We are analyzing https://link.springer.com/article/10.1186/s13059-018-1494-1.

Title:
Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence | Genome Biology
Description:
Background 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. Results 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. Conclusions 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.
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Keywords {🔍}

pubmed, cells, foxf, article, enhapois, cas, google, scholar, enhancer, senescence, ois, motif, cell, enhancers, fig, activity, expression, analysis, screen, gene, transcription, central, sgrnaap, data, functional, oncogenic, res, additional, sgrnas, dna, performed, genome, human, targeting, required, target, file, control, stress, crispr, results, pcr, proliferation, cancer, binding, regions, bjindrasgv, oht, luciferase, elements,

Topics {✒️}

article download pdf modulate oncogene-induced senescence milipore steriflip hv/pvdf gov/geo/query/acc promoting jun-jun homodimers htert-immortalized bj cells exploiting bi-directional transcription typical bi-directional transcription open-access database erc-itn rna train bypassing oncogene-induced senescence p53 chromatin immunoprecipitation-sequencing call crispr-ap1-enhlib crispr-based screen aimed promoter-distal cis-res high-throughput reporter assays typically transcribed bi-directionally apply genome-wide profiling 50 mm tris-hcl ph 7 10 mm tris-hcl ph 7 regulates oncogene-induced senescence crispr-ap1-enhlib library anti-brdu antibody oncogene-induced senescence bypass high-throughput sequencing data veronica della chiara fast gapped-read alignment cis-located target genes gene-set enrichment analysis foxf1 ko + p53 ko related subjects acc=gse112458 korkmaz analyzed rna-seq data crispr-based screens screen detected enhap1-ois1 cas9-mediated dna cleavage enhancer-binding transcription factor cas9-madiated dna cut functional genetic screens target senescence-induced enhancers functional regulatory elements sa-β-gal staining defined bi-directional tus enriched jun/fos motif pgl3-enhap1-ois1-fw pgl3-enhap1-ois1-rv sgrna-ap171+ p53 ko ap-1 transcription factors neuronal activity-regulated enhancers crispr library construction

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WebPage:
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         headline:Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence
         description: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.
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      headline:Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence
      description: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.
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         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      name:Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
      name:Oncode Institute, Amsterdam, The Netherlands
      name:Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
      name:Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
      name:Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
      name:Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
      name:Oncode Institute, Amsterdam, The Netherlands
      name:Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
      name:Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
      name:Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
      name:Department of Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
      name:Oncode Institute, Amsterdam, The Netherlands

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