2025
Emerging roles of transcriptional condensates as temporal signal integrators
Meyer K, Huang B, Weiner O. Emerging roles of transcriptional condensates as temporal signal integrators. Nature Reviews Genetics 2025, 1-12. PMID: 40240649, DOI: 10.1038/s41576-025-00837-y.Peer-Reviewed Original ResearchGene regulatory networksTranscriptional condensatesRegulatory networksControl cell physiologyTemporal signal integrationMethod to probeSignaling networksSignaling specificityCell physiologyGene activationTranscription factorsSignaling DynamicsBiophysical frameworkSignal adaptationTranscriptionGenesSignalDecoding mechanismSignal integrityFrequency of signalsPhysiologyMechanism
2024
DNA methylation in mammalian development and disease
Smith Z, Hetzel S, Meissner A. DNA methylation in mammalian development and disease. Nature Reviews Genetics 2024, 26: 7-30. PMID: 39134824, DOI: 10.1038/s41576-024-00760-8.Peer-Reviewed Original ResearchLong-read sequencing technologiesDNA methylation fieldDNA methylation landscapeGenome functionMethylation landscapeSequencing technologiesEpigenetic codeGenomic characterizationRegulatory layerDNA methylationCell physiologyMammalian developmentMammalian lifespanGenetic featuresFunctional understandingSingle-cellDNAMechanistic discoveriesSomatic transitionsPhases of discoveryDevelopmental potentialDiscoveryPhenotypeSenescencePhysiology
2023
Cell protrusions and contractions generate long-range membrane tension propagation
De Belly H, Yan S, Borja da Rocha H, Ichbiah S, Town J, Zager P, Estrada D, Meyer K, Turlier H, Bustamante C, Weiner O. Cell protrusions and contractions generate long-range membrane tension propagation. Cell 2023, 186: 3049-3061.e15. PMID: 37311454, PMCID: PMC10330871, DOI: 10.1016/j.cell.2023.05.014.Peer-Reviewed Original ResearchConceptsActomyosin contractionPropagation of membrane tensionDual-trap optical tweezersMembrane tensionActin-driven protrusionsActin-based protrusionsCell membraneOptical tweezersActin cortexCell protrusionsCell polarityMembrane flowCell physiologyTension propagationActomyosinTension transmissionCellsMembraneMechanical forcesPropagationProtrusionTweezersActinPolarization
2022
Endoplasmic Reticulum Membrane Contact Sites, Lipid Transport, and Neurodegeneration.
Guillén-Samander A, De Camilli P. Endoplasmic Reticulum Membrane Contact Sites, Lipid Transport, and Neurodegeneration. Cold Spring Harbor Perspectives In Biology 2022, 15: a041257. PMID: 36123033, PMCID: PMC10071438, DOI: 10.1101/cshperspect.a041257.Peer-Reviewed Original ResearchConceptsMembrane contact sitesEndoplasmic reticulumEndoplasmic reticulum membrane contact sitesContact sitesLipid transportER membrane contact sitesCross talkLipid transfer proteinMutations of genesFamilial neurodegenerative diseasesIntracellular membranous organellesEndomembrane systemLipid trafficVesicular transportCell physiologyPlasma membraneMembranous organellesMembrane lipidsLipid exchangeTransfer proteinCell compartmentProteinNeurodegenerative diseasesMultiplicity of rolesDendritic tipsCyclobutane Pyrimidine Dimer Hyperhotspots as Sensitive Indicators of Keratinocyte UV Exposure†
