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
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 collection
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 developmentChromatinTranscriptionHumansMethylationA 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 ResearchConceptsEnhancer-gene interactionsTarget genesGene prediction methodsGenome-wide collectionCis-regulatory elementsCell typesEpigenomic dataDevelopment of computational methodsPredicted target genesGenomic interactionsPublished computational methodsTargetFinderComputational methodsGenesConclusionsOur resultsCCREsDistance methodCellsResultsToInteractionConclusionsOurTypePEPPrediction method
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