Abstract
Cellular stresses activate the tumor suppressor p53 protein leading to selective binding to DNA response elements (REs) and gene transactivation from a large pool of potential p53 REs (p53REs). To elucidate how p53RE sequences and local chromatin context interact to affect p53 binding and gene transactivation, we mapped genome-wide binding localizations of p53 and H3K4me3 in untreated and doxorubicin (DXR)-treated human lymphoblastoid cells. We examined the relationships among p53 occupancy, gene expression, H3K4me3, chromatin accessibility (DNase 1 hypersensitivity, DHS), ENCODE chromatin states, p53RE sequence, and evolutionary conservation. We observed that the inducible expression of p53-regulated genes was associated with the steady-state chromatin status of the cell. Most highly inducible p53-regulated genes were suppressed at baseline and marked by repressive histone modifications or displayed CTCF binding. Comparison of p53RE sequences residing in different chromatin contexts demonstrated that weaker p53REs resided in open promoters, while stronger p53REs were located within enhancers and repressed chromatin. p53 occupancy was strongly correlated with similarity of the target DNA sequences to the p53RE consensus, but surprisingly, inversely correlated with pre-existing nucleosome accessibility (DHS) and evolutionary conservation at the p53RE. Occupancy by p53 of REs that overlapped transposable element (TE) repeats was significantly higher (p<10−7) and correlated with stronger p53RE sequences (p<10−110) relative to nonTE-associated p53REs, particularly for MLT1H, LTR10B, and Mer61 TEs. However, binding at these elements was generally not associated with transactivation of adjacent genes. Occupied p53REs located in L2-like TEs were unique in displaying highly negative PhyloP scores (predicted fast-evolving) and being associated with altered H3K4me3 and DHS levels. These results underscore the systematic interaction between chromatin status and p53RE context in the induced transactivation response. This p53 regulated response appears to have been tuned via evolutionary processes that may have led to repression and/or utilization of p53REs originating from primate-specific transposon elements.
Highlights
Tumor suppressor p53 is activated in response to DNA damage and cellular stress signals and regulates the expression of target genes to elicit cell-growth arrest, DNA damage repair, or apoptosis to prevent the propagation of damaged or compromised cells [1,2]
We assessed genome-wide in vivo p53 occupancy, H3K4me3, DNase I hypersensitivity (DHS) and gene expression in human lymphoblastoid cells treated with the DNA-damaging chemotherapeutic agent DXR
Previous studies of functional regulatory variation indicate that lymphoblastoid cell lines (LCL) are responsive to a variety of treatments [28], including p53
Summary
Tumor suppressor p53 is activated in response to DNA damage and cellular stress signals and regulates the expression of target genes to elicit cell-growth arrest, DNA damage repair, or apoptosis to prevent the propagation of damaged or compromised cells [1,2]. About two hundred p53REs have been characterized in detail but p53 chromatin immunoprecipitation sequencing (ChIP-seq) experiments indicate there are thousands of p53 targets and numerous exposure-specific patterns of binding and transactivation [4,5,6,7,8,9]. These patterns have been variously attributed to sequence-specific binding [5,6], p53 post-translational modifications [10], targeting coactivators/factors [11], post-transcriptional effects [12], as well as, chromatin status at the binding site [13,14,15]. The rules governing the sequence specificity and functional output of regulatory interactions between p53 and the genome are not yet fully understood
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