2023
Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube
Afzal Z, Lange J, Nolte C, McKinney S, Wood C, Paulson A, De Kumar B, Unruh J, Slaughter B, Krumlauf R. Shared retinoic acid responsive enhancers coordinately regulate nascent transcription of Hoxb coding and non-coding RNAs in the developing mouse neural tube. Development 2023, 150: dev201259. PMID: 37102683, PMCID: PMC10233718, DOI: 10.1242/dev.201259.Peer-Reviewed Original ResearchConceptsNascent transcriptionDynamic regulatory interactionsHox gene expressionCis-regulatory elementsRetinoic acid response elementMouse neural tubeTranscription of genesNon-coding RNAAcid response elementSingle-molecule fluorescentRetinoic acid responseMutant embryosHOXB clusterHox expressionAxial identityHoxb genesRegulatory interactionsTranscriptional mechanismsGene expressionDependent enhancersTranscriptionResponse elementResponsive enhancerNeural tubeCompetitive interactions
2022
HiChIPdb: a comprehensive database of HiChIP regulatory interactions
Zeng W, Liu Q, Yin Q, Jiang R, Wong H. HiChIPdb: a comprehensive database of HiChIP regulatory interactions. Nucleic Acids Research 2022, 51: d159-d166. PMID: 36215037, PMCID: PMC9825415, DOI: 10.1093/nar/gkac859.Peer-Reviewed Original ResearchConceptsRegulatory interactionsChromatin conformation capture methodsCell typesArchitecture of DNADiverse cell typesComprehensive annotationGene regulationRegulatory genesHiChIPInteraction databasesRegulatory mechanismsTissue homeostasisCell differentiationFunctional interactionsComprehensive databaseCell linesDisease developmentGenesCellsCapture methodCohesinGWASH3K27acChromatinSNPs
2021
Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube
Parker H, De Kumar B, Pushel I, Bronner M, Krumlauf R. Analysis of lamprey meis genes reveals that conserved inputs from Hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube. Developmental Biology 2021, 479: 61-76. PMID: 34310923, DOI: 10.1016/j.ydbio.2021.07.014.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesBody PatterningConserved SequenceEnhancer Elements, GeneticGene ExpressionGene Expression Regulation, DevelopmentalGenes, HomeoboxHomeodomain ProteinsLampreysMyeloid Ecotropic Viral Integration Site 1 ProteinNeural CrestNeural TubePre-B-Cell Leukemia Transcription Factor 1RhombencephalonTranscription FactorsConceptsMeis genesTALE proteinsDivergence of jawedSea lamprey genomeEvolution of vertebratesNeural crest cellsLamprey genomeTALE factorsPattern of expressionPbx proteinsJawed vertebratesVertebrate evolutionDeep ancestryJawless vertebratesLamprey embryosRhombomeric domainsTransgenic reporterNeural enhancerSimilar relative positionsRegulatory interactionsPharyngeal archesReporter expressionHead developmentCrest cellsSequence alignmentMultiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help
Tejero E, Lashgari D, García-Valiente R, Gao X, Crauste F, Robert P, Meyer-Hermann M, Martínez M, van Ham S, Guikema J, Hoefsloot H, van Kampen A. Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help. Frontiers In Immunology 2021, 11: 620716. PMID: 33613551, PMCID: PMC7892951, DOI: 10.3389/fimmu.2020.620716.Peer-Reviewed Original ResearchMeSH KeywordsAsymmetric Cell DivisionB-LymphocytesCD40 AntigensCell LineageComputer SimulationGene Regulatory NetworksGerminal CenterHumansImmunologic MemoryInterferon Regulatory FactorsLymphopoiesisModels, ImmunologicalPlasma CellsPositive Regulatory Domain I-Binding Factor 1Proto-Oncogene Proteins c-bcl-6Signal TransductionT Follicular Helper CellsTime FactorsConceptsB cell to plasma cell differentiationAsymmetric divisionRegulatory interactions of transcription factorsPlasma cell differentiationInteraction of transcription factorsCore gene regulatory networkGene regulatory networksCell differentiationCell-fate decisionsTemporal switchB cell receptor affinityGerminal center reactionB cellsCD40 signaling pathwayRegulatory networksRegulatory interactionsTranscription factorsEffective immune protectionCenter reactionSignaling pathwayAdaptive immune systemT Follicular Helper CellsPlasma cell generationMemory B cellsMolecular modules
