Dissecting the DNA binding landscape and gene regulatory network of p63 and p53
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Germany
- Max Planck Institute for Molecular Genetics, Germany
- Queen's University Belfast, United Kingdom
Abstract
The transcription factor p53 is the best-known tumor suppressor, but its sibling p63 is a master regulator of epidermis development and a key oncogenic driver in squamous cell carcinomas (SCC). Despite multiple gene expression studies becoming available, the limited overlap of reported p63-dependent genes has made it difficult to decipher the p63 gene regulatory network. Particularly, analyses of p63 response elements differed substantially among the studies. To address this intricate data situation, we provide an integrated resource that enables assessing the p63-dependent regulation of any human gene of interest. We use a novel iterative de novo motif search approach in conjunction with extensive ChIP-seq data to achieve a precise global distinction between p53 and p63 binding sites, recognition motifs, and potential co-factors. We integrate these data with enhancer:gene associations to predict p63 target genes and identify those that are commonly de-regulated in SCC representing candidates for prognosis and therapeutic interventions.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files.
-
Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiationNCBI Gene Expression Omnibus, GSE59824.
-
p63 attenuates epithelial to mesenchymal potential in an experimental prostate cell modelNCBI Gene Expression Omnibus, GSE43111.
-
Ras and TGF-β signaling enhance cancer progression by promoting the ΔNp63 transcriptional programNCBI Gene Expression Omnibus, GSE60814.
-
SOX2 and p63 colocalize at genetic loci in squamous cell carcinomasNCBI Gene Expression Omnibus, GSE46837.
-
ΔNp63α Suppresses TGFB2 Expression and RHOA Activity to Drive Cell Proliferation in Squamous Cell CarcinomasNCBI Gene Expression Omnibus, GSE111619.
-
p63 regulates an adhesion programme and cell survival in epithelial cellsNCBI Gene Expression Omnibus, GSE20286.
-
ΔNp63α represses anti-proliferative genes via H2A.Z depositionNCBI Gene Expression Omnibus, GSE40462.
-
Control of p53-dependent transcription and enhancer activity by the p53 family member p63NCBI Gene Expression Omnibus, GSE111009.
-
p63 establishes epithelial enhancers at critical craniofacial development genesNCBI Gene Expression Omnibus, GSE126397.
-
TP63-Mediated Enhancer Reprogramming Drives the Squamous Subtype of Pancreatic Ductal AdenocarcinomaNCBI Gene Expression Omnibus, GSE115462.
-
SOX2 and p63 colocalize at genetic loci in squamous cell carcinomasNCBI Gene Expression Omnibus, GSE47058.
Article and author information
Author details
Funding
Deutsche Forschungsgemeinschaft (FI 1993/2-1)
- Martin Fischer
Bundesministerium für Bildung und Forschung (031L016D)
- Steve Hoffmann
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Ashish Lal, National Institutes of Health, United States
Version history
- Received: September 21, 2020
- Accepted: December 1, 2020
- Accepted Manuscript published: December 2, 2020 (version 1)
- Version of Record published: December 14, 2020 (version 2)
Copyright
© 2020, Riege et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,403
- views
-
- 372
- downloads
-
- 28
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Dissecting the DNA binding landscape and gene regulatory network of p63 and p53
eLife 9:e63266.
https://doi.org/10.7554/eLife.63266
Further reading
-
- Chromosomes and Gene Expression
Extrachromosomal DNA is a common cause of oncogene amplification in cancer. The non-chromosomal inheritance of ecDNA enables tumors to rapidly evolve, contributing to treatment resistance and poor outcome for patients. The transcriptional context in which ecDNAs arise and progress, including chromosomally-driven transcription, is incompletely understood. We examined gene expression patterns of 870 tumors of varied histological types, to identify transcriptional correlates of ecDNA. Here, we show that ecDNA-containing tumors impact four major biological processes. Specifically, ecDNA-containing tumors up-regulate DNA damage and repair, cell cycle control, and mitotic processes, but down-regulate global immune regulation pathways. Taken together, these results suggest profound alterations in gene regulation in ecDNA-containing tumors, shedding light on molecular processes that give rise to their development and progression.
-
- Chromosomes and Gene Expression
- Genetics and Genomics
ASARs are a family of very-long noncoding RNAs that control replication timing on individual human autosomes, and are essential for chromosome stability. The eight known ASAR lncRNAs remain closely associated with their parent chromosomes. Analysis of RNA-protein interaction data (from ENCODE) revealed numerous RBPs with significant interactions with multiple ASAR lncRNAs, with several hnRNPs as abundant interactors. An ~7 kb domain within the ASAR6-141 lncRNA shows a striking density of RBP interaction sites. Genetic deletion and ectopic integration assays indicate that this ~7 kb RNA binding protein domain contains functional sequences for controlling replication timing of entire chromosomes in cis. shRNA-mediated depletion of 10 different RNA binding proteins, including HNRNPA1, HNRNPC, HNRNPL, HNRNPM, HNRNPU, or HNRNPUL1, results in dissociation of ASAR lncRNAs from their chromosome territories, and disrupts the synchronous replication that occurs on all autosome pairs, recapitulating the effect of individual ASAR knockouts on a genome-wide scale. Our results further demonstrate the role that ASARs play during the temporal order of genome-wide replication, and we propose that ASARs function as essential RNA scaffolds for the assembly of hnRNP complexes that help maintain the structural integrity of each mammalian chromosome.
