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
2022
Building integrative functional maps of gene regulation
Xu J, Pratt HE, Moore JE, Gerstein MB, Weng Z. Building integrative functional maps of gene regulation. Human Molecular Genetics 2022, 31: r114-r122. PMID: 36083269, PMCID: PMC9585680, DOI: 10.1093/hmg/ddac195.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsMeSH KeywordsChromosome MappingDNAGene Expression RegulationGenome, HumanHumansRegulatory Sequences, Nucleic AcidConceptsGene regulationRegulatory mapSame genetic informationNon-coding genesSuch regulatory elementsEvolutionary analysisHuman genomeRegulatory elementsGenetic informationGene expressionType diversityRegulatory roleGenomeBase pairsIndividual cellsFunctional assaysSpecific functionsRegulationCellsFunctional mapsGenesDNADiversityCopiesSequence
2021
Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types
Moore J, Zhang X, Elhajjajy S, Fan K, Pratt H, Reese F, Mortazavi A, Weng Z. Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome Research 2021, 32: gr.275723.121. PMID: 34949670, PMCID: PMC8805725, DOI: 10.1101/gr.275723.121.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression RegulationGenome-Wide Association StudyHumansPromoter Regions, GeneticTranscription Initiation SiteConceptsTranscription start site annotationTranscription start siteGenome-wide association studiesStart siteAccurate transcription start siteCell type-specific usageMapping of promotersPaired-end informationPaired-end readsAnalysis of gene expressionTranscriptomic data setsGENCODE genesRNA annotationGWAS genesPaired-endGenomic positionsGene collectionTissue typesAssociation studiesTranscriptional regulationTranscription assaysBiological communitiesGene expressionHuman diseasesHuman cellsFactorbook: 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 ResearchMeSH KeywordsBinding SitesDatabases, GeneticGene Expression RegulationHumansNucleotide MotifsRegulatory Sequences, Nucleic AcidTranscription FactorsConceptsChIP-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 collectionInvestigating the Potential Roles of SINEs in the Human Genome
Zhang X, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annual Review Of Genomics And Human Genetics 2021, 22: 1-20. PMID: 33792357, DOI: 10.1146/annurev-genom-111620-100736.Peer-Reviewed Original ResearchMeSH KeywordsGene Expression RegulationGenome, HumanHumansRNA Polymerase IIIShort Interspersed Nucleotide ElementsTranscription, GeneticConceptsShort interspersed nuclear elementsHuman genomePol II-transcribed genesFunctional regulatory elementsGene-rich regionsRNA polymerase IIIProximity to genesInterspersed nuclear elementsRegulate gene expressionPotential regulatory functionsSINE RNAsNonautonomous retrotransposonsPolymerase IIIGene regulationRegulatory elementsAutonomous retroelementsGenomeNuclear elementsGene expressionGenesRNARNA levelsPolPotential roleRetrotransposons
2020
A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods
Moore J, Pratt H, Purcaro M, Weng Z. A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. Genome Biology 2020, 21: 17. PMID: 31969180, PMCID: PMC6977301, DOI: 10.1186/s13059-019-1924-8.Peer-Reviewed Original ResearchMeSH KeywordsBenchmarkingData CurationEnhancer Elements, GeneticGene Expression RegulationGenomicsMachine LearningConceptsEnhancer-gene interactionsTarget genesGene prediction methodsGenome-wide collectionCis-regulatory elementsCell typesEpigenomic dataDevelopment of computational methodsPredicted target genesGenomic interactionsPublished computational methodsTargetFinderComputational methodsGenesConclusionsOur resultsCCREsDistance methodCellsResultsToInteractionConclusionsOurTypePEPPrediction method