2025
Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase
Devarkar S, Budding C, Pathirage C, Kavoor A, Herbert C, Limbach P, Musier-Forsyth K, Xiong Y. Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase. Nucleic Acids Research 2025, 53: gkaf114. PMID: 40036503, PMCID: PMC11878792, DOI: 10.1093/nar/gkaf114.Peer-Reviewed Original ResearchConceptsTransfer ribonucleic acidHuman lysyl-tRNA synthetaseLysyl-tRNA synthetaseHigh-resolution cryo-electron microscopyPost-transcriptional modificationsCryo-electron microscopyD-loopCatalytic stepStructural basisAminoacylationCryo-EMProtein synthesisCatalytic efficiencyFunctional impactSynthetaseRibonucleic acidActive siteMachineryLysRSMetazoansMs2t6ATRNALys3Mcm5s2UR37Integral role
2024
The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus
Kojima M, Hoppe C, Giraldez A. The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus. Nature Reviews Genetics 2024, 26: 245-267. PMID: 39587307, PMCID: PMC11928286, DOI: 10.1038/s41576-024-00792-0.Peer-Reviewed Original Research
2021
VPS13D bridges the ER to mitochondria and peroxisomes via Miro
Guillén-Samander A, Leonzino M, Hanna MG, Tang N, Shen H, De Camilli P. VPS13D bridges the ER to mitochondria and peroxisomes via Miro. Journal Of Cell Biology 2021, 220: e202010004. PMID: 33891013, PMCID: PMC8077184, DOI: 10.1083/jcb.202010004.Peer-Reviewed Original ResearchConceptsLipid transport proteinsHigher eukaryotesER-mitochondriaSecretory pathwayAccessory factorsMitochondrial dynamicsDisease pathogenesisTransport proteinsParkin substratesLipid transferSplice variantsParkinson's disease pathogenesisVps13Lipid supplyMitochondriaMiroVPS13DERMESYeastMost lipidsTransport domainEukaryotesGem1MetazoansER
2017
Purification of Zygotically Transcribed RNA through Metabolic Labeling of Early Zebrafish Embryos
Heyn P, Neugebauer KM. Purification of Zygotically Transcribed RNA through Metabolic Labeling of Early Zebrafish Embryos. Methods In Molecular Biology 2017, 1605: 121-131. PMID: 28456961, DOI: 10.1007/978-1-4939-6988-3_8.Peer-Reviewed Original Research
2015
Coilin: The first 25 years
Machyna M, Neugebauer KM, Staněk D. Coilin: The first 25 years. RNA Biology 2015, 12: 590-596. PMID: 25970135, PMCID: PMC4615369, DOI: 10.1080/15476286.2015.1034923.Peer-Reviewed Original Research
2014
Versatile microRNA biogenesis in animals and their viruses
Xie M, Steitz JA. Versatile microRNA biogenesis in animals and their viruses. RNA Biology 2014, 11: 673-681. PMID: 24823351, PMCID: PMC4156499, DOI: 10.4161/rna.28985.Peer-Reviewed Original ResearchConceptsEssential cellular processesMiRNA regulatory networkPost-transcriptional levelUbiquitous gene regulatorsNon-canonical pathwayMost miRNAsCytoplasmic DicerMicroRNA biogenesisMolecular machineryCellular processesRegulatory networksPrimary transcriptGene regulatorsNuclear DroshaCellular RNABiogenesisDroshaAlternative mechanismFundamental roleCleavage stepMetazoansDicerMiRNAsMicroRNAsMiRNA
2013
Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets
López-Giráldez F, Moeller AH, Townsend JP. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.Peer-Reviewed Original ResearchConceptsPhylogenomic data setsPhylogenetic informativenessPhylogenetic signalEffects of homoplasyPoor phylogenetic resolutionPhylogenetic resolutionSister cladeOutgroup taxaPhylogenetic researchTaxonomic groupsPhylogenetic inferenceAdvantageous genesGenesMetazoansCladeTaxaDiverse groupDiverse time scalesHomoplasyHaphazard samplingMammalsFungiOrganismsFungalMarkers
2012
Nuclear noncoding RNA surveillance: is the end in sight?
