Distinct Regulatory Mechanisms and Functions for p53-Activated and p53-Repressed DNA Damage Response Genes in Embryonic Stem Cells

Abstract

SUMMARY p53 is critical in regulating the differentiation of ES and induced pluripotent stem (iPS) cells. Here, we report a whole-genome study of p53-mediated DNA damage signaling in mouse ES cells. Systems analyses reveal that binding of p53 at promoter region significantly correlates with gene activation but not with repression. Unexpectedly, we identify a regulatory mode for p53-mediated repression through interfering with distal enhancer activity. Importantly, many ES cell-enriched core transcription factors are p53-repressed genes. Further analyses demonstrate that p53-repressed genes are functionally associated with ES/iPS cell status while p53-activated genes are linked to differentiation. p53-activated genes and -repressed genes also display distinguishable features of expression levels and epigenetic markers. Upon DNA damage, p53 regulates the self-renewal and pluripotency of ES cells. Together, these results support a model that, in response to DNA damage, p53 affects the status of ES cells through activating differentiation-associated genes and repressing ES cell-enriched genes.

p53 suppresses muscle differentiation at the myogenin step in response to genotoxic stress

“…Corresponding RNA sequencing analysis showed reduced myogenin mRNA 41 (Supplementary Figure 6a). The same binding region was also identified when mESCs were exposed to doxorubicin 42 (Supplementary Figure 6b). This p53RE shares 95% sequence similarity with the canonical element 43 (Figure 4a).…”

“…26 Molecular mechanisms of p53-mediated transcriptional repression are less understood in comparison with transcriptional activation mechanisms. 7,42,43 Here we report for the first time that p53 binds to a highly conserved p53RE in a distal enhancer region of the myogenin gene and transcriptionally represses myogenin in response to genotoxic stress. Using luciferase reporter assays, we found that this p53RE can be 6,7,42,43,57 the exact mechanism of myogenin repression by p53 is still unclear to us.…”

“…We speculate that p53 or p63 enrichment on myogenin regulatory elements previously observed in non-myogenic cells, such as MEFs, 41 mESC, 42 or primary keratinocytes, 46 may reflect a poised global surveillance system that maintains cell identity and prevents, at least, a myogenic fate transition in response to stress signals. This notion is supported by the observation that elimination of p53 enhances cellular plasticity and efficiency of reprogramming somatic cells to pluripotency 58 and differentiated hepatocytes to malignant cell fates.…”

“…Global ChIP sequencing analysis has shown that p53-repressed genes tend to associate with p53 peak enrichment at the distal enhancers in mESC exposed to doxorubicin. 42 A recent study on mapping the genome-wide histone marks during myogenic differentiation identified three upstream enhancers, R1, R2, and R3, in the distal region upstream of the mouse myogenin gene 47 ( Figure 4a). These three enhancers are proposed to function as a switch control that regulates myogenin expression from proliferation to differentiation.…”

Ribosome biogenesis dysfunction leads to p53-mediated apoptosis and goblet cell differentiation of mouse intestinal stem/progenitor cells

“…In response to DNA damage in embryonic stem cells, p53 induces differentiation through direct repression and activation of pluripotency-and differentiation-associated genes respectively. 32 In adult melanocyte and hematopoietic stem cells, premature differentiation in response to genotoxic stress occurs independently of p53. 33,34 Muc2 expression was upregulated both in NleVilcKO crypts and in CX-5641-treated organoids.…”