2019
Structures of ligand-occupied β-Klotho complexes reveal a molecular mechanism underlying endocrine FGF specificity and activity
Kuzina ES, Ung PM, Mohanty J, Tome F, Choi J, Pardon E, Steyaert J, Lax I, Schlessinger A, Schlessinger J, Lee S. Structures of ligand-occupied β-Klotho complexes reveal a molecular mechanism underlying endocrine FGF specificity and activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 7819-7824. PMID: 30944224, PMCID: PMC6475419, DOI: 10.1073/pnas.1822055116.Peer-Reviewed Original ResearchConceptsFGF receptorsPleiotropic cellular responsesFibroblast growth factor (FGF) familyPrimary high-affinity receptorsKlotho proteinChimeric mutantsGrowth factor familyCatalytic subunitFGFR functionRegulatory interactionsTerminal tailPleiotropic cellular effectsFactor familyP motifS motifExtracellular domainMolecular mechanismsIntracellular signalingCellular responsesSame binding siteCellular effectsGeneral mechanismEndocrine FGFsBinary complexBinding sitesA Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates
Parker H, De Kumar B, Green S, Prummel K, Hess C, Kaufman C, Mosimann C, Wiedemann L, Bronner M, Krumlauf R. A Hox-TALE regulatory circuit for neural crest patterning is conserved across vertebrates. Nature Communications 2019, 10: 1189. PMID: 30867425, PMCID: PMC6416258, DOI: 10.1038/s41467-019-09197-8.Peer-Reviewed Original ResearchConceptsNeural crestHox genesAncestral mechanismRegulatory circuitsUpstream regulatory componentsNeural crest patterningAncient paraloguesPbx proteinsJawed vertebratesAncient conservationExtant vertebratesAncestral activityRegulatory interactionsHOX2 genesRegulatory componentsVertebratesJaw formationGenesGnathostomesEnhancerHoxLampreyParaloguesImportant roleHoxa2
2017
Understanding Tissue-Specific Gene Regulation
Sonawane A, Platig J, Fagny M, Chen C, Paulson J, Lopes-Ramos C, DeMeo D, Quackenbush J, Glass K, Kuijjer M. Understanding Tissue-Specific Gene Regulation. Cell Reports 2017, 21: 1077-1088. PMID: 29069589, PMCID: PMC5828531, DOI: 10.1016/j.celrep.2017.10.001.Peer-Reviewed Original ResearchConceptsTissue specificityTissue-specific gene regulationGenotype-Tissue Expression projectControl tissue specificityTissue-specific genesTranscription factor targetsTissue-specific functionsGene expression patternsGene Set Enrichment AnalysisTissue-specific mannerTissue-specific processesInvestigate gene expressionGene regulationRegulatory interactionsTranscriptional controlTranscription factor expressionTranscription factorsExpression projectEnrichment analysisGene expressionExpression patternsGenesRegulation nodeFactor targetsTranscriptionReciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition
Musante V, Li L, Kanyo J, Lam TT, Colangelo CM, Cheng SK, Brody AH, Greengard P, Le Novère N, Nairn AC. Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition. ELife 2017, 6: e24998. PMID: 28613156, PMCID: PMC5515580, DOI: 10.7554/elife.24998.Peer-Reviewed Original ResearchConceptsARPP-16ARPP-19Protein phosphatase 2A inhibitionProtein phosphatase PP2A.Inhibition of PP2ASwitch-like responseKinase inhibitsPhosphatase PP2A.Regulatory interactionsPKA phosphorylationAntagonistic interplayReciprocal regulationBasal phosphorylationPhosphorylationMAST3PP2APKAENSAKinaseStriatal signalingPP2A.Multiple sitesInhibitionMitosisSignaling
2014
Structure and Regulatory Interactions of the Cytoplasmic Terminal Domains of Serotonin Transporter