Wolin SL, Sim S, Chen X. Nuclear noncoding RNA surveillance: is the end in sight? Trends In Genetics 2012, 28: 306-313. PMID: 22475369, PMCID: PMC3378728, DOI: 10.1016/j.tig.2012.03.005.Peer-Reviewed Original ResearchConceptsRNA surveillance pathwaySurveillance pathwayAberrant RNAsSteady-state transcriptomeYeast counterpartEukaryotic cellsProtein cofactorsMammalian cellsRNA determinantsHuman diseasesSubsequent degradationRNACofactorPathwayKey roleRecent studiesMetazoansExoribonucleasesAccessible endTranscriptomeNcRNAsCellsYeastNucleaseProtein
2011
Mechanisms of Insulin Action
White M, White M. Mechanisms of Insulin Action. 2011, 19-38. DOI: 10.1007/978-1-4614-1028-7_2.Peer-Reviewed Original ResearchInsulin-like growth factor 2Receptor tyrosine kinasesTyrosine kinaseInsulin-like signalingInsulin-like peptidesG protein-coupled receptorsInsulin-like growth factor-1Caenorhabditis elegansEnvironmental signalsHuman genomeFruit flyRelease of nutrientsGrowth factor 2Factor 1Factor 2Somatic growthKinaseLower animalsGrowth factor-1Common mechanismSimilar peptidesInsulin actionWide arrayMetabolismMetazoansHigher-level metazoan relationships: recent progress and remaining questions
Edgecombe G, Giribet G, Dunn C, Hejnol A, Kristensen R, Neves R, Rouse G, Worsaae K, Sørensen M. Higher-level metazoan relationships: recent progress and remaining questions. Organisms Diversity & Evolution 2011, 11: 151-172. DOI: 10.1007/s13127-011-0044-4.Peer-Reviewed Original ResearchThousands of genesTarget gene approachSister-group relationBilaterian phylogenyBilaterian animalsPhylogenomic approachProtostome cladeMain cladesTaxonomic sampleSequencing projectsAcoelomorph flatwormsPhylogenetic analysisSister groupMultiple lociCladeProtostomesStable corePlacozoaBilateriansBilateriaDeuterostomesMetazoansSpiraliansPlatyzoaDeuterostomia
2009
The Role of Insulin‐like Signaling for the Central and Peripheral Regulation of Nutrient Homeostasis and Life Span
White M. The Role of Insulin‐like Signaling for the Central and Peripheral Regulation of Nutrient Homeostasis and Life Span. The FASEB Journal 2009, 23: 329.2-329.2. DOI: 10.1096/fasebj.23.1_supplement.329.2.Peer-Reviewed Original ResearchInsulin-like signalingNutrient homeostasisHigher animalsInsulin receptor substrateLife spanAge-related diseasesMammalian lifespanLower metazoansReceptor substrateInsulin resistanceInsulin secretionNutrient storageNarrow physiologic rangeSignalingMetazoansAction of insulinReduced insulin secretionRole of insulinHomeostasisBlood glucose concentrationCompensatory hyperinsulinemiaGlucose intolerancePeripheral regulationPeripheral tissuesGlucose homeostasisA Hypervariable Invertebrate Allodeterminant
Nicotra ML, Powell AE, Rosengarten RD, Moreno M, Grimwood J, Lakkis FG, Dellaporta SL, Buss LW. A Hypervariable Invertebrate Allodeterminant. Current Biology 2009, 19: 583-589. PMID: 19303297, PMCID: PMC2681180, DOI: 10.1016/j.cub.2009.02.040.Peer-Reviewed Original ResearchConceptsColonial marine invertebratesGreatest sequence similarityPutative transmembrane receptorField-derived strainChimeric coloniesInvertebrate allorecognitionMarine invertebratesLower metazoansSequence similarityIntraspecific competitionTransmembrane receptorsHydractinia symbiolongicarpusMolecular basisExtracellular domainHistocompatibility responsesAllorecognition responsesInvertebratesModel systemGenesColoniesMetazoansCnidariansProtochordatesVertebratesPhyla
2008
Insulin-Like Signaling, Nutrient Homeostasis, and Life Span
Taguchi A, White M. Insulin-Like Signaling, Nutrient Homeostasis, and Life Span. Annual Review Of Physiology 2008, 70: 191-212. PMID: 17988211, DOI: 10.1146/annurev.physiol.70.113006.100533.Peer-Reviewed Original Research
2006
A low diversity of ANTP class homeobox genes in Placozoa
