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Series GSE76653 Query DataSets for GSE76653
Status Public on May 07, 2016
Title Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic [CHEQ-seq]
Organism Homo sapiens
Experiment type Other
Summary Analysis of p53 binding sites using multiplex enhancer reporter assays, ChIP-seq data and RNA-seq data.

Transcription factors establish and maintain the specific transcriptome of a cell by binding to genomic regulatory regions, thereby regulating the transcription of their target genes. Like many transcription factors, the DNA sequence-specific binding preferences of p53 are known. However, it remains largely unclear what distinguishes functional enhancers from other bound genomic regions that have no regulatory activity. In addition, the genome is scattered with seemingly perfect recognition sequences that remain unoccupied. To disentangle the rules of genome-wide p53 binding, we employed two complementary techniques of multiplex enhancer-reporter assays, one using barcoded reporters and the other using enhancer self-transcription. We compared the activity of more than one thousand candidate p53 enhancers under loss and gain of p53 conditions and identified several hundred high-confidence p53-responsive enhancers. Strikingly, the large majority (99%) of these target enhancers can be characterized and distinguished from negative sequences by the occurrence of a single p53 binding site. By training a machine learning classifier on these data, and integrating the resulting genome-wide predictions with fifteen publicly available human p53 ChIP-seq data sets, we identified a consensus set of 1148 functional p53 binding sites in the human genome. Unexpectedly, this direct p53 cistrome is invariably used between cell types and experimental conditions, while differences between experiments can be largely attributed to indirect non-functional binding. Our data suggest that direct p53 enhancers function in a context-independent manner and do not contain obvious combinatorial complexity of binding sites for multiple transcription factors. They represent a class of unsophisticated cell-autonomous enhancers with a single binding site, distinct from complex developmental enhancers that integrate signals from multiple transcription factors. This suggests that context-dependent regulation of p53 target genes is not encoded in the p53 enhancer, but at different upstream or downstream layers of the cell's gene regulatory network.
Overall design CHEQ-seq multiplex enhancer reporter assay to identify and validate p53-responsive enhancers.
Contributor(s) Verfaillie A, Aerts S
Citation(s) 27197205
Submission date Jan 07, 2016
Last update date May 15, 2019
Contact name Zeynep Kalender Atak
Organization name KULeuven
Street address Herestraat 49
City Leuven
ZIP/Postal code 3001
Country Belgium
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL21311 PacBio RS II (Homo sapiens)
Samples (12)
GSM2033048 CS_plasmid_N1
GSM2033049 CS_plasmid_WT1
GSM2033050 CS_plasmid_KD1
This SubSeries is part of SuperSeries:
GSE76657 Multiplex enhancer-reporter assays uncover unsophisticated p53 enhancer logic
BioProject PRJNA308237
SRA SRP068216

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE76653_RAW.tar 13.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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