Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence
Open Access
- 17 August 2018
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 19 (1), 1-13
- https://doi.org/10.1186/s13059-018-1494-1
Abstract
Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncogene-induced senescence, a cellular state of irreversible proliferation arrest that is enforced following excessive oncogenic activity, is a major barrier against cancer transformation; therefore, bypassing oncogene-induced senescence is a critical step in tumorigenesis. Here, we aim at further identification of enhancer elements that are required for the establishment of this state. We first apply genome-wide profiling of enhancer-RNAs (eRNAs) to systematically identify enhancers that are activated upon oncogenic stress. DNA motif analysis of these enhancers indicates AP-1 as a major regulator of the transcriptional program induced by oncogene-induced senescence. We thus constructed a CRISPR-Cas9 sgRNA library designed to target senescence-induced enhancers that are putatively regulated by AP-1 and used it in a functional screen. We identify a critical enhancer that we name EnhAP1-OIS1 and validate that mutating the AP-1 binding site within this element results in oncogene-induced senescence bypass. Furthermore, we identify FOXF1 as the gene regulated by this enhancer and demonstrate that FOXF1 mediates EnhAP1-OIS1 effect on the senescence phenotype. Our study elucidates a novel cascade mediated by AP-1 and FOXF1 that regulates oncogene-induced senescence and further demonstrates the power of CRISPR-based functional genomic screens in deciphering the function of non-coding regulatory elements in the genome.Keywords
This publication has 51 references indexed in Scilit:
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusionsGenome Biology, 2013
- An integrated encyclopedia of DNA elements in the human genomeNature, 2012
- Landscape of transcription in human cellsNature, 2012
- Functional and Mechanistic Diversity of Distal Transcription EnhancersCell, 2011
- Transcriptional Enhancers in Animal Development and EvolutionCurrent Biology, 2010
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell IdentitiesMolecular Cell, 2010
- Widespread transcription at neuronal activity-regulated enhancersNature, 2010
- Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active TranscriptionDevelopmental Cell, 2008
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genomeNature Genetics, 2007
- Expression of a β-globin gene is enhanced by remote SV40 DNA sequencesCell, 1981