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ΔNp63α modulates histone methyl transferase SETDB1 to transcriptionally repress target genes in cancers

Cell Death Discovery volume 2, Article number: 16015 (2016) | Download Citation

ΔNp63α is primarily expressed in the epithelial tissue, including the mammary gland and epidermis, where it is indispensable to maintain the high proliferative potential of somatic stem cells.1 Although mutations of p63 are extremely rare in human cancers, several tumors, including primary head and neck squamous cell carcinomas (HNSCCs), squamous cell epithelial lung malignancies, non-small-cell lung cancers and basal-like subtypes of breast cancer,2,​3,​4,​5,​6 often display elevated levels of ΔNp63, which is associated with poor prognosis. However, the mechanism of action of ΔNp63α in tumors remains mostly unknown. ΔNp63 isoforms, the amino-deleted isoforms encoded by TP63, lack the N-terminal transactivation (TA) domain, but are still able to transcriptionally regulate a distinct subset of genes due to the presence of a second TA domain (TA2). Thus, ΔNp63α has been shown to function both as a transcriptional activator and as a transcriptional repressor. Although the ΔNp63 transcriptional profile has been extensively characterized in normal epithelial cells and in cancer cell lines, little is known about how ΔNp63α directly transactivates genes, and which co-activators are required at enhancer and promoter sites. Furthermore, detailed information precisely mapping the TA2 domain is still missing. In contrast, much more information is available on the mechanisms of ΔNp63α-mediated transcriptional repression. ΔNp63α represses transcription by directly antagonizing p53 family members or by modulating the chromatin landscape near target genes (Figure 1). In the past several years, one prevalent hypothesis in the literature has been that ΔNp63α represses TAp73/p53 target genes simply by acting as dominant-negative to prevent TAp73/p53 occupancy at the shared DNA responsive elements (Figure 1a). For example, p63 knockdown in HNSCC cell lines results in TAp73-dependent apoptosis via PUMA and NOXA upregulation. In this system, ΔNp63α forms hetero-tetramers with TAp73, preventing the binding of TAp73 to PUMA enhancers.7 Although this notion is still valid, it did not explain several results obtained in HNSCC2 and in other cancer types suggesting that alternative TAp73/p53-independent mechanisms, employed by ΔNp63α, are engaged. Indeed, in keratinocytes and in HNSCC cell lines, ΔNp63α physically interacts with the histone deacetylases HDAC1 and HDAC2, and recruits these enzymes to p63 and p53 enhancer sites, thus mediating histone H3 and H4 deacetylation and consequent transcriptional inhibition (Figure 1b).8 Another ΔNp63α-dependent mechanism of repression is the recruitment of the SRCAP chromatin remodelling complex, via a physical interaction with the SAMD9L subunit.2 SRCAP complex is involved in H2A/H2A.Z exchange, mediating H2A.Z deposition near p63 response elements, thus creating a chromatin environment that is in a repressed conformation; this has been demonstrated in keratinocytes, lung SCC and HNSCC cell lines (Figure 1c).

Figure 1
Figure 1

Schematic view of different mechanisms of ΔNp63α-mediated inhibition in different cancer types. (a) ΔNp63α, by direct interaction with p53-like responsive elements and/or by forming mixed inactive tetramers, inhibits the transcription of TAp73/p53 target genes, acting in a dominant-negative fashion. This mechanism has been demonstrated in keratinocytes and HNSCCs.7 (b) ΔNp63α, by physical interaction with the histone deacetylases HDAC1 and HDAC2, recruits these enzymes to chromatin, resulting in deacetylation of histone H4 and consequent transcription inhibition. This has been shown in JHU-029 SCC cell line.8 (c) ΔNp63α recruits components of the H2A.Z exchange complex to facilitate H2A.Z incorporation to repress transcription. This mechanism has been observed in the lung SCC cell line H226.2 (d) ΔNp63α, by physical interaction with the histone lysine methyl transferases SETDB1, may repress transcription of target genes9 by SETDB1 deposition of histone H3 lysine 9 dimethylation and of histone H3 lysine 9 trimethylation marks. This mechanism has been observed in breast cancer cell lines.9

Recently, using a yeast two-hybrid assay, Regina et al. 9 showed that ΔNp63α interacts with SETDB1, a histone lysine methyl transferase (HMT) that is important in epigenetic regulation (Figure 1d). SETDB1 belongs to the SET (Suppression of variegation, Enhancer of zeste, Trithorax)-domain containing enzymes. HMTs catalyze the transfer of one to three methyl groups from S-adenosyl-methionine to specific lysine residues on histone proteins.10 Depending on the site and degree of methylation, this modification can have various effects, including regulation of chromatin organization and gene transcription. Among the different HMTs, SETDB1 has been of increasing interest due to its involvement in melanoma, where it is located in a recurrently amplified chromosome fragment.11 SETDB1 amplification has been also described in lung tumors.12 Regina et al.9 demonstrated that SETB1 is also overexpressed in different breast cancer cell lines and in primary tumors. Knockdown of SETDB1 resulted in growth-inhibitory effects. The authors also identified a list of 30 genes possibly repressed by ΔNp63 in a SETDB1-dependent manner, some of which correlated with the survival of breast cancer patients, suggesting that the ΔNp63α−SETDB1 interaction has a relevant and functional role in breast tumorigenesis.

These findings indicate a third mechanism through which ΔNp63α represses transcription, demonstrating that ΔNp63α uses different partners in a combinatorial fashion and in a cell-type-specific manner. Understanding mechanistically how ΔNp63α recruits chromatin remodelers, and identifying repressed target genes in different cells and cancer types, could be important in the future to modulate senescence/proliferation in epithelial cells and to block rapid cancer expansion.


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This work was mainly supported by AIRC grant to EC (IG13387) and partially supported by ‘Fondazione Roma’ NCD grant to GM and ‘Ricerca Finalizzata’ IDI-IRCCS to GM.

Author information


  1. Department of Experimental Medicine and Surgery , University of Rome ‘Tor Vergata’, Via Montpellier 1, Rome 00133, Italy

    • C Regina
    • , M Compagnone
    • , AM Lena
    • , G Melino
    •  & E Candi
  2. Institute of Cell Biology and Neurobiology (IBCN), CNR, Rome, Italy

    • A Peschiaroli
  3. IDI-IRCCS, Biochemistry Laboratory, Via Monti di Creta 104, Rome 00166, Italy

    • E Candi


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The authors declare no conflict of interest.

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Correspondence to E Candi.

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