Fenollar-Ferrer C, Stockner T, Schwarz TC, Pal A, Gotovina J, Hofmaier T, Jayaraman K, Adhikary S, Kudlacek O, Mehdipour AR, Tavoulari S, Rudnick G, Singh SK, Konrat R, Sitte HH, Forrest LR. Structure and Regulatory Interactions of the Cytoplasmic Terminal Domains of Serotonin Transporter. Biochemistry 2014, 53: 5444-5460. PMID: 25093911, PMCID: PMC4147951, DOI: 10.1021/bi500637f.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCircular DichroismCytoplasmFluorescence Resonance Energy TransferHumansMagnetic Resonance SpectroscopyModels, MolecularMolecular Sequence DataProtein ConformationProtein FoldingProtein Structure, SecondaryProtein Structure, TertiarySerotonin Plasma Membrane Transport ProteinsConceptsTerminal domainStructures of homologuesYellow fluorescent protein tagProtein-protein interactionsFluorescent protein tagsFluorescence resonance energy transfer signalN-terminal domainCarboxy-terminal endHelix-breaking residuesCyan fluorescent proteinEnergy transfer signalHuman serotonin transporterNSS familyConformational cycleCircular dichroism spectroscopyProtein tagsCytoplasmic segmentRegulatory interactionsTransmembrane regionUptake of neurotransmittersInteraction partnersRegulatory mechanismsSerotonin transporterBiophysical approachesFluorescent protein
2011
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M. Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. PLOS Computational Biology 2011, 7: e1002190. PMID: 22125477, PMCID: PMC3219617, DOI: 10.1371/journal.pcbi.1002190.Peer-Reviewed Original ResearchConceptsTranscription factorsRegulatory networksGenome-wide ChIP-seqIntegrated Regulatory NetworkHigh-throughput sequencing dataTargets of miRNAsProtein-protein interactionsMulti-level regulationRNA-seq dataRNA-seq profilesHigh-throughput datasetsSet of TFsModENCODE projectHigher eukaryotesC. elegansMotif enrichmentChIP-seqRegulatory interactionsHost genesTarget genesNegative regulatorSequencing dataMiRNAsNetwork motifsConservation information
2010
How B cells influence bone biology in health and disease
Horowitz MC, Fretz JA, Lorenzo JA. How B cells influence bone biology in health and disease. Bone 2010, 47: 472-479. PMID: 20601290, PMCID: PMC2941392, DOI: 10.1016/j.bone.2010.06.011.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsHematopoietic stem cellsB cell differentiationCell differentiationTranscription factorsBone cellsImportant regulatory interactionsBone phenotypeRegulatory interactionsB cellsTemporal mannerSupportive nicheStem cellsAdaptive immune systemBone biologyDifferentiationRANKL-RANKActivated B cellsEndosteal bone surfaceNormal bone remodelingNicheSpecific responsesPhenotypeCellsImportant roleImmune system
2008
Two GATA Transcription Factors Are Downstream Effectors of Floral Homeotic Gene Action in Arabidopsis
Mara CD, Irish VF. Two GATA Transcription Factors Are Downstream Effectors of Floral Homeotic Gene Action in Arabidopsis. Plant Physiology 2008, 147: 707-718. PMID: 18417639, PMCID: PMC2409029, DOI: 10.1104/pp.107.115634.Peer-Reviewed Original ResearchConceptsTranscription factorsChlorophyll biosynthesisMADS-box transcription factorsSpecification of petalGATA transcription factor familyNutrient-responsive genesFloral organ identityComplex regulatory interplayDirect regulatory interactionsGATA transcription factorsTranscription factor familyExpression of suitesStamen identityOrgan identityTranscriptional cascadeAPETALA3Regulatory interplayChromatin immunoprecipitationCombinatorial actionFloral organogenesisResponsive genesRedundant rolesRegulatory interactionsGene actionPromoter sequencesPrioritization of gene regulatory interactions from large-scale modules in yeast
Lee HJ, Manke T, Bringas R, Vingron M. Prioritization of gene regulatory interactions from large-scale modules in yeast. BMC Bioinformatics 2008, 9: 32. PMID: 18211684, PMCID: PMC2244593, DOI: 10.1186/1471-2105-9-32.Peer-Reviewed Original ResearchConceptsTranscriptional modulesRegulatory interactionsTarget genesTranscription factorsChIP-chip binding dataTF-gene interactionsGene regulatory interactionsCo-regulated proteinsCo-regulated genesNormal growth conditionsGenome-wide dataCell wall synthesisChIP-chip dataRegulatory linkWall synthesisFunctional categoriesRegulatory proteinsYeast dataGenesCoherent modulesGrowth conditionsProteinBiological systemsDifferent reference datasetsNumerous modules
2007
[18] Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters
Zwir I, Harari O, Groisman EA. [18] Gene Promoter Scan Methodology for Identifying and Classifying Coregulated Promoters. Methods In Enzymology 2007, 422: 361-385. PMID: 17628149, PMCID: PMC3755887, DOI: 10.1016/s0076-6879(06)22018-4.Peer-Reviewed Original ResearchConceptsCoregulated promotersTwo-component regulatory systemCis-acting regulatory elementsDistinct regulatory networksSingle transcription factorPhoP/PhoQPhoP proteinGenomic approachesCoregulated genesPhoP regulonRegulatory networksRegulatory interactionsTranscription factorsRegulatory featuresGene transcriptionRegulatory elementsPostgenomic eraNovel memberDifferential expressionGenesEscherichia coliRegulatory systemSalmonella entericaPromoterMultiple mechanisms
2006
A Misclassification Model for Inferring Transcriptional Regulatory Networks
Vannucci M, Sun N, Zhao H. A Misclassification Model for Inferring Transcriptional Regulatory Networks. 2006, 347-365. DOI: 10.1017/cbo9780511584589.019.Peer-Reviewed Original ResearchTranscriptional regulatory networksGene expression dataRegulatory networksExpression dataUnderlying transcriptional regulatory networksProtein-DNA binding dataNetwork reconstructionSet of proteinsYeast cell cycleMutual regulatory interactionsRegulatory network reconstructionGene regulationRegulatory interactionsSpecific genesCell cycleGenesBiological researchExpression levelsProteinTRNBinding dataHigh connectivityTransient stimulationRecent advancesStatistical framework
2005
Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation
Zwir I, Huang H, Groisman EA. Analysis of differentially-regulated genes within a regulatory network by GPS genome navigation. Bioinformatics 2005, 21: 4073-4083. PMID: 16159917, DOI: 10.1093/bioinformatics/bti672.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsArtificial IntelligenceCluster AnalysisComputational BiologyDatabases, GeneticEscherichia coliEscherichia coli ProteinsGene Expression RegulationGene Expression Regulation, BacterialGenomeGenomicsPromoter Regions, GeneticResponse ElementsSalmonella entericaSoftwareTranscription, GeneticConceptsPhoP proteinRegulatory featuresGene expressionEnteric bacteria Escherichia coliCis-regulatory featuresCo-regulated promotersPost-genomic eraTranscription initiationRegulatory networksRegulatory interactionsGene transcriptionNovel memberExpression patternsBacteria Escherichia coliGenesEscherichia coliSalmonella entericaMultiple mechanismsProteinFundamental mechanismsExpressionRegulonTranscriptionPromoterReduced dataset
2003
Making informed decisions: regulatory interactions between two-component systems
Bijlsma JJ, Groisman EA. Making informed decisions: regulatory interactions between two-component systems. Trends In Microbiology 2003, 11: 359-366. PMID: 12915093, DOI: 10.1016/s0966-842x(03)00176-8.Peer-Reviewed Original ResearchConceptsTwo-component systemTwo-component regulatory systemPost-transcriptional mechanismsMultitude of stressesResponse regulatorBacterial adaptationRegulatory interactionsComplex nichePhosphoryl transferMolecular levelRegulatory systemSpecific signalsMultiple signalsPhosphorelayMultifaceted environmentNicheRegulatorBacteriaPhosphataseMechanismStressAdaptation
2000
Cellular Mechanisms Regulating Protein Phosphatase-1 A KEY FUNCTIONAL INTERACTION BETWEEN INHIBITOR-2 AND THE TYPE 1 PROTEIN PHOSPHATASE CATALYTIC SUBUNIT*
Frederick D, Huang H, Yang J, Helps N, Cohen P, Nairn A, DePaoli-Roach A, Tatchell K, Connor J, Shenolikar S. Cellular Mechanisms Regulating Protein Phosphatase-1 A KEY FUNCTIONAL INTERACTION BETWEEN INHIBITOR-2 AND THE TYPE 1 PROTEIN PHOSPHATASE CATALYTIC SUBUNIT*. Journal Of Biological Chemistry 2000, 275: 18670-18675. PMID: 10748125, DOI: 10.1074/jbc.m909312199.Peer-Reviewed Original ResearchConceptsPP1 catalytic subunitCatalytic subunitType 1 protein phosphatase catalytic subunitAmino acidsProtein phosphatase catalytic subunitN-terminusProtein serine/threonineN-terminal 35 amino acidsInhibitor 2Phosphatase catalytic subunitTwo-hybrid analysisNovel regulatory interactionsProtein phosphatase 1Serine/threoninePull-down assaysSite-directed mutagenesisN-terminal sequencePP1 mutantsKey functional interactionsPP1 inhibitorPP1 enzymesPP1 inhibitionPhosphatase 1Regulatory interactionsSaccharomyces cerevisiae
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