2024
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements
Pratt H, Andrews G, Shedd N, Phalke N, Li T, Pampari A, Jensen M, Wen C, Consortium P, Gandal M, Geschwind D, Gerstein M, Moore J, Kundaje A, Colubri A, Weng Z. Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science Advances 2024, 10: eadj4452. PMID: 38781344, PMCID: PMC11114231, DOI: 10.1126/sciadv.adj4452.Peer-Reviewed Original ResearchConceptsEpigenetic dataCell-type-specific gene regulationCis-regulatory elementsComprehensive atlasGenetic variants associated with psychiatric disordersLineage-specific transcription factorsBrain cell typesMammalian elementsPsychENCODE ConsortiumNoncoding regionsEvolutionary historyGene regulationRegulatory elementsSequence mutationsTranscription factorsSequence syntaxRegulatory informationPrimate-specific sequencesBinding sitesHuman traitsCell typesFunctional implicationsPsychiatric disordersSequenceFetal brain development
2021
YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte‐Like Cells
Smith J, Rodríguez T, Mou H, Kwan S, Pratt H, Zhang X, Cao Y, Liang S, Ozata D, Yu T, Yin Q, Hazeltine M, Weng Z, Sontheimer E, Xue W. YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte‐Like Cells. Hepatology 2021, 73: 1011-1027. PMID: 32452550, PMCID: PMC8500588, DOI: 10.1002/hep.31389.Peer-Reviewed Original ResearchConceptsYes-associated protein 1Tumor cellsTumor regressionB-cateninStage IV hepatoblastomaResidual tumor cellsPediatric liver tumorsTherapeutic targetLong-term regressionTherapeutic differentiationHepatocyte-like morphologyFunctional hepatocyte-like cellsChildren's HbHB tumorsHepatocyte gene expressionHepatocyte-like cellsTranscription factor occupancyChemotherapeutic advancesTargeted therapyTumor landscapeLiver tumorsMurine modelHepatoblastomaTumorPromote cell deathAnnotation of chromatin states in 66 complete mouse epigenomes during development
van der Velde A, Fan K, Tsuji J, Moore J, Purcaro M, Pratt H, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Communications Biology 2021, 4: 239. PMID: 33619351, PMCID: PMC7900196, DOI: 10.1038/s42003-021-01756-4.Peer-Reviewed Original ResearchConceptsChromatin stateMouse epigenomesPolycomb repressive complex proteinsBivalent chromatin stateTranscription start siteRepressive mark H3K27me3Silence target genesCharacteristics of promotersChromHMM algorithmUnique epigenomeGene expression programsENCODE projectTranscribed regionsMulticellular organismsStart siteRepressed regionsActive marksMammalian developmentComplex proteinsEpigenomeTissue specificityTarget genesExpression programsCell typesIntegrated analysis
2020
Expanded encyclopaedias of DNA elements in the human and mouse genomes
Moore J, Purcaro M, Pratt H, Epstein C, Shoresh N, Adrian J, Kawli T, Davis C, Dobin A, Kaul R, Halow J, Van Nostrand E, Freese P, Gorkin D, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams B, Mortazavi A, Keller C, Zhang X, Elhajjajy S, Huey J, Dickel D, Snetkova V, Wei X, Wang X, Rivera-Mulia J, Rozowsky J, Zhang J, Chhetri S, Zhang J, Victorsen A, White K, Visel A, Yeo G, Burge C, Lécuyer E, Gilbert D, Dekker J, Rinn J, Mendenhall E, Ecker J, Kellis M, Klein R, Noble W, Kundaje A, Guigó R, Farnham P, Cherry J, Myers R, Ren B, Graveley B, Gerstein M, Pennacchio L, Snyder M, Bernstein B, Wold B, Hardison R, Gingeras T, Stamatoyannopoulos J, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 2020, 583: 699-710. PMID: 32728249, PMCID: PMC7410828, DOI: 10.1038/s41586-020-2493-4.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatinDatabases, GeneticDeoxyribonuclease IDNADNA FootprintingDNA MethylationDNA Replication TimingGenomeGenome, HumanGenomicsHistonesHumansMiceMice, TransgenicMolecular Sequence AnnotationRegistriesRegulatory Sequences, Nucleic AcidRNA-Binding ProteinsTranscription, GeneticTransposasesConceptsMouse genomeCandidate cis-regulatory elementsCis-regulatory elementsDNA Elements (ENCODE) projectMouse fetal developmentChromatin structureGene regulationRespective genomesCellular contextDNA elementsDNA methylationENCODE dataTranscription factorsRNA transcriptionWeb-based serverGenomeExpansive resourceRNAEncyclopediaProteinFetal developmentChromatinTranscriptionHumansMethylation
2018
Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers
Fu S, Wang Q, Moore J, Purcaro M, Pratt H, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Research 2018, 46: 11184-11201. PMID: 30137428, PMCID: PMC6265487, DOI: 10.1093/nar/gky753.Peer-Reviewed Original ResearchConceptsPeak callersH3K27ac peaksDevelopmental enhancersHistone modificationsDistal cis-regulatory elementsAnalysis of chromatin accessibilityChIP-seq peaksPeak-calling algorithmsDepleted of nucleosomesCis-regulatory elementsModulate gene expressionTransgenic mouse assaysF-SeqDNase-seqHeart enhancersChromatin accessibilityH3K27ac signalH3K27acDNaseGene expressionHistoneDNase peakMouse assayPredicted enhancersDistant tissues
2013
Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling
Giallourakis C, Benita Y, Molinie B, Cao Z, Despo O, Pratt H, Zukerberg L, Daly M, Rioux J, Xavier R. Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling. The Journal Of Immunology 2013, 190: 5578-5587. PMID: 23616578, PMCID: PMC3703829, DOI: 10.4049/jimmunol.1203471.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCluster AnalysisComputational BiologyDatabases, Nucleic AcidDNA-Binding ProteinsExpressed Sequence TagsGene Expression ProfilingGene Regulatory NetworksGenome-Wide Association StudyGenomicsHumansImmune SystemImmune System DiseasesLymphoma, B-CellMiceMolecular Sequence AnnotationReproducibility of ResultsRNA, Long NoncodingTranscription FactorsTranscriptomeConceptsExpressed sequence tagsExpressed sequence tag profilingEncyclopedia of DNA ElementsHuman expressed sequence tagsGenome-wide analysisIdentification of transcriptsMicroarray-based studiesImmune system genesRNA sequencing analysisStudies of mRNADNA elementsSequence tagsNovel genesMetabolic gene signatureNoncoding genesSequence analysisTranscriptome analysisImmune systemMicroarray studiesOverexpressed genesSystem genesGene expressionGenesFunctional studiesNoncoding RNAs