2025
Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment
Pal A, Noble M, Morales M, Pal R, Baumgartner M, Yang J, Yim K, Uebbing S, Noonan J. Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment. Cell 2025, 188: 1504-1523.e27. PMID: 39889695, PMCID: PMC11928272, DOI: 10.1016/j.cell.2025.01.007.Peer-Reviewed Original ResearchQuantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks
Chen S, Xie Y, Alvarez M, Sheng Y, Bouchibti Y, Chang V, Lebrilla C. Quantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks. Analytical Chemistry 2025, 97: 1584-1593. PMID: 39805041, PMCID: PMC11780575, DOI: 10.1021/acs.analchem.4c04134.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProtein interaction networkCell surface glycansTerminal sialic acidAbundant membrane proteinProtein pairsCross-linking mass spectrometrySurface glycansAffinity purificationInteraction networkSialylated glycoformsMembrane proteinsLysine residuesProtein networkTarget proteinsSialic acidGlycansBiotin groupPolypeptide moietyProteinInteractomeExtensive interactionsCell membranePeptide pairsPolypeptide
2024
An atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms
Hart T, Sonnert N, Tang X, Chaurasia R, Allen P, Hunt J, Read C, Johnson E, Arora G, Dai Y, Cui Y, Chuang Y, Yu Q, Rahman M, Mendes M, Rolandelli A, Singh P, Tripathi A, Ben Mamoun C, Caimano M, Radolf J, Lin Y, Fingerle V, Margos G, Pal U, Johnson R, Pedra J, Azad A, Salje J, Dimopoulos G, Vinetz J, Carlyon J, Palm N, Fikrig E, Ring A. An atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms. Cell 2024, 187: 4113-4127.e13. PMID: 38876107, PMCID: PMC11959484, DOI: 10.1016/j.cell.2024.05.023.Peer-Reviewed Original ResearchCell invasionHost-microbe interactionsArthropod-borne pathogensHost sensingMicrobe interactionsTranscriptional regulationLyme disease spirocheteMicrobial interactionsExtracellular proteinsMicrobial pathogenesisEpidermal growth factorTissue colonizationEnvironmental cuesBacterial selectivityIntracellular pathogensPutative interactionsNext-generation therapeuticsPathogensFunctional investigationsInteractomeVector-borne diseasesImmune evasionPathogenic mechanismsStrainUnmet medical needA host–microbiota interactome reveals extensive transkingdom connectivity
Sonnert N, Rosen C, Ghazi A, Franzosa E, Duncan-Lowey B, González-Hernández J, Huck J, Yang Y, Dai Y, Rice T, Nguyen M, Song D, Cao Y, Martin A, Bielecka A, Fischer S, Guan C, Oh J, Huttenhower C, Ring A, Palm N. A host–microbiota interactome reveals extensive transkingdom connectivity. Nature 2024, 628: 171-179. PMID: 38509360, DOI: 10.1038/s41586-024-07162-0.Peer-Reviewed Original ResearchNiche colonizationHost–microorganism interactionsHost-microbiota interactionsInvade host tissuesStrain-specific interactionsHost cells in vitroConspecific strainsEffect of indigenous microorganismsHost biologyHost proteinsSecreted proteinsCommensal microorganismsExoproteinsBacterial strainsDiverse phylogenyMolecular basisMyriad microorganismsTissue of originTissue isolationCells in vitroInteractomeBinding patternsHost tissuesBiological logicHost immune system in vivo
2023
Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome
Rahman S, Dong P, Apontes P, Fernando M, Kosoy R, Townsley K, Girdhar K, Bendl J, Shao Z, Misir R, Tsankova N, Kleopoulos S, Brennand K, Fullard J, Roussos P. Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Research 2023, 51: 11142-11161. PMID: 37811875, PMCID: PMC10639075, DOI: 10.1093/nar/gkad798.Peer-Reviewed Original ResearchConceptsChromatin interactomeNeural developmentSpecific gene expressionEnhancer-promoter loopsDistinct cell typesGenome compartmentalizationRepressive compartmentGenome architectureFine-scale changesGenome structureChromatin loopsGWAS lociTAD boundariesTranscriptional inactivationActive promotersGene expressionInteractomeGenomeCell typesComplex organDisease mechanismsHuman brainAdult prefrontal cortexAdult human brainNeurodevelopmental processesUnannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5