Garcia‐Ruiz A, Kornacker K, Brash DE. Cyclobutane Pyrimidine Dimer Hyperhotspots as Sensitive Indicators of Keratinocyte UV Exposure†. Photochemistry And Photobiology 2022, 98: 987-997. PMID: 35944237, PMCID: PMC9802031, DOI: 10.1111/php.13683.Peer-Reviewed Original ResearchConceptsCyclobutane pyrimidine dimersGenomic averageSequence motifsHigh-throughput DNA sequencing methodsETS family transcription factorsNucleotide resolution analysisRNA processing genesNeonatal human epidermal keratinocytesDNA sequencing methodsTranscription factorsCpG islandsSites hundredsCell physiologyProcessing genesPromoter regionCell deathDNA damageSequencing methodsBiological importanceHuman epidermal keratinocytesPyrimidine dimersGenesMotifEpidermal keratinocytesMelanocytes
2021
Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline
Ferkowicz M, Winfree S, Sabo A, Kamocka M, Khochare S, Barwinska D, Eadon M, Cheng Y, Phillips C, Sutton T, Kelly K, Dagher P, El-Achkar T, Dunn K, Project F, Knight R, Lecker S, Stillman I, Mcmahon G, Waikar S, Weins A, Hacohen N, Hoover P, Aulisio M, Cooperman L, Herlitz L, O'toole J, Poggio E, Sedor J, Appelbaum P, Barasch J, Bomback A, D'agati V, Kiryluk K, Mehl K, Shang N, Weng C, Barisoni L, Alexandrov T, Ashkar T, Barwinska D, Dagher P, Dunn K, Eadon M, Ferkowicz M, Kelly K, Sutton T, Winfree S, Menez S, Parikh C, Rosenberg A, Villalobos P, Slack A, Rosas S, Williams M, Azeloglu E, He C, Iyengar R, Parikh S, Anderton C, Pasa-Tolic L, Velickovic D, Oliver G, Ardayfio J, Bebiak J, Brown K, Campbell T, Campbell C, Hayashi L, Jefferson N, Koewler R, Roberts G, Saul J, Shpigel A, Stutzke E, Wright L, Miegs L, Pinkeney R, Sealfon R, Troyanskaya O, Tuttle K, Goltsev Y, Lake B, Zhang K, Dobi D, Joanes M, Laszik Z, Nolan G, Schroeder A, Balis U, He O, Hodgin J, Kretzler M, Mariani L, Menon R, Otto E, Schaub J, Steck B, Elder M, Hall D, Kellum J, Kruth M, Murugan R, Palevsky P, Randhawa P, Rosengart M, Sims-Lucas S, Stefanick M, Stull S, Tublin M, Alpers C, De Boer I, Fullerton M, Himmelfarb J, Mcclelland R, Mooney S, Shankland S, Williams K, Blank K, Dighe A, Carson J, Dowd F, Drager Z, Sharma K, Zhang G, Kermani A, Lee S, Lu C, Miller T, Moe O, Park H, Sambandam K, Sanchez F, Torrealba J, Robert T, Vazquez M, Wang N, Gaut J, Jain S, Vijayan A, Luciano R, Moledina D, Ugochukwu U, Wilson F. Large-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline. Laboratory Investigation 2021, 101: 661-676. PMID: 33408350, PMCID: PMC8363780, DOI: 10.1038/s41374-020-00518-w.Peer-Reviewed Original ResearchConceptsSingle-cell techniquesCell physiologyTissue cytometryClinical tissue samplesHuman kidney tissueTissue samplesPersonalized medicineMolecular informationQuantitative censusAdvent of personalized medicineSpectral confocal microscopyRenal biopsyConfocal microscopyDiabetic nephropathyPathology of kidney diseaseKidney diseaseFlow cytometryIntact tissueCellsHuman nephrectomyHuman kidneyCytometryVolumetric Tissue Exploration
2019
Genomic sites hypersensitive to ultraviolet radiation
Premi S, Han L, Mehta S, Knight J, Zhao D, Palmatier MA, Kornacker K, Brash DE. Genomic sites hypersensitive to ultraviolet radiation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 24196-24205. PMID: 31723047, PMCID: PMC6883822, DOI: 10.1073/pnas.1907860116.Peer-Reviewed Original ResearchMeSH Keywords5' Untranslated RegionsCells, CulturedDNA DamageFibroblastsGene Expression RegulationGenome, HumanHigh-Throughput Nucleotide SequencingHumansMelanocytesMelanomaMutationPromoter Regions, GeneticProtein BiosynthesisPyrimidine DimersPyrimidine NucleotidesSkin NeoplasmsTOR Serine-Threonine KinasesUltraviolet RaysConceptsCyclobutane pyrimidine dimersETS family transcription factorsIndividual gene promotersFamily transcription factorsRNA-binding proteinPrimary human melanocytesSingle-base resolutionEpigenetic marksGenomic averageTranslation regulationGenomic sitesMotif locationsTranscription factorsCell physiologyGene promoterCancer driversGenomeHuman melanocytesCell typesTumor evolutionCell pathwaysRare mutationsUV targetPyrimidine dimersApurinic sitesProteostasis Environment Shapes Higher-Order Epistasis Operating on Antibiotic Resistance
Guerrero R, Scarpino S, Rodrigues J, Hartl D, Ogbunugafor C. Proteostasis Environment Shapes Higher-Order Epistasis Operating on Antibiotic Resistance. Genetics 2019, 212: 565-575. PMID: 31015194, PMCID: PMC6553834, DOI: 10.1534/genetics.119.302138.Peer-Reviewed Original ResearchConceptsHigher-order epistasisSNPs associated with resistancePatterns of epistasisControlled genetic backgroundSets of mutationsProteostasis environmentComplex traitsEpistatic interactionsBacterial enzymesEssential enzymeCell physiologyGenotypic contextEpistasisAntibiotic resistanceGenetic backgroundBackground sequencesAntimicrobial resistanceProteostasisBacterial resistanceGenetic modification technologyMutationsProteinEnzymeTraitsAntibiotics
2018
Cell-Penetrating Peptide Mediates Intracellular Membrane Passage of Human Papillomavirus L2 Protein to Trigger Retrograde Trafficking
Zhang P, da Silva G, Deatherage C, Burd C, DiMaio D. Cell-Penetrating Peptide Mediates Intracellular Membrane Passage of Human Papillomavirus L2 Protein to Trigger Retrograde Trafficking. Cell 2018, 174: 1465-1476.e13. PMID: 30122350, PMCID: PMC6128760, DOI: 10.1016/j.cell.2018.07.031.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCapsid ProteinsCell-Penetrating PeptidesEndosomesGolgi ApparatusGreen Fluorescent ProteinsHEK293 CellsHeLa CellsHuman papillomavirus 16HumansMutagenesisOncogene Proteins, ViralProtein TransportRecombinant Fusion ProteinsSequence AlignmentVirus AttachmentVirus InternalizationConceptsCell-penetrating peptidesTrans-Golgi networkNormal cell physiologyL2 proteinRetrograde transport pathwayShort protein segmentsHPV L2 proteinTrafficking factorsRetrograde traffickingCationic cell-penetrating peptidesCell physiologyEndosomal membranesProtein segmentsC-terminusBiological roleNon-enveloped virusesRetrograde pathwayL2 capsid proteinsMembrane passageCell penetrating peptideCapsid proteinViral proteinsProteinRetromerTransport pathways
2017
Contacts between the endoplasmic reticulum and other membranes in neurons
Wu Y, Whiteus C, Xu CS, Hayworth KJ, Weinberg RJ, Hess HF, De Camilli P. Contacts between the endoplasmic reticulum and other membranes in neurons. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e4859-e4867. PMID: 28559323, PMCID: PMC5474793, DOI: 10.1073/pnas.1701078114.Peer-Reviewed Original ResearchConceptsEndoplasmic reticulumER–plasma membrane contactsER-PM contactsMembrane contactSmaller focal contactsRegulation of CaInterorganelle communicationOrganelle biogenesisDifferent neuronal compartmentsCell physiologyIntracellular membranesFocal contactsMultivesicular bodiesER contactsIntracellular organellesER cisternaeLipid homeostasisBiochemical studiesTubulovesicular structuresMembrane appositionNeuronal compartmentsImportant functionsMitochondriaReticulumMembraneEndoplasmic Reticulum—Plasma Membrane Contact Sites
