1 | CCDC51 | CPEB2 | LPXN | SARS | |
PPM1D | SLC12A4 | APOBEC3C | EPS8L2 | BCL6 | VCAN | PLTP | CDH8 | CPSF4 | LRPAP1 | SCIN | |
SULF2 | ATF3 | ASTN2 | FAM210B | BLCAP | ADCK3 | PLXNB1 | DUSP11 | DNAJB2 | MFAP3L | SCN3B | |
XPC | BBC3 | CD82 | GLS2 | C17orf82 | AK3 | PLXNB2 | GCC2 | DOCK8 | MKNK2 | SDC4 | |
AEN | CCDC90B | CDIP1 | GPX1 | COL7A1 | ALDH1A3 | PRKAB2 | METTL8 | DUSP5 | MON2 | SDPR | |
BLOC1S2 | DYRK3 | CPE | GRHL3 | CPEB4 | BBS2 | PRKX | PPP1R3C | DUSP7 | MRPL49 | SMAD3 | |
FAS | EDA2R | CSF1 | HHAT | CSNK1G1 | BTG1 | PRODH | STEAP3 | EBI3 | MYBPHL | SNX2 | |
GPR87 | EPHA2 | DCP1B | IGDCC4 | DGKA | CEL | PTPRU | ABHD4 | EFNB1 | MYLK | SOCS4 | |
NINJ1 | FAM13C | ENC1 | IKBIP | FAM49A | CLCA2 | RGMA | ABTB2 | EI24 | MYOF | TAB3 | |
PLK2 | FAM198B | FOSL1 | LAPTM5 | FAM84B | CLDN1 | RGS16 | ADGRG1 | EML2 | NFKBIA | TCAIM | |
PSTPIP2 | FAM212B | FUCA1 | MAST4 | GNAI1 | CLP1 | RND3 | AIFM2 | ENPP2 | NHLH2 | TEP1 | |
SESN1 | FDXR | IER5 | MICALL1 | INPP1 | CROT | RNF144B | AMOTL1 | ETV7 | NLRP1 | TET2 | |
TP53I3 | LIF | PADI4 | NOTCH1 | ITGA3 | CYP4F3 | S100A2 | AMZ2 | FAM196A | NYNRIN | TEX9 | |
TP53INP1 | NADSYN1 | PANK1 | RABGGTA | KRT15 | DAPK1 | SCN2A | ARC | FAM98C | P3H2 | TMEM63B |
p53 responsive-elements
The canonical p53 response-element (p53-RE) consists of two copies of the
palindromic
half-site RRRCWWGYYY
where each p53 monomer binds five nucleotides (R = purine, W= A or T and Y = pyrimidine).
A list of putative canonical and non-canonical p53 REs identified in the human genome by Tebaldi et al., 2017
can be downloaded
here.
Below are some example of p53RE:
p53-RE name | Gene/Protein activity | Tetrameric p53-RE sequence (5’→3’)(a)(b) | p53-RE location | PubMed |
---|---|---|---|---|
PG13 | 13 copies of p53CON | 1588974 | ||
14-3-3s | Cell cycle arrest | AGGCATGTgC cAcCATGCCC | 2,5 kb | 9659898 |
GtAGCAttAGCCC AGACATGTCC | 1,8 kb | 9659898 | ||
BAX | Apoptosis | tcACAAGTTaGAGACAAGCCT | -113 to -93 | 10559267 |
AGACAAGCCT GGGCgTGggC | -102 to -83 | 10559267 | ||
AGACAAGCCTGGGCGTGGGCTAtaTT | -102 to -77 | 10559267 | ||
BTG2 | Cell cycle arrest | AGtCcgGgCAGAGcCcgagCa | -122 to -74 | 11814693 |
CD95-Fas | Apoptosis | GGACAAGCCC tGACAAGCCa | intron 1 | 9841917 |
GADD45 | Cell cycle arrest | GAACATGTCT AAGCATGCTg | intron 3 | 8226988 |
IGF-BP3-boxA | Apoptosis | AAACAAGCCaCcAACATGCTT | intron 1 | 7566179 |
IGF-BP3-boxB | GGGCAAGaCC tGcCAAGCCT | intron 2 | 7566179 | |
KILLER/DR5 | Apoptosis | GGGCATGTCC GGGCAAGaCg | intron 1 | 10777207 |
MDM2 | p53 regulation | GGtCAAGTTC AGACAcGTCC | intron 1 | 7651818 |
AGttAAGTCC tGACTTGTCT | intron 1 | 7651818 | ||
NOXA | Apoptosis | AGGCTTGCCC cGGCAAGTTg | -174 to -155 | 10807576 |
P53DINP1 | Regulation of p53-dependent apoptosis | GAACTTGggg GAACATGTTT | intron 2 | 11511362 |
P53R2 | DNA repair | tGACATGCCC AGGCATGTCT | intron 1 | 10716435 |
P53RFP | p21WAF1 regulation | AGACAgGTCC tGACAAGCag | -157 to -137 | 12853982 |
SESN1 | Oxydative metabolism | GGACAAGTCT ccACAAGTTC | intron 2 | 9926927 |
PCNA | DNA repair / Replication | GAACAAGTCC GGGCATaTgT | -236 to -217 | 8570655 |
PIDD | Apoptosis | AGGCcTGCCTGCGTGCTGGGACATGTCT | -54 to -26 | 10973264 |
PIG3 | Apoptosis | cAGCTTGCCC AccCATGCTC | -328 to -308 | 9305847 |
PUMA | Apoptosis | ctcCTTGCCTTGGGCTAGgCC | -230 | 11463391 |
ctGCAAGTCC tGACTTGTCC | -144 | 11463391 | ||
RGC | Ribosomes synthesis | GGACTTGCCT GGcCTTGCCT | NA | 2047879 |
WAF15’ | Cell cycle arrest | GAACATGTCC cAACATGTTg | -2.3 kb | 8242752 |
WAF1 3’ | GAAgAAGaCT GGGCATGTCT | -1.4 kb | 9679054 |
(a) Non-functional putative p53-RE are indicated in italic.
(b) Bases that do not correspond to the p53-RE consensus sequence are in lowercase.
(b) Bases that do not correspond to the p53-RE consensus sequence are in lowercase.