Chen Y, Su H, Zhao J, Na Z, Jiang K, Bacchiocchi A, Loh K, Halaban R, Wang Z, Cao X, Slavoff S. Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5. Cell Reports 2023, 42: 113145. PMID: 37725512, PMCID: PMC10629662, DOI: 10.1016/j.celrep.2023.113145.Peer-Reviewed Original ResearchConceptsG2/M phaseWD40-repeat protein WDR5Mitotic spindle lengthMultiple interaction partnersM phaseOff-target genesLate G1 phaseWDR5 interactionMitotic functionsH3K4me3 levelsWDR5Interaction partnersMultiple proteinsExpression maximaCell cycleSpindle lengthG1 phaseGenesCell proliferationOff-target bindingBindingInteractomeChromatinTranscriptionKIF2A.Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes
Lou S, Yang M, Li T, Zhao W, Cevasco H, Yang Y, Gerstein M. Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes. PLOS Computational Biology 2023, 19: e1011222. PMID: 37410793, PMCID: PMC10325097, DOI: 10.1371/journal.pcbi.1011222.Peer-Reviewed Original ResearchConceptsProtein-coding genesHuman protein-coding genesProtein-protein interactionsFull interactomeDirect protein-protein interactionHuman protein-protein interactionsSingle-cell sequencing dataHuman genesExogenous microbesHuman microRNAsSequencing dataInteractomeGenesPathway structureMicrobesMiRNAsNetwork propagationRothia mucilaginosaInitial linkageComprehensive understandingMicroRNAsViral infectionMillions of deathsAbundanceSimilar patternChemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides
Chen Y, Cao X, Loh K, Slavoff S. Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides. Biochemical Society Transactions 2023, 51: 1071-1082. PMID: 37171061, PMCID: PMC10317152, DOI: 10.1042/bst20221074.Peer-Reviewed Original ResearchConceptsChemical labelingAlternative open reading framesOpen reading frameLimited sequence homologyMammalian genomesGene classesProtein domainsQuantitative proteomicsReading frameSequence homologyBiological roleProteomic discoveryMolecular levelSmORFsCell proliferationProteomicsInteractomeGenomeSpecific propertiesExperimental techniquesLabelingHomologyPolypeptideProteinFunctionalizationProteome-wide screening for mitogen-activated protein kinase docking motifs and interactors
Shi G, Song C, Torres Robles J, Salichos L, Lou H, Lam T, Gerstein M, Turk B. Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science Signaling 2023, 16: eabm5518. PMID: 36626580, PMCID: PMC9995140, DOI: 10.1126/scisignal.abm5518.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinaseDocking motifSequence motifsDocking sequenceShort linear sequence motifsLinear sequence motifsSubstrate recruitmentHuman proteomeProtein kinaseCatalytic cleftExchange mutantsEssential functionsCultured cellsScreening pipelineWide screeningInteractorsMotifSequenceLimited repertoireSelective bindingInteractomeCombinatorial librariesMKK6ProteomeMKK7
2022
Orientia tsutsugamushi OtDUB Is Expressed and Interacts with Adaptor Protein Complexes during Infection
Adcox H, Berk J, Hochstrasser M, Carlyon J. Orientia tsutsugamushi OtDUB Is Expressed and Interacts with Adaptor Protein Complexes during Infection. Infection And Immunity 2022, 90: e00469-22. PMID: 36374099, PMCID: PMC9753657, DOI: 10.1128/iai.00469-22.Peer-Reviewed Original ResearchConceptsObligate intracellular lifestyleClathrin adaptor protein complex 1Adaptor protein complex 1Non-integral membrane proteinsAdaptor protein complexesHost endocytic pathwayMembrane traffic regulatorsCell wall proteinsWall proteinsProtein complexesIntracellular lifestyleRho GTPasesAdapter proteinEndocytic pathwayMembrane proteinsUbiquitin bindingCellular pathwaysCell wallStructured illumination microscopyPhospholipid phosphatidylserineIntact bacteriaO. tsutsugamushi infectionProteinRecombinant versionInteractome
2020
A reference map of the human binary protein interactome
Luck K, Kim D, Lambourne L, Spirohn K, Begg B, Bian W, Brignall R, Cafarelli T, Campos-Laborie F, Charloteaux B, Choi D, Coté A, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy M, Kishore N, Knapp J, Kovács I, Lemmens I, Mee M, Mellor J, Pollis C, Pons C, Richardson A, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin S, Choi S, Colabella C, Coppin G, D’Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson J, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman G, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere J, Wang Y, Weatheritt R, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader G, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill D, Vidal M, Roth F, Calderwood M. A reference map of the human binary protein interactome. Nature 2020, 580: 402-408. PMID: 32296183, PMCID: PMC7169983, DOI: 10.1038/s41586-020-2188-x.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsBinary protein interactionsTissue-specific networksContext-specific functionsTissue-specific phenotypesSubcellular rolesGenome functionProtein interactomeInteractome networkMendelian diseasesInteractome mapCurated interactionsProtein interactionsCellular contextCellular functionsPhenotypic outcomesCellular organizationMolecular mechanismsInteractomeReference mapGlobal insightGenomeHuriComprehensive understandingInteraction
