2024
Machine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cells
2023
DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ
Pramio D, Vieceli F, Varella-Branco E, Goes C, Kobayashi G, da Silva Pelegrina D, de Moraes B, El Allam A, De Kumar B, Jara G, Farfel J, Bennett D, Kundu S, Viapiano M, Reis E, de Oliveira P, Dos Santos E Passos-Bueno M, Rothlin C, Ghosh S, Schechtman D. DNA methylation of the promoter region at the CREB1 binding site is a mechanism for the epigenetic regulation of brain-specific PKMζ. Biochimica Et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2023, 1866: 194909. PMID: 36682583, PMCID: PMC10037092, DOI: 10.1016/j.bbagrm.2023.194909.Peer-Reviewed Original ResearchConceptsInduced pluripotent stem cellsInternal promoterNeuronal differentiationEpigenetic mechanismsDNA methylationUpstream promoterProtein kinase C ζHuman neuronal differentiationSite-specific hypermethylationAberrant DNA hypermethylationPluripotent stem cellsEpigenetic regulationSame epigenetic mechanismsLong-term memory formationDNA hypermethylationDemethylated regionsEpigenetic factorsPromoter regionTissue specificityMolecular mechanismsPRKCZ geneDifferentiated neuronsPromoterProtein kinase M zetaLong-term potentiation
2022
Within subject cross‐tissue analyzes of epigenetic clocks in substance use disorder postmortem brain and blood
Cabrera‐Mendoza B, Stertz L, Najera K, Selvaraj S, Teixeira A, Meyer T, Fries G, Walss‐Bass C. Within subject cross‐tissue analyzes of epigenetic clocks in substance use disorder postmortem brain and blood. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2022, 192: 13-27. PMID: 36056652, PMCID: PMC9742183, DOI: 10.1002/ajmg.b.32920.Peer-Reviewed Original ResearchConceptsSubstance use disordersStimulant use disorderUse disordersPostmortem brainsAlcohol use disorderBrains of individualsBlood tissueBiological agingSubgroup analysisBrain valuesEpigenetic clocksSUD groupPeripheral measuresAging StudyDisordersBrainPatientsBloodDNA methylation changesSame individualTissueIndividualsMethylation changesOpioidsTissue specificity
2021
Annotation of chromatin states in 66 complete mouse epigenomes during development
van der Velde A, Fan K, Tsuji J, Moore J, Purcaro M, Pratt H, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Communications Biology 2021, 4: 239. PMID: 33619351, PMCID: PMC7900196, DOI: 10.1038/s42003-021-01756-4.Peer-Reviewed Original ResearchConceptsChromatin stateMouse epigenomesPolycomb repressive complex proteinsBivalent chromatin stateTranscription start siteRepressive mark H3K27me3Silence target genesCharacteristics of promotersChromHMM algorithmUnique epigenomeGene expression programsENCODE projectTranscribed regionsMulticellular organismsStart siteRepressed regionsActive marksMammalian developmentComplex proteinsEpigenomeTissue specificityTarget genesExpression programsCell typesIntegrated analysis
2018
HOXA5 protein expression and genetic fate mapping show lineage restriction in the developing musculoskeletal system
Holzman MA, Bergmann JM, Feldman M, Landry-Truchon K, Jeannotte L, Mansfield JH. HOXA5 protein expression and genetic fate mapping show lineage restriction in the developing musculoskeletal system. The International Journal Of Developmental Biology 2018, 62: 785-796. PMID: 30604848, PMCID: PMC8783609, DOI: 10.1387/ijdb.180214jm.Peer-Reviewed Original ResearchConceptsLateral plate mesodermHOXA5 expressionSkeletal patterningPlate mesodermNon-cell autonomous functionCell-autonomous roleProtein expressionSatellite cell lineageLineage restrictionGenetic lineagesEmbryonic cellsCell lineagesLateral sclerotomeTissue specificitySomite stageSkeletal developmentLineagesAutonomous roleDirect roleMusculoskeletal morphologyTissue typesMesodermHOXA5SomitesAutonomous functions
2017
Genetic effects on gene expression across human tissues
Aguet F, Brown A, Castel S, Davis J, He Y, Jo B, Mohammadi P, Park Y, Parsana P, Segrