2023
Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer
de Miguel F, Gentile C, Feng W, Silva S, Sankar A, Exposito F, Cai W, Melnick M, Robles-Oteiza C, Hinkley M, Tsai J, Hartley A, Wei J, Wurtz A, Li F, Toki M, Rimm D, Homer R, Wilen C, Xiao A, Qi J, Yan Q, Nguyen D, Jänne P, Kadoch C, Politi K. Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer. Cancer Cell 2023, 41: 1516-1534.e9. PMID: 37541244, PMCID: PMC10957226, DOI: 10.1016/j.ccell.2023.07.005.Peer-Reviewed Original ResearchConceptsMammalian SWI/SNF chromatinSWI/SNF chromatinMSWI/SNF complexesGenome-wide localizationGene regulatory signaturesNon-genetic mechanismsEpithelial cell differentiationEGFR-mutant cellsChromatin accessibilitySNF complexCellular programsRegulatory signaturesTKI-resistant lung cancerGene targetsKinase inhibitor resistanceCell differentiationMesenchymal transitionTKI resistancePharmacologic disruptionTyrosine kinase inhibitor resistanceCell proliferationChromatinInhibitor resistanceEGFR-mutant lungKinase inhibitors
2017
Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling
Stanton KP, Jin J, Lederman RR, Weissman SM, Kluger Y. Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling. Nucleic Acids Research 2017, 45: e173-e173. PMID: 28981893, PMCID: PMC5716106, DOI: 10.1093/nar/gkx799.Peer-Reviewed Original ResearchConceptsChIP-seqNext-generation high-throughput DNA sequencing technologiesHigh-throughput DNA sequencing technologiesGenome-wide localizationGenome-wide scaleTF-binding sitesTranscription factor bindingDNA sequencing technologiesENCODE consortiumResultant readsChromatin immunoprecipitationReference genomeDiverse biological effectsModification eventsFactor bindingOmics techniquesSequencing technologiesOmics experimentsSequencing costsWide localizationPeak callingChip targetArtifactual peaksPeak callersBiological effects
2014
Using Native Chromatin Immunoprecipitation to Interrogate Histone Variant Protein Deposition in Embryonic Stem Cells
Tseng Z, Wu T, Liu Y, Zhong M, Xiao A. Using Native Chromatin Immunoprecipitation to Interrogate Histone Variant Protein Deposition in Embryonic Stem Cells. Methods In Molecular Biology 2014, 1176: 11-22. PMID: 25030915, DOI: 10.1007/978-1-4939-0992-6_2.Peer-Reviewed Original ResearchConceptsNative chromatin immunoprecipitationHigh-throughput sequencingEmbryonic stem cellsChromatin immunoprecipitationHistone variantsMouse embryonic stem cellsGenome-wide localizationChromatin-associated factorsStem cellsProtein of interestMassive parallel sequencingHistone modificationsChromatin regionsChromatin pelletEpigenetic techniquesDNA fragmentsParallel sequencingImmunoprecipitationLibrary constructionSequencingEnzymatic digestionProtein depositionCellsH2A.XSpecific antibodies
2012
Linking DNA Methyltransferases to Epigenetic Marks and Nucleosome Structure Genome-wide in Human Tumor Cells
Jin B, Ernst J, Tiedemann R, Xu H, Sureshchandra S, Kellis M, Dalton S, Liu C, Choi J, Robertson K. Linking DNA Methyltransferases to Epigenetic Marks and Nucleosome Structure Genome-wide in Human Tumor Cells. Cell Reports 2012, 2: 1411-1424. PMID: 23177624, PMCID: PMC3625945, DOI: 10.1016/j.celrep.2012.10.017.Peer-Reviewed Original ResearchMeSH KeywordsCarcinoma, EmbryonalCell LineChromatinCpG IslandsDNADNA (Cytosine-5-)-Methyltransferase 1DNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3AEmbryonic Stem CellsEpigenomicsGenes, OverlappingGenetic LociGenome, HumanHCT116 CellsHistonesHumansMaleNucleosomesProtein BindingTesticular NeoplasmsTranscription, GeneticConceptsDNA methylationDNA methyltransferasesDifferentiated stateGenome-wide localizationCancerous stem cellsEpigenetic marksMammalian developmentHistone modificationsNucleosome structureCellular transformationDNA hypermethylationLocalization patternsHuman tumor cellsMethylationDNMTsHuman tumor cell linesTumor cell linesStem cellsMethyltransferasesCancer cellsCell linesLociCellsTumor cellsEpigenome
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