2024
Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes
Maury E, Jones A, Seplyarskiy V, Nguyen T, Rosenbluh C, Bae T, Wang Y, Abyzov A, Khoshkhoo S, Chahine Y, Zhao S, Venkatesh S, Root E, Voloudakis G, Roussos P, Network B, Park P, Akbarian S, Brennand K, Reilly S, Lee E, Sunyaev S, Walsh C, Chess A. Somatic mosaicism in schizophrenia brains reveals prenatal mutational processes. Science 2024, 386: 217-224. PMID: 39388546, PMCID: PMC11490355, DOI: 10.1126/science.adq1456.Peer-Reviewed Original ResearchConceptsTranscription Factor Binding SitesWhole-genome sequencingOpen chromatinMutational processesSomatic mutationsFactor binding sitesSchizophrenia casesSchizophrenia risk genesSomatic mosaicismSomatic variantsRisk genesG mutationGene expressionGermline mutationsBinding sitesGenesMutationsIncreased somatic mutationsChromatinMosaic somatic mutationsPrenatal neurogenesisContext of schizophreniaBrain neuronsSchizophrenia brainVariants42. STRESS EXPOSURE DYNAMICALLY REGULATES EQTL ACTIVITY IN THE POST-MORTEM BRAIN AND IN HIPSC-DERIVED NEURONS
Seah C, Signer R, Young H, Hicks E, Rusielewicz T, Bader H, Xu C, Breen M, Paull D, Yehuda R, Girgenti M, Brennand K, Huckins L. 42. STRESS EXPOSURE DYNAMICALLY REGULATES EQTL ACTIVITY IN THE POST-MORTEM BRAIN AND IN HIPSC-DERIVED NEURONS. European Neuropsychopharmacology 2024, 87: 71-72. DOI: 10.1016/j.euroneuro.2024.08.156.Peer-Reviewed Original ResearchPost-mortem brainsTranscription Factor Binding SitesAbsence of cellular stressCombat-exposed veteransFactor binding sitesImpact gene expressionBinding sitesGR binding sitesPositive regulatory activityMotif enrichmentSequence readsCRISPRi screenOpen chromatinFunctional annotationBrain regionsTraumatic stressCRISPR screensEQTLTraumatic experiencesLeading locusPTSDPerturbed genesRegulatory architectureTranscriptomic activityTranscriptomic response
2019
DeepHistone: a deep learning approach to predicting histone modifications
Yin Q, Wu M, Liu Q, Lv H, Jiang R. DeepHistone: a deep learning approach to predicting histone modifications. BMC Genomics 2019, 20: 193. PMID: 30967126, PMCID: PMC6456942, DOI: 10.1186/s12864-019-5489-4.Peer-Reviewed Original ResearchConceptsHistone modificationsHistone markersGenetic variantsDisease-associated genetic variantsTranscription Factor Binding SitesDetection of histone modificationsAnalysis of histone modificationsHigh-throughput experimental techniquesChromatin accessibility dataFactor binding sitesHistone modification landscapeSingle nucleotide polymorphismsFunctional single nucleotide polymorphismsChIP-seqChromosome packagingModification landscapeSequence signaturesEpigenomic signalsDNA sequencesSequence informationEpigenomic studiesRegulatory signaturesLarge-scale analysisComprehensive validation experimentsTranscriptional activity
2013
Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes
Duke JL, Liu M, Yaari G, Khalil AM, Tomayko MM, Shlomchik MJ, Schatz DG, Kleinstein SH. Multiple Transcription Factor Binding Sites Predict AID Targeting in Non-Ig Genes. The Journal Of Immunology 2013, 190: 3878-3888. PMID: 23514741, PMCID: PMC3689293, DOI: 10.4049/jimmunol.1202547.Peer-Reviewed Original ResearchConceptsTranscription Factor Binding SitesAID-induced lesionsNon-Ig genesGenome instabilityTranscription factorsAberrant targetingSequence dataCertain genesGenesAID targetingGerminal center B cellsSomatic mutationsLikely targetBinding sitesAID targetsTargetingClassification tree modelMistargetingB cellsLociMechanismTargetMutationsSites
2010
Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria
Harari O, Park SY, Huang H, Groisman EA, Zwir I. Defining the Plasticity of Transcription Factor Binding Sites by Deconstructing DNA Consensus Sequences: The PhoP-Binding Sites among Gamma/Enterobacteria. PLOS Computational Biology 2010, 6: e1000862. PMID: 20661307, PMCID: PMC2908699, DOI: 10.1371/journal.pcbi.1000862.Peer-Reviewed Original ResearchMeSH KeywordsArtificial IntelligenceBacterial ProteinsBase SequenceBinding SitesChromatin ImmunoprecipitationCluster AnalysisComputational BiologyConsensus SequenceDNA, BacterialEnterobacteriaceaeEvolution, MolecularGene Expression ProfilingGenome, BacterialModels, GeneticMolecular Sequence DataNucleic Acid ConformationOligonucleotide Array Sequence AnalysisPattern Recognition, AutomatedSequence AlignmentTranscription FactorsConceptsGene expressionSite sequenceKey cis-regulatory elementsExpression of dozensGenome-wide analysisCis-regulatory elementsTranscription Factor Binding SitesDifferential gene expressionSpecific DNA sequencesDNA consensus sequencePhoP proteinAncestral geneTarget promotersDistant speciesHigh conservationTranscriptional regulatorsInter-species differencesChromatin immunoprecipitationRelated speciesRNA polymeraseDNA sequencesTarget genesRegulatory proteinsMolecular basisConsensus sequence
