2023
Isoform Function Prediction Based on Heterogeneous Graph Attention Networks
Guo K, Li Y, Chen H, Shen H, Yang Y. Isoform Function Prediction Based on Heterogeneous Graph Attention Networks. 2023, 00: 522-527. DOI: 10.1109/bibm58861.2023.10386048.Peer-Reviewed Original ResearchIsoform function predictionFunction predictionIsoform functionGene OntologyMechanisms of gene regulationFunctions of isoformsProtein language modelsFunctional labelsProtein sequencesGO annotationsGene regulationSequence featuresGO termsMRNA moleculesIsoform levelsGene levelBiological processesGenesIsoformsSpecies datasetInteraction dataIntricate mechanismsProteinHeterogeneous graph attention networkAnnotationInsights into RAG Evolution from the Identification of “Missing Link” Family A RAGL Transposons
Martin E, Le Targa L, Tsakou-Ngouafo L, Fan T, Lin C, Xiao J, Huang Z, Yuan S, Xu A, Su Y, Petrescu A, Pontarotti P, Schatz D. Insights into RAG Evolution from the Identification of “Missing Link” Family A RAGL Transposons. Molecular Biology And Evolution 2023, 40: msad232. PMID: 37850912, PMCID: PMC10629977, DOI: 10.1093/molbev/msad232.Peer-Reviewed Original ResearchConceptsJawed vertebratesTransposon familyRAG1-RAG2 recombinaseRecombination signal sequencesHemichordate Ptychodera flavaMolecular domesticationSignal sequenceP. flavaDNA bindingPtychodera flavaSequence featuresTransposition activityVertebratesTransposonCritical enzymeHinge regionGenomeDomesticationFlavaProteinPivotal stepAdaptive immunityCritical intermediateRAGRAGLChromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy
Poulet A, Kratkiewicz A, Li D, van Wolfswinkel J. Chromatin analysis of adult pluripotent stem cells reveals a unique stemness maintenance strategy. Science Advances 2023, 9: eadh4887. PMID: 37801496, PMCID: PMC10558129, DOI: 10.1126/sciadv.adh4887.Peer-Reviewed Original ResearchConceptsAdult pluripotent stem cellsPluripotent stem cellsStem cell genesStem cellsCell genesPluripotency-related gene expressionStem cell-specific genesTissue-specific genesCell-specific genesTissue-specific promotersChromatin stateChromatin organizationRegenerative organismsChromatin analysisConstitutive genesRegulatory logicTranscription factorsGene expressionSequence featuresGenesDefault statePromoterLong-term maintenanceCellsISWI
2019
Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition
Yadav D, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky P. Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition. Nucleic Acids Research 2019, 48: 2091-2106. PMID: 31875226, PMCID: PMC7038937, DOI: 10.1093/nar/gkz1163.Peer-Reviewed Original ResearchConceptsDsRNA binding proteinSpecific mRNA targetsGroove sideMinor groove recognitionCytoplasmic mRNA levelsMRNA decayMRNA transportTranslational controlLoop anchorsMRNA targetsMinor groove sideMajor groove sideStaufen1Helix α1Sequence featuresDsRNABinding proteinGroove recognitionPhosphodiester backboneSpecific recognitionGuanine baseMRNA levels
2017
Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation
Roden C, Gaillard J, Kanoria S, Rennie W, Barish S, Cheng J, Pan W, Liu J, Cotsapas C, Ding Y, Lu J. Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation. Genome Research 2017, 27: 374-384. PMID: 28087842, PMCID: PMC5340965, DOI: 10.1101/gr.208900.116.Peer-Reviewed Original ResearchConceptsPri-miRNA processingHuman genetic variationGenetic variationPrimary sequence motifsPrimary microRNA processingMiRNA biogenesisDisease-causing mutationsPri-miRNAsPrimary miRNAsSequence motifsMiRNA hairpinsMicroRNA processingMature microRNAsSequence featuresRNA hairpinsComputational pipelineNovel determinantStem lengthUnpaired basesHairpinTranscriptsStemBiogenesisGenomeMiRNAs
2016
STarMir Tools for Prediction of microRNA Binding Sites
Kanoria S, Rennie W, Liu C, Carmack CS, Lu J, Ding Y. STarMir Tools for Prediction of microRNA Binding Sites. Methods In Molecular Biology 2016, 1490: 73-82. PMID: 27665594, PMCID: PMC5353976, DOI: 10.1007/978-1-4939-6433-8_6.Peer-Reviewed Original ResearchConceptsMessenger RNAEndogenous short noncoding RNAsGene expressionMammalian biological processesHigh-throughput miRNATarget messenger RNAsShort noncoding RNAsMicroRNA Binding SitesCertain human diseasesCross-species validationTranslational repressionMiRNA functionGene regulationSeedless sitesMRNA degradationNoncoding RNAsRegulatory moleculesBiological processesSequence featuresHuman diseasesImmunoprecipitation studiesMiRNAComputational predictionsBinding sitesMiRNAsIntegrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer
Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nature Communications 2016, 7: 10982. PMID: 26975529, PMCID: PMC4796315, DOI: 10.1038/ncomms10982.Peer-Reviewed Original ResearchMeSH KeywordsAdenocarcinomaBlotting, WesternCell FractionationCell ProliferationChromatin ImmunoprecipitationGene Expression Regulation, NeoplasticGene Regulatory NetworksHCT116 CellsHumansIn Situ Hybridization, FluorescenceMaleMicroRNAsPolycomb Repressive Complex 2Prostatic NeoplasmsPTEN PhosphohydrolaseReverse Transcriptase Polymerase Chain ReactionRNA TransportRNA, Long NoncodingConceptsRegulatory networksPolycomb repressive complex 2Protein-coding genesProtein-coding transcriptsRepressive complex 2Cancer driver genesGene expression profilesTumor suppressive functionTranscriptional regulationSponge lncRNAsCytoplasmic localizationExpression profilesIntegrative analysisSequence featuresDriver genesLncRNAsPTEN expressionFunctional significanceRegulationGenesRNAExpressionComplexes 2Important roleMicroRNAs
