2023
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Rozowsky J, Gao J, Borsari B, Yang Y, Galeev T, Gürsoy G, Epstein C, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun M, Wright J, Chang J, Cameron C, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona G, Chee S, Chhetri S, Cortez Martins G, Danyko C, Davis C, Farid D, Farrell N, Gabdank I, Gofin Y, Gorkin D, Gu M, Hecht V, Hitz B, Issner R, Jiang Y, Kirsche M, Kong X, Lam B, Li S, Li B, Li X, Lin K, Luo R, Mackiewicz M, Meng R, Moore J, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt H, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber J, Sedlazeck F, See L, Sherman R, Shi X, Shi M, Sloan C, Strattan J, Tan Z, Tanaka F, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry J, Mendenhall E, Noble W, Weng Z, Levine M, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers R, Snyder M, Choudhary J, Milosavljevic A, Schatz M, Bernstein B, Guigó R, Gingeras T, Gerstein M. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell 2023, 186: 1493-1511.e40. PMID: 37001506, PMCID: PMC10074325, DOI: 10.1016/j.cell.2023.02.018.Peer-Reviewed Original Research
2021
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Pratt H, Andrews G, Phalke N, Huey J, Purcaro M, van der Velde A, Moore J, Weng Z. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Research 2021, 50: d141-d149. PMID: 34755879, PMCID: PMC8728199, DOI: 10.1093/nar/gkab1039.Peer-Reviewed Original ResearchConceptsChIP-seqHT-SELEXTranscription factorsDNA-binding transcription factorsHT-SELEX experimentsChIP-seq dataChIP-seq experimentsAnnotation of variantsTF binding sitesCis-regulatory elementsTranscriptional regulatory proteinsDatabase of annotationsIntegrated analysisENCODE projectHuman genomeMotif modelsTrait heritabilityRegulatory proteinsBinding specificityGene expressionMotifBinding sitesCell typesRegulatory effectsComprehensive collectionYAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation
He L, Pratt H, Gao M, Wei F, Weng Z, Struhl K. YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation. ELife 2021, 10: e67312. PMID: 34463254, PMCID: PMC8463077, DOI: 10.7554/elife.67312.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingCell Line, TumorCell Transformation, NeoplasticDatabases, GeneticFemaleGene Expression Regulation, NeoplasticHumansIntracellular Signaling Peptides and ProteinsProtein BindingProtein Interaction Domains and MotifsSignal TransductionSTAT3 Transcription FactorTranscription Factor AP-1Transcription FactorsTranscriptional ActivationTranscriptional Coactivator with PDZ-Binding Motif ProteinsTriple Negative Breast NeoplasmsYAP-Signaling ProteinsConceptsTranscriptional co-activatorAP-1 proteinsAP-1Cellular transformationTarget siteNon-overlapping genesStimulated transcriptional activityAssociated with poor survival of breast cancer patientsPoor survival of breast cancer patientsSTAT3 motifTEAD proteinsSequence motifsGene classesWW domainEpigenetic switchTaz paralogTAZ-specificTranscriptional activityTranscription factorsTEADYAP/TAZSTAT3MotifTAZJunBGenome-wide detection and analysis of CRISPR-Cas off-targets
Rodríguez T, Dadafarin S, Pratt H, Liu P, Amrani N, Zhu L. Genome-wide detection and analysis of CRISPR-Cas off-targets. Progress In Nucleic Acid Research And Molecular Biology 2021, 181: 31-43. PMID: 34127199, DOI: 10.1016/bs.pmbts.2021.01.012.Peer-Reviewed Original ResearchConceptsProtospacer-adjacent motifOff-target identificationGUIDE-seqGenome-wide detectionHigh-throughput sequencingShort Palindromic Repeats (CRISPR) technologyOff-target sitesSequencing platformsThroughput sequencingTreat human diseasesOpen-source pipelineDocker imageHuman diseasesGene editingOff-targetsBiological studiesIncreased multiplexingProfiling approachSequenceIn vivoBioconductorSgRNAMotifRNAIdentification