Monteiro A, Schierwater B, Dellaporta S, Holland P. A low diversity of ANTP class homeobox genes in Placozoa. Evolution & Development 2006, 8: 174-182. PMID: 16509895, DOI: 10.1111/j.1525-142x.2006.00087.x.Peer-Reviewed Original ResearchConceptsANTP class genesClass genesGene familyHomeobox genesLow diversityANTP class homeobox genesTight gene clusterClass homeobox genesDistinct cell typesPRD classBilaterian animalsTrichoplax adhaerensGene clusterBody patterningBody organizationMarine animalsTrichoplaxExtensive screenGenesCell typesMetazoansLarge diversitySitu hybridizationDiversityFamily
2004
Molecular Regulation of Müllerian Development by Hox Genes
DU H, TAYLOR HS. Molecular Regulation of Müllerian Development by Hox Genes. Annals Of The New York Academy Of Sciences 2004, 1034: 152-165. PMID: 15731308, DOI: 10.1196/annals.1335.018.Peer-Reviewed Original ResearchConceptsHox genesMolecular regulationCommon genetic systemConserved transcription factorHox gene expressionAspects of morphogenesisNormal embryonic developmentEmbryonic patterningGenetic systemTranscription factorsEmbryonic developmentDevelopmental processesGene expressionRegulatory moleculesCell differentiationGenesReproductive tract developmentAdult functionHOXA10 geneTract developmentEmbryonic periodReproductive tractRegulationMullerian tractMetazoansGuide RNAs with 5′ Caps and Novel Box C/D snoRNA-like Domains for Modification of snRNAs in Metazoa
Tycowski KT, Aab A, Steitz JA. Guide RNAs with 5′ Caps and Novel Box C/D snoRNA-like Domains for Modification of snRNAs in Metazoa. Current Biology 2004, 14: 1985-1995. PMID: 15556860, DOI: 10.1016/j.cub.2004.11.003.Peer-Reviewed Original ResearchConceptsModification guide RNAsGuide RNABox C/D snoRNAsInvariant G residueKink-turn structureGuide RNA genesShort guide RNASmall ribonucleoprotein particlesMetazoan organismsAncestral metazoanGuanosine capMetazoan cellsSingle intronD snoRNAsRNA genesSpliceosomal snRNAsTelomerase RNARibosomal RNASuch RNAsRibonucleoprotein particleMetazoansUpstream promoterIntronsG residuesCommon modificationA molecular link between SR protein dephosphorylation and mRNA export
Huang Y, Yario TA, Steitz JA. A molecular link between SR protein dephosphorylation and mRNA export. Proceedings Of The National Academy Of Sciences Of The United States Of America 2004, 101: 9666-9670. PMID: 15210956, PMCID: PMC470732, DOI: 10.1073/pnas.0403533101.Peer-Reviewed Original ResearchConceptsNuclear export factor 1Multiple RNA-binding proteinsMRNA-protein complexesSR protein dephosphorylationMRNA nuclear exportASF/SF2RNA-binding proteinMRNA exportProtein dephosphorylationProtein complexesProtein adaptersNuclear exportSpliced mRNAPhosphorylation stateMolecular linkFactor 1MRNAHigh affinityMetazoansDephosphorylationExportComplexesSerineAdapterProtein
2003
Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis
Shepard K, Gerber A, Jambhekar A, Takizawa P, Brown P, Herschlag D, DeRisi J, Vale R. Widespread cytoplasmic mRNA transport in yeast: Identification of 22 bud-localized transcripts using DNA microarray analysis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 11429-11434. PMID: 13679573, PMCID: PMC208774, DOI: 10.1073/pnas.2033246100.Peer-Reviewed Original ResearchConceptsDNA microarray analysisBud tipRNA transportMRNA localizationMicroarray analysisCell wall maintenanceCytoplasmic mRNA transportCytoplasmic mRNA localizationAsymmetric localizationMRNA transportYeast SaccharomycesRNA reportersProtein activityUntranslated regionCell asymmetryStress responseSecondary screenYeastMRNAProteinLocalizationShe2pMetazoansMyo4pShe3p
2000
The Role of HOX Genes in the Development and Function of the Female Reproductive Tract
Taylor H. The Role of HOX Genes in the Development and Function of the Female Reproductive Tract. Seminars In Reproductive Medicine 2000, 18: 081-090. PMID: 11299523, DOI: 10.1055/s-2000-13478.Peer-Reviewed Original ResearchConceptsHox genesCommon genetic systemHox gene mutationsAdult functionReproductive tractEmbryonic patterningRegulatory genesGenetic systemTranscription factorsEmbryonic developmentFemale reproductive tractGenesReproductive tract developmentTract developmentGene mutationsMetazoansHuman endometrial developmentSpeciesRoleMutationsRegulationPatterningFunctionEndometrial developmentMüllerian system
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