EXPLORING THE P53 TRANSCRIPTIONAL NETWORK THROUGH
INTEGRATIVE GENOMICS REVEALS NEW CANDIDATE TARGET GENES
AND CO-FACTORS.
Annelien Verfaillie1, Rekin’s Janky1, Hana Imrichova1, Valerie Chistiaens1 and Stein
Aerts1
1
Laboratory of Computational Biology, Center for Human Genetics, University of
Leuven, Belgium
As tumor suppressor many roles have been ascribed to p53 like cell cycle arrest and
apoptosis but also metabolism and developmental processes. p53 functions as a
transcription factor (TF) by interacting with a variety of target genes of which many have
been reported but p53’s full targetome is likely incomplete. In addition, many other
aspects of p53’s activity require further investigation. To address these questions we
performed RNA-seq on MCF7-cells, revealing a list of differentially expressed genes. On
this set we applied an in-house developed motif discovery tool called iRegulon,
generating subsets of direct and indirect target genes. It also enabled us to retrieve
possible master regulators like p53 itself but also possible new co-factors like AP-1. We
observed E2F as regulator of the downregulated targets with a pronounced absence of the
p53 motifs amongst these genes supporting the possibility of a p21-Rb-E2F approach for
p53-repression. Next, we performed both ChIP-seq and FAIRE-seq in order to get a
comprehensive view on the genomic landscape of p53 binding. While the p53 ChIP peaks
improved our predicted set of p53 targets, the FAIRE profile established a correlation
between open chromatin regions and upregulated genes. Finally we selected four
enhancers from our direct targets for in vitro validation. Three of four enhancers showed
the ability to functionally drive gene expression. In conclusion, by using NGS
experiments, motif discovery and experimental validation we were able to address key
questions about p53’s transcriptional mechanism and identify several new candidate
target genes.