2019
Neurofilament-lysosomal genetic intersections in the cortical network of stuttering
Benito-Aragón C, Gonzalez-Sarmiento R, Liddell T, Diez I, d'Oleire Uquillas F, Ortiz-Terán L, Bueichekú E, Chow H, Chang S, Sepulcre J. Neurofilament-lysosomal genetic intersections in the cortical network of stuttering. Progress In Neurobiology 2019, 184: 101718. PMID: 31669185, PMCID: PMC6938554, DOI: 10.1016/j.pneurobio.2019.101718.Peer-Reviewed Original ResearchConceptsCytoskeleton organizationNeurofilament genesCortical networksGenetic expression levelsMannose-6-phosphateGenetic interactomesInteractome networkTranscriptome dataLarge-scale cortical networksLysosomal pathwayAllen Human Brain AtlasPresence of stutteringGenetic intersectionFunctional connectivity MRIBiological functionsNeuronal circuitsSpatial similarity analysisGenesHuman Brain AtlasTarget pathwaysFunctional linkInteractomeNeurobiological underpinningsCo-localizationLysosomal dysfunctionProximity labeling reveals novel interactomes in live Drosophila tissue
Mannix KM, Starble RM, Kaufman RS, Cooley L. Proximity labeling reveals novel interactomes in live Drosophila tissue. Development 2019, 146: dev176644. PMID: 31208963, PMCID: PMC6679357, DOI: 10.1242/dev.176644.Peer-Reviewed Original ResearchMeSH KeywordsActin CytoskeletonActinsAnimalsAnimals, Genetically ModifiedCell CommunicationCell DifferentiationCytological TechniquesCytoskeletonDNA-(Apurinic or Apyrimidinic Site) LyaseDrosophila melanogasterFemaleGenes, ReporterGerm CellsIntercellular JunctionsMolecular ImagingOocytesOogenesisProtein BindingProtein Interaction MapsStaining and LabelingConceptsProximity labelingIntercellular bridgesProximity-dependent biotinylationStable intercellular bridgesRC proteinDynamic actin cytoskeletonProtein interactome analysisRNA interference screenNovel interactomePrey genesUncharacterized proteinsDistinct interactomesDrosophila tissuesActin cytoskeletonInterference screenInteractome analysisLive tissueMultiple proteinsProximity ligationInteractomeGerm cellsIntercellular communicationRespective preyFunctional roleProtein
2018
The number of titrated microRNA species dictates ceRNA regulation
Chiu H, Martínez M, Komissarova E, Llobet-Navas D, Bansal M, Paull E, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Research 2018, 46: gky286-. PMID: 29684207, PMCID: PMC5961349, DOI: 10.1093/nar/gky286.Peer-Reviewed Original ResearchConceptsCo-regulationPrediction of gene expressionMiRNA speciesTumor suppressor PTENCeRNA regulationGene expressionCeRNA interactionsMicroRNA speciesBiochemical assaysMultiple miRNAsSpeciesOncogene CCND1Non-tumour contextsRegulating microRNAsMiRNAsInteraction kineticsEndogenous RNAIndependent tumorsCeRNA networkHIF1AInteractomeCeRNAGenesRNAOncogene
2017
Mapping Protein–Protein Interactions Using Affinity Purification and Mass Spectrometry
Lee CM, Adamchek C, Feke A, Nusinow DA, Gendron JM. Mapping Protein–Protein Interactions Using Affinity Purification and Mass Spectrometry. Methods In Molecular Biology 2017, 1610: 231-249. PMID: 28439867, DOI: 10.1007/978-1-4939-7003-2_15.Peer-Reviewed Original ResearchConceptsAP-MSHigher-order protein complexesAffinity purificationMapping protein-protein interactionsProtein-protein interaction networkProtein-protein interactionsMeaningful complexesProtein interactomeProtein complexesProtein-specific antibodiesMass spectrometry technologyInteraction networksCellular pathwaysTransient interactionsMass spectrometryInteractomeNonspecific interactionsSpectrometry technologyUnbiased methodComplexesPurificationComprehensive knowledgeCrucial stepPlantsProteinSingle-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface
Pavličev M, Wagner GP, Chavan AR, Owens K, Maziarz J, Dunn-Fletcher C, Kallapur SG, Muglia L, Jones H. Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface. Genome Research 2017, 27: 349-361. PMID: 28174237, PMCID: PMC5340963, DOI: 10.1101/gr.207597.116.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomicsG protein-coupled receptorsCell communication networksGene expression profilesReceptor-ligand pairsCell type identificationOrganismal functionInteraction hubTrophoblast cellsGene expressionExpression profilesEndometrial stromal fibroblastsSpecific expressionCell typesInteractomeTranscriptomicsRich resourceCell interactionsPlacental trophoblast cellsDecidual cellsImmune signalsStromal cellsGrowth factorStromal fibroblastsEndometrial stromal cells
2016
The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome
McCann KL, Teramoto T, Zhang J, Hall T, Baserga SJ. The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome. ELife 2016, 5: e16381. PMID: 27077951, PMCID: PMC4859800, DOI: 10.7554/elife.16381.Peer-Reviewed Original ResearchMeSH KeywordsAlopeciaCircular DichroismEndocrine System DiseasesHumansIntellectual DisabilityMagnetic Resonance SpectroscopyModels, BiologicalMutant ProteinsProtein BindingProtein FoldingProtein Interaction MapsRibonucleoproteins, Small NucleolarRibosome Subunits, LargeRNA PrecursorsRNA Processing, Post-TranscriptionalRNA-Binding ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsConceptsProtein-protein interactionsANE syndromeMolecular basisDefective protein foldingRRNA processing defectsRNA recognition motifMature ribosomesRibosome assemblyHub proteinsRRNA processingNucleolar proteinsDomain foldingProtein foldingRecognition motifHuman diseasesProcessing defectsInteractomeMutationsCircular dichroismHub functionModel systemYeastFoldingProteinNOP4
2015
A comparative study of disease genes and drug targets in the human protein interactome
Sun J, Zhu K, Zheng W, Xu H. A comparative study of disease genes and drug targets in the human protein interactome. BMC Bioinformatics 2015, 16: s1. PMID: 25861037, PMCID: PMC4402590, DOI: 10.1186/1471-2105-16-s5-s1.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesDisease genesDrug targetsHuman protein-coding genesHuman protein-protein interaction networkProtein-protein interaction networkProtein-coding genesHuman protein interactomeComplex diseasesNovel drug targetsProtein interactomeAnatomical Therapeutic Chemical (ATC) classificationInteraction networksDisease proteinAssociation studiesGenesDisease categoriesInteractomeProteinMajor disease categoriesDifferent disease categoriesFirst comprehensive comparisonTargetTreatment efficacyHigh betweennessA Survey of the Interactome of Kaposi's Sarcoma-Associated Herpesvirus ORF45 Revealed Its Binding to Viral ORF33 and Cellular USP7, Resulting in Stabilization of ORF33 That Is Required for Production of Progeny Viruses
Gillen J, Li W, Liang Q, Avey D, Wu J, Wu F, Myoung J, Zhu F. A Survey of the Interactome of Kaposi's Sarcoma-Associated Herpesvirus ORF45 Revealed Its Binding to Viral ORF33 and Cellular USP7, Resulting in Stabilization of ORF33 That Is Required for Production of Progeny Viruses. Journal Of Virology 2015, 89: 4918-4931. PMID: 25694600, PMCID: PMC4403494, DOI: 10.1128/jvi.02925-14.Peer-Reviewed Original ResearchConceptsUbiquitin-specific protease 7Kaposi's sarcoma-associated herpesvirusSarcoma-associated herpesvirusKSHV lytic replicationORF45 proteinKaposi's Sarcoma-Associated Herpesvirus ORF45Lytic replicationCarboxyl-terminal 19 amino acidsKSHV ORF45Copurified proteinsConsensus motifMultifunctional proteinKinase proteinInteractomeCarboxyl terminusKSHV genomeORF45Tegument proteinsWeight complexesProtein accumulationORF33Progeny virionsAmino acidsHuman cancersProtein
2014
More Than a Pore: Ion Channel Signaling Complexes
Lee A, Fakler B, Kaczmarek LK, Isom LL. More Than a Pore: Ion Channel Signaling Complexes. Journal Of Neuroscience 2014, 34: 15159-15169. PMID: 25392484, PMCID: PMC4228125, DOI: 10.1523/jneurosci.3275-14.2014.Peer-Reviewed Original ResearchConceptsIon channelsHeterologous expression systemIon channel complexSignaling ComplexFunctional dissectionHuman genomeMolecular basisExpression systemSecond messengerHuman diseasesChannel complexCellular excitabilityProteinNew insightsSuch interactionsInteractomeGenomeUnexpected propertiesComplexesMessengerPathwayInteractionDysregulationLocalizationVivo
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