Saheki Y, De Camilli P. Endoplasmic Reticulum—Plasma Membrane Contact Sites. Annual Review Of Biochemistry 2017, 86: 1-26. PMID: 28301744, DOI: 10.1146/annurev-biochem-061516-044932.Peer-Reviewed Original ResearchConceptsPlasma membraneEndoplasmic reticulumProtein tethersEndoplasmic reticulum-plasma membrane contact sitesNonvesicular lipid transportER-PM contactsMembrane contact sitesLipid transfer proteinLipid trafficCell physiologyContact sitesMembranous organellesLipid transportBroad localizationTransfer proteinCross talkIntracellular CaDirect physical contactMultiplicity of rolesFunctional state
2015
Phosphoinositide Signaling in the Control of Membrane Dynamics and Interactions
De Camilli P. Phosphoinositide Signaling in the Control of Membrane Dynamics and Interactions. The FASEB Journal 2015, 29 DOI: 10.1096/fasebj.29.1_supplement.90.1.Peer-Reviewed Original ResearchPlasma membraneEndoplasmic reticulumIntrinsic membrane proteinsKey regulatory roleIntracellular second messengerMembrane identityE-SytsExtended synaptotagminsDifferent phosphoinositidesEndocytic membranesPutative functionsMembrane proteinsCell physiologyMembrane dynamicsCytosolic proteinsSecond messengerRegulatory rolePhosphatidyl inositolPhosphoinositideCell membraneInositol groupProteinMembranePhosphorylated metabolitesCa 2
2014
Spatial and temporal control of Rho GTPase functions
Moissoglu K, Schwartz MA. Spatial and temporal control of Rho GTPase functions. Cellular Logistics 2014, 4: e943618. PMID: 25610718, PMCID: PMC4279778, DOI: 10.4161/21592780.2014.943618.Peer-Reviewed Original ResearchCellular compartmentsRho GTPase biologyRho GTPases functionRho GTPase functionMultiple cellular compartmentsDifferent cellular compartmentsTemporal controlGTPase inactivationMembrane targetingGTPases functionGTPase functionCellular functionsRho GTPaseCell physiologyBiochemical regulationEffector activationMultiple regulatorsMultiple effectorsWealth of knowledgeSame cellsRegulationCompartmentsNano-scale dynamicsGTPaseMajor questionsManipulation of Plasma Membrane Phosphoinositides Using Photoinduced Protein–Protein Interactions
Idevall-Hagren O, De Camilli P. Manipulation of Plasma Membrane Phosphoinositides Using Photoinduced Protein–Protein Interactions. Methods In Molecular Biology 2014, 1148: 109-128. PMID: 24718798, DOI: 10.1007/978-1-4939-0470-9_8.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsArabidopsis ProteinsCatalytic DomainCell MembraneChlorocebus aethiopsCOS CellsCryptochromesHeLa CellsHumansLightMiceMolecular Sequence DataPhosphatidylinositolsPhosphoric Monoester HydrolasesPhotochemical ProcessesProtein Interaction Domains and MotifsProtein MultimerizationRecombinant Fusion ProteinsConceptsPlasma membraneCryptochrome 2Plasma membrane phosphatidylinositolProtein-protein interactionsLight-dependent conversionLipid-binding domainLive-cell imagingCritical regulatory roleMembrane lipid metabolismPhosphoinositide speciesSpatiotemporal regulationDimerization moduleCell physiologyMembrane phosphatidylinositolRegulatory roleTypes of cellsInositol phospholipidsPhosphorylated productsDimerization methodLipid metabolismMembraneCIB1DephosphorylationPhosphatidylinositolPhosphoinositide
2013
Hypoxia and DNA repair.
