ArticlePloS one2014
Identification of proteins associated with an IFNγ-responsive promoter by a retroviral expression system for enChIP using CRISPR.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Review
- PROBER identifies proteins associated with programmable sequence-specific DNA in living cells.Nature methods · 2022Article
- Control of Foxp3 induction and maintenance by sequential histone acetylation and DNA demethylation.Cell reports · 2021Article
- Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer.Molecular cancer · 2021Review
- MSCV-based retroviral plasmids expressing 3xFLAG-Sp-dCas9 for enChIP analysis.Biology methods & protocols · 2021Article
- pSIR-bsr, a self-inactivating retrovirus vector expressing the blasticidin S-resistance gene.Biology methods & protocols · 2021Article
- CRISPR/Cas System and Factors Affecting Its Precision and Efficiency.Frontiers in cell and developmental biology · 2021Review
- Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer.Clinical & experimental metastasis · 2020Article
- Article
- FGF6 and FGF9 regulate UCP1 expression independent of brown adipogenesis.Nature communications · 2020Article
- Functional Genomics in Pancreatic β Cells: Recent Advances in Gene Deletion and Genome Editing Technologies for Diabetes Research.Frontiers in endocrinology · 2020Review
- The next generation of CRISPR-Cas technologies and applications.Nature reviews. Molecular cell biology · 2019Review
- Purification of specific DNA species using the CRISPR system.Biology methods & protocols · 2019Review
- CRISPR-based reagents to study the influence of the epigenome on gene expression.Clinical and experimental immunology · 2018Review
- CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9.Current protocols in molecular biology · 2018Article
- FOXC1-induced non-canonical WNT5A-MMP7 signaling regulates invasiveness in triple-negative breast cancer.Oncogene · 2018Article
- enChIP systems using different CRISPR orthologues and epitope tags.BMC research notes · 2018Article
- Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Application of CRISPR/Cas9 to the study of brain development and neuropsychiatric disease.Molecular and cellular neurosciences · 2017Review
- Overview of CRISPR-Cas9 Biology.Cold Spring Harbor protocols · 2016Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Isolation of specific genomic regions retaining molecular interactions is essential for comprehensive identification of molecules associated with the genomic regions. Recently, we developed the engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technology for purification of specific genomic regions. Here, we developed a retroviral expression system for enChIP using CRISPR. We showed that the target genomic locus can be purified with high efficiency by using this system. We also showed that contamination of potential off-target sites is negligible by using this system if the guide RNA (gRNA) for the target site has a sufficiently long unique sequence in its seed sequence. enChIP combined with stable isotope labeling using amino acids in cell culture (SILAC) analysis identified proteins whose association with the interferon (IFN) regulatory factor-1 (IRF-1) promoter region increases in response to IFNγ stimulation. The list of the associated proteins contained many novel proteins in the context of IFNγ-induced gene expression as well as proteins related to histone deacetylase complexes whose involvement has been suggested in IFNγ-mediated gene expression. Finally, we confirmed IFNγ-induced increased association of the identified proteins with the IRF-1 promoter by ChIP. Thus, our results showed that the retroviral enChIP system using CRISPR would be useful for biochemical analysis of genome functions including transcription and epigenetic regulation.
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