2009
Transcriptional features of genomic regulatory blocks
Akalin A, Fredman D, Arner E, Dong X, Bryne J, Suzuki H, Daub C, Hayashizaki Y, Lenhard B. Transcriptional features of genomic regulatory blocks. Genome Biology 2009, 10: r38. PMID: 19374772, PMCID: PMC2688929, DOI: 10.1186/gb-2009-10-4-r38.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationBase SequenceCell DifferentiationConserved SequenceCpG IslandsEpigenesis, GeneticGene Expression RegulationGene Regulatory NetworksGenome, HumanHumansMacrophagesModels, GeneticPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidTranscription Initiation SiteTranscription, GeneticConceptsTranscription start siteRegulatory inputsTarget genesStart siteRegulatory blocksMapping of transcription start sitesTranscription Factor Binding SitesAlternative transcription start sitesGenomic regulatory blocksLong CpG islandFactor binding sitesRepressive histone modificationsTarget gene promotersResponse of genesTarget gene expressionMouse embryonic stem cell linesGene desertChromosomal regionsCpG islandsHistone modificationsExpression dataAcetylation stateEpigenetic featuresTranscriptional activityTranscription factors
2007
Divergence of Transcription Factor Binding Sites Across Related Yeast Species
Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. Divergence of Transcription Factor Binding Sites Across Related Yeast Species. Science 2007, 317: 815-819. PMID: 17690298, DOI: 10.1126/science.1140748.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBinding SitesCandida albicansChromatin ImmunoprecipitationDNA-Binding ProteinsEvolution, MolecularFungal ProteinsGene Expression Regulation, FungalGene Regulatory NetworksGenes, FungalOligonucleotide Array Sequence AnalysisRegulatory Sequences, Nucleic AcidSaccharomycesSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription FactorsConceptsS. mikataeGene regulationS. bayanusRelated yeast speciesYeast Saccharomyces cerevisiaeTranscription factor bindingTranscription Factor Binding SitesDNA microarray analysisOrthologous genesChromatin immunoprecipitationRelated speciesPhenotypic diversityTranscription factorsFactor bindingSaccharomyces cerevisiaeS. cerevisiaeYeast speciesMolecular basisMicroarray analysisInterspecies variationSte12SpeciesBinding sitesCerevisiaeBayanus
2005
Chicken TAP genes differ from their human orthologues in locus organisation, size, sequence features and polymorphism
Walker B, van Hateren A, Milne S, Beck S, Kaufman J. Chicken TAP genes differ from their human orthologues in locus organisation, size, sequence features and polymorphism. Immunogenetics 2005, 57: 232-247. PMID: 15900495, DOI: 10.1007/s00251-005-0786-2.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsATP-Binding Cassette TransportersBase SequenceCell LineChickensChromosome MappingConserved SequenceDNA, ComplementaryExonsGenes, MHC Class IHaplotypesInterferon-gammaMajor Histocompatibility ComplexMolecular Sequence DataPolymorphism, GeneticPolymorphism, Single-Stranded ConformationalPromoter Regions, GeneticRecombinant ProteinsRNA, MessengerSequence Homology, Amino AcidSpecies SpecificityUp-RegulationConceptsTAP genesClass I genesSequence featuresI geneTranscription Factor Binding SitesProtein sequence featuresLevel of polymorphismFactor binding sitesChicken major histocompatibility complexEndoplasmic reticulum retentionBi-directional promoterClass I gene promoterInbred lines of chickensGene sizeGene structureBind ATPHuman orthologueProcessing genesExon 1Tapasin bindingHeterodimer formationTransporters associated with antigen processing genesLines of chickensHuman TAPInbred linesAnalysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites
Rozowsky J, Bertone P, Royce T, Weissman S, Snyder M, Gerstein M. Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. Lecture Notes In Computer Science 2005, 3594: 28-29. DOI: 10.1007/11532323_4.Peer-Reviewed Original ResearchGenomic tiling microarraysTiling microarraysNovel genomic featuresTranscription Factor Binding SitesGenomic tiling arraysDifferent splice isoformsNon-repetitive DNA sequencesGenome annotationTiling arraysChromatin immunoprecipitationNovel transcriptsTranscription factorsTranscript mappingGenomic featuresDNA sequencesSplice isoformsChIP experimentsShort oligonucleotide probesPCR ampliconsOligonucleotide probesUnbiased fashionBinding sitesMicroarrayGenomeTranscripts
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