Glazer PM, Hegan DC, Lu Y, Czochor J, Scanlon SE. Hypoxia and DNA repair. The Yale Journal Of Biology And Medicine 2013, 86: 443-51. PMID: 24348208, PMCID: PMC3848098.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsDNA repairHomology-dependent repairDNA repair pathwaysNucleotide excision repairDNA mismatch repairGenomic integrityDependent repairCell physiologyRepair pathwaysExcision repairHypoxic cancer cellsCell metabolismGenetic instabilityMismatch repairInduction of angiogenesisCancer progressionCell growthCancer cellsNeoplastic developmentRepairSolid tumorsKey componentHypoxiaProfound changesApoptosisCalcium oscillations-coupled conversion of actin travelling waves to standing oscillations
Wu M, Wu X, De Camilli P. Calcium oscillations-coupled conversion of actin travelling waves to standing oscillations. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 1339-1344. PMID: 23297209, PMCID: PMC3557052, DOI: 10.1073/pnas.1221538110.Peer-Reviewed Original ResearchConceptsPlasma membraneActin regulatory proteinsActin cytoskeletonActin dynamicsActive Cdc42Cell cortexCell physiologyRegulatory proteinsActin polymerizationDynamic spatial patternsMacromolecular assembliesCalcium oscillationsSpatial patternsActinMembraneFBP17Cdc42CellsCytoskeletonFeedback mechanismProteinPhysiologyAntigen stimulationGlobal fluctuationsMechanismDynamin triple knockout cells reveal off target effects of commonly used dynamin inhibitors
Park RJ, Shen H, Liu L, Liu X, Ferguson SM, De Camilli P. Dynamin triple knockout cells reveal off target effects of commonly used dynamin inhibitors. Journal Of Cell Science 2013, 126: 5305-5312. PMID: 24046449, PMCID: PMC3828596, DOI: 10.1242/jcs.138578.Peer-Reviewed Original ResearchConceptsDynamin 1Dynamin inhibitorTKO cellsPeripheral membrane rufflingDouble knockoutDynamin 3 geneClathrin-mediated endocytosisTriple-knockout cellsDynamin-dependent processFluid-phase endocytosisDyngo-4aMembrane fissionMembrane rufflingDKO cellsDynamin 2Knockout cellsLow-level expressionCell physiologyDynaminEndocytosisTarget effectsDKO fibroblastsGenesCellsKO fibroblasts
2012
Science Signaling Podcast: 12 June 2012
Ferguson S, VanHook A. Science Signaling Podcast: 12 June 2012. Science Signaling 2012, 5 DOI: 10.1126/scisignal.2003263.Commentaries, Editorials and LettersTranscription factorsLysosomal homeostasisNuclear translocationActivity of TFEBExpression of genesDamaged organellesKinase mTORTFEB activityCell physiologyLysosomal proteinsLysosomal stressCellular wasteLysosomal functionTFEBInternalized materialScience SignalingMTOROrganellesTranslocationHomeostasisNormal conditionsDephosphorylationGenesSignalingCytoplasm
2009
Revisiting the parietal cell
Kopic S, Murek M, Geibel JP. Revisiting the parietal cell. American Journal Of Physiology - Cell Physiology 2009, 298: c1-c10. PMID: 19889964, DOI: 10.1152/ajpcell.00478.2009.Peer-Reviewed Original ResearchHow form follows functional genomics: gene expression profiling gastric epithelial cells with a particular discourse on the parietal cell
Capoccia BJ, Huh WJ, Mills JC. How form follows functional genomics: gene expression profiling gastric epithelial cells with a particular discourse on the parietal cell. Physiological Genomics 2009, 37: 67-78. PMID: 19208773, PMCID: PMC2685495, DOI: 10.1152/physiolgenomics.90408.2008.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsFunctional genomic studiesFunctional genomicsGene expressionGenomic studiesCell lineagesEntire cellular transcriptomeGene ontology analysisDifferentiated cell lineagesGene expression patternsCellular transcriptomeParietal cellsVascular endothelial growth factor BIndividual genesLineage-specific markersOntology analysisCell physiologyGene productsMolecular anatomyGastric parietal cellsExpression patternsMicroarray analysisMolecular mechanismsCell-specific markersGastric epithelial cellsGrowth factor B
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