Smeenk Leonie, van Heeringen Simon J, Koeppel Max, van Driel Marc A, Bartels Stefanie J J, Akkers Robert C, Denissov Sergei, Stunnenberg Hendrik G, Lohrum Marion
Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands.
Nucleic Acids Res. 2008 Jun;36(11):3639-54. doi: 10.1093/nar/gkn232. Epub 2008 May 12.
The tumor suppressor p53 is a sequence-specific transcription factor, which regulates the expression of target genes involved in different stress responses. To understand p53's essential transcriptional functions, unbiased analysis of its DNA-binding repertoire is pivotal. In a genome-wide tiling ChIP-on-chip approach, we have identified and characterized 1546 binding sites of p53 upon Actinomycin D treatment. Among those binding sites were known as well as novel p53 target sites, which included regulatory regions of potentially novel transcripts. Using this collection of genome-wide binding sites, a new high-confidence algorithm was developed, p53scan, to identify the p53 consensus-binding motif. Strikingly, this motif was present in the majority of all bound sequences with 83% of all binding sites containing the motif. In the surrounding sequences of the binding sites, several motifs for potential regulatory cobinders were identified. Finally, we show that the majority of the genome-wide p53 target sites can also be bound by overexpressed p63 and p73 in vivo, suggesting that they can possibly play an important role at p53 binding sites. This emphasizes the possible interplay of p53 and its family members in the context of target gene binding. Our study greatly expands the known, experimentally validated p53 binding site repertoire and serves as a valuable knowledgebase for future research.
肿瘤抑制因子p53是一种序列特异性转录因子，可调节参与不同应激反应的靶基因的表达。为了解p53的基本转录功能，对其DNA结合序列进行无偏分析至关重要。在全基因组平铺芯片ChIP实验中，我们鉴定并表征了放线菌素D处理后p53的1546个结合位点。这些结合位点中既有已知的p53靶位点，也有新发现的靶位点，其中包括潜在新转录本的调控区域。利用这一全基因组结合位点集合，我们开发了一种新的高可信度算法p53scan，用于识别p53共有结合基序。令人惊讶的是，该基序存在于大多数结合序列中，83%的结合位点都含有该基序。在结合位点的周边序列中，还鉴定出了几种潜在调控共结合因子的基序。最后，我们发现全基因组范围内的大多数p53靶位点在体内也能被过表达的p63和p73结合，这表明它们可能在p53结合位点发挥重要作用。这强调了p53及其家族成员在靶基因结合方面可能存在相互作用。我们的研究极大地扩展了已知的、经过实验验证的p53结合位点集合，为未来的研究提供了宝贵的知识库。
