2021
Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer
Chen H, Yao J, Bao R, Dong Y, Zhang T, Du Y, Wang G, Ni D, Xun Z, Niu X, Ye Y, Li HB. Cross-talk of four types of RNA modification writers defines tumor microenvironment and pharmacogenomic landscape in colorectal cancer. Molecular Cancer 2021, 20: 29. PMID: 33557837, PMCID: PMC7869236, DOI: 10.1186/s12943-021-01322-w.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorColorectal NeoplasmsCombined Modality TherapyComputational BiologyDisease ManagementDisease SusceptibilityEpithelial-Mesenchymal TransitionGene Expression ProfilingGene Expression Regulation, NeoplasticHumansLymphocytes, Tumor-InfiltratingPharmacogeneticsPrognosisProportional Hazards ModelsRNA Processing, Post-TranscriptionalTranscription, GeneticTranscriptomeTumor MicroenvironmentConceptsColorectal cancerConsensus molecular subtypesTumor microenvironmentRNA modification patternsTME cell-infiltrating characteristicsWorse patient overall survivalDevelopment of CRCInhibitory immune cellsPD-L1 blockadeEfficacy of immunotherapyCharacteristics of TMEPatients' overall survivalPotential clinical utilityTherapeutic liabilityOverall survivalClinical featuresClinical benefitPatient survivalImmune cellsM2 macrophagesCRC samplesImmune responseMolecular subtypesClinical utilitySurvival advantage
2012
Nature and function of insulator protein binding sites in the Drosophila genome
Schwartz Y, Linder-Basso D, Kharchenko P, Tolstorukov M, Kim M, Li H, Gorchakov A, Minoda A, Shanower G, Alekseyenko A, Riddle N, Jung Y, Gu T, Plachetka A, Elgin S, Kuroda M, Park P, Savitsky M, Karpen G, Pirrotta V. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Research 2012, 22: 2188-2198. PMID: 22767387, PMCID: PMC3483548, DOI: 10.1101/gr.138156.112.Peer-Reviewed Original ResearchConceptsInsulator proteinsQuantitative genome-wide analysisInsulator elementsGenome-wide analysisEnhancer-blocking assaysRepressive histone methylationDrosophila chromatinDrosophila genomeEukaryotic genomesCombinatorial bindingH3K27me3 marksHistone methylationRNAi knockdownAdjacent genesGenome expressionFunctional characterizationAssociated proteinsGenomeCultured cellsProteinSpecific regulationGenesMajor alterationsDifferent classesChromatin