2015
Characterization of the mammalian miRNA turnover landscape
Guo Y, Liu J, Elfenbein SJ, Ma Y, Zhong M, Qiu C, Ding Y, Lu J. Characterization of the mammalian miRNA turnover landscape. Nucleic Acids Research 2015, 43: 2326-2341. PMID: 25653157, PMCID: PMC4344502, DOI: 10.1093/nar/gkv057.Peer-Reviewed Original ResearchConceptsMiRNA turnoverStable small RNAsMammalian cell typesCultured mammalian cellsSubset of miRNAsTurnover kineticsMiRNA biogenesisMost miRNAsMiR-222-5pNucleotide biasSmall RNAsMiRNA maturationMammalian cellsSame miRNAMiRNA poolExpression profilingHsp90 associationSequence determinantsDeep sequencingHsp90 inhibitionTurnover rateMiRNA isoformsDifferent turnover ratesSequence featuresCell types
2013
77 Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
Wang J, Zhuang J, Iyer S, Lin X, Whitfield T, Greven M, Pierce B, Dong X, Kundaje A, Cheng Y, Rando O, Birney E, Myers R, Noble W, Snyder M, Weng Z. 77 Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Journal Of Biomolecular Structure And Dynamics 2013, 31: 49-50. DOI: 10.1080/07391102.2013.786511.Peer-Reviewed Original ResearchChIP-seqTF bindingGC-richSecondary motifsTranscription factor (TFChIP-seq dataTF binding sitesDNase I-sensitive regionsHuman transcription factorsNucleosomes in vivoHigh-throughput sequencingDNase I digestionHistone deacetylase HDAC2Cell type-specificCell linesENCODE consortiumGenome-wideSequence motifsGenomic regionsCanonical motifsNucleosome-depletedChromatin structureMotif sitesTethered bindingSequence features
2012
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
Wang J, Zhuang J, Iyer S, Lin X, Whitfield T, Greven M, Pierce B, Dong X, Kundaje A, Cheng Y, Rando O, Birney E, Myers R, Noble W, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research 2012, 22: 1798-1812. PMID: 22955990, PMCID: PMC3431495, DOI: 10.1101/gr.139105.112.Peer-Reviewed Original ResearchMeSH KeywordsBase CompositionBinding SitesCell LineChromatin Assembly and DisassemblyChromatin ImmunoprecipitationCluster AnalysisComputational BiologyDeoxyribonuclease IGenome, HumanHigh-Throughput Nucleotide SequencingHumansInternetMolecular Sequence AnnotationNucleosomesNucleotide MotifsOrgan SpecificityProtein BindingTranscription FactorsConceptsChIP-seqTF bindingGC-richSecondary motifsRegions genome-wideChIP-seq dataTF binding sitesDNase I-sensitive regionsHuman transcription factorsNucleosomes in vivoHigh-throughput sequencingDNase I digestionHistone deacetylase HDAC2Cell type-specificCell linesENCODE consortiumGenome-wideSequence motifsGenomic regionsNucleosome-depletedCanonical motifsChromatin structureMotif sitesTethered bindingSequence featurespiRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism
Beyret E, Liu N, Lin H. piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism. Cell Research 2012, 22: 1429-1439. PMID: 22907665, PMCID: PMC3463270, DOI: 10.1038/cr.2012.120.Peer-Reviewed Original ResearchConceptsPIWI proteinsPing-pong mechanismSmall non-coding RNAsSame DNA strandNon-coding RNAsPiRNA biogenesisGermline developmentDiverse organismsEpigenetic regulationPiRNAsMIWIRepeat sequencesMILISame locusSequence featuresNucleotide positionsPostnatal testisBroad functionsAdult testisMouse testisDNA strandsAdult spermatogenesisProteinBiogenesisPrimary pathway
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 lines
2003
The properties of the single chicken MHC classical class II α chain (B-LA) gene indicate an ancient origin for the DR/E-like isotype of class II molecules
Salomonsen J, Marston D, Avila D, Bumstead N, Johansson B, Juul-Madsen H, Olesen G, Riegert P, Skjødt K, Vainio O, Wiles M, Kaufman J. The properties of the single chicken MHC classical class II α chain (B-LA) gene indicate an ancient origin for the DR/E-like isotype of class II molecules. Immunogenetics 2003, 55: 605-614. PMID: 14608490, DOI: 10.1007/s00251-003-0620-7.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAmino Acid SequenceAnimalsBlotting, SouthernChickensChromosomesCloning, MolecularDNA, ComplementaryExonsFemaleGenes, MHC Class IIHaplotypesHLA-DP AntigensHLA-DQ AntigensHLA-DR AntigensIntronsMaleMicrosatellite RepeatsMolecular Sequence DataPolymerase Chain ReactionSequence Homology, Amino AcidConceptsPeptide-binding residuesIsotypes of class II moleculesSouthern blot analysis of genomic DNALow level of polymorphismAnalysis of genomic DNALevel of polymorphismGenomic DNA sequencesNon-mammalian vertebratesSouthern blot analysisChicken sequencesBack-cross familiesSequence diversitySequence featuresDNA sequencesGenomic DNAMHC lociChain locusChain transcriptsChain geneAmino acidsClass II moleculesBack-crossGenesSequenceCDNA
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