2018
Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder
Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, Moran Losada P, Khan Z, Mleczko J, Xia Y, Dai R, Wang D, Yang YT, Xu M, Fish K, Hof PR, Warrell J, Fitzgerald D, White K, Jaffe AE, Peters M, Gerstein M, Liu C, Iakoucheva L, Pinto D, Geschwind D, Ashley-Koch A, Crawford G, Garrett M, Song L, Safi A, Johnson G, Wray G, Reddy T, Goes F, Zandi P, Bryois J, Jaffe A, Price A, Ivanov N, Collado-Torres L, Hyde T, Burke E, Kleiman J, Tao R, Shin J, Akbarian S, Girdhar K, Jiang Y, Kundakovic M, Brown L, Kassim B, Park R, Wiseman J, Zharovsky E, Jacobov R, Devillers O, Flatow E, Hoffman G, Lipska B, Lewis D, Haroutunian V, Hahn C, Charney A, Dracheva S, Kozlenkov A, Belmont J, DelValle D, Francoeur N, Hadjimichael E, Pinto D, van Bakel H, Roussos P, Fullard J, Bendl J, Hauberg M, Mangravite L, Peters M, Chae Y, Peng J, Niu M, Wang X, Webster M, Beach T, Chen C, Jiang Y, Dai R, Shieh A, Liu C, Grennan K, Xia Y, Vadukapuram R, Wang Y, Fitzgerald D, Cheng L, Brown M, Brown M, Brunetti T, Goodman T, Alsayed M, Gandal M, Geschwind D, Won H, Polioudakis D, Wamsley B, Yin J, Hadzic T, De La Torre Ubieta L, Swarup V, Sanders S, State M, Werling D, An J, Sheppard B, Willsey A, White K, Ray M, Giase G, Kefi A, Mattei E, Purcaro M, Weng Z, Moore J, Pratt H, Huey J, Borrman T, Sullivan P, Giusti-Rodriguez P, Kim Y, Sullivan P, Szatkiewicz J, Rhie S, Armoskus C, Camarena A, Farnham P, Spitsyna V, Witt H, Schreiner S, Evgrafov O, Knowles J, Gerstein M, Liu S, Wang D, Navarro F, Warrell J, Clarke D, Emani P, Gu M, Shi X, Xu M, Yang Y, Kitchen R, Gürsoy G, Zhang J, Carlyle B, Nairn A, Li M, Pochareddy S, Sestan N, Skarica M, Li Z, Sousa A, Santpere G, Choi J, Zhu Y, Gao T, Miller D, Cherskov A, Yang M, Amiri A, Coppola G, Mariani J, Scuderi S, Szekely A, Vaccarino F, Wu F, Weissman S, Roychowdhury T, Abyzov A. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science 2018, 362 PMID: 30545856, PMCID: PMC6443102, DOI: 10.1126/science.aat8127.Peer-Reviewed Original ResearchConceptsTranscriptome-wide association studyTranscriptome-wide characterizationPathogenic dysregulationTranscriptomic organizationDifferential splicingCoexpression networkGenetic enrichmentRegulatory regionsGenomic dataGene expressionAssociation studiesDisease locusComprehensive resourceMechanistic insightsCis effectSplicingBipolar disorderNeural-immune mechanismsMolecular pathologyTherapeutic developmentAutism spectrum disorderExpressionMajor psychiatric disordersBrain expressionDiseased brainIsoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq
Carlyle B, Kitchen RR, Zhang J, Wilson R, Lam T, Rozowsky JS, Williams KR, Sestan N, Gerstein M, Nairn AC. Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq. Journal Of Proteome Research 2018, 17: 3431-3444. PMID: 30125121, PMCID: PMC6392456, DOI: 10.1021/acs.jproteome.8b00310.Peer-Reviewed Original ResearchConceptsRNA-seqProteomic dataGene expressionLiquid chromatography-tandem mass spectrometry proteomicsTandem mass spectrometry proteomicsHigh-throughput proteomic dataTranscriptomic profiling methodsDistinct amino acid sequencesTranscript-level expressionAmino acid sequenceMass spectrometry proteomicsHEK293 cell culturesTranslatome dataMost genesProfound functional implicationsProtein isoformsAlternate isoformsGene productsAcid sequenceCellular controlBiosynthetic stateGeneration of peptidesCell typesFunctional relevanceFunctional implications
2001
ARPP‐16/ARPP‐19: a highly conserved family of cAMP‐regulated phosphoproteins
Dulubova I, Horiuchi A, Snyder G, Girault J, Czernik A, Shao L, Ramabhadran R, Greengard P, Nairn A. ARPP‐16/ARPP‐19: a highly conserved family of cAMP‐regulated phosphoproteins. Journal Of Neurochemistry 2001, 77: 229-238. DOI: 10.1046/j.1471-4159.2001.00191.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCHO CellsConserved SequenceCorpus StriatumCricetinaeCyclic AMPCyclic AMP-Dependent Protein KinasesHumansIn Vitro TechniquesMaleMiceMultigene FamilyOrgan SpecificityPhosphoproteinsPhosphorylationProtein IsoformsRatsRats, Sprague-DawleyReceptors, Dopamine D1Receptors, Dopamine D2Sequence Homology, Amino AcidConceptsProtein kinase AARPP-19ARPP-16Family of cAMPImportant cellular functionsActivation of PKAIsoform-specific antibodiesYeast genomeD. melanogasterC. elegansProtein familyCellular functionsNon-neuronal cellsSignal transductionConsensus sitesKinase ARelated proteinsΑ-endosulfinePhosphorylated formIntact cellsIntracellular messengerBi-directional regulationDopamine receptorsFamily membersPhosphorylationARPP-16/ARPP-19: a highly conserved family of cAMP-regulated phosphoproteins.
Dulubova I, Horiuchi A, Snyder G, Girault J, Czernik A, Shao L, Ramabhadran R, Greengard P, Nairn A. ARPP-16/ARPP-19: a highly conserved family of cAMP-regulated phosphoproteins. Journal Of Neurochemistry 2001, 77: 229-38. PMID: 11279279, DOI: 10.1046/j.1471-4159.2001.t01-1-00191.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsCHO CellsConserved SequenceCorpus StriatumCricetinaeCyclic AMPCyclic AMP-Dependent Protein KinasesHumansIn Vitro TechniquesMaleMiceMultigene FamilyOrgan SpecificityPhosphoproteinsPhosphorylationProtein IsoformsRatsRats, Sprague-DawleyReceptors, Dopamine D1Receptors, Dopamine D2Sequence Homology, Amino AcidConceptsProtein kinase AARPP-19ARPP-16Family of cAMPImportant cellular functionsActivation of PKAIsoform-specific antibodiesYeast genomeD. melanogasterC. elegansProtein familyCellular functionsNon-neuronal cellsSignal transductionConsensus sitesType dopamine receptorsKinase ARelated proteinsPhosphorylated formIntact cellsDopamine receptorsIntracellular messengerBi-directional regulationFamily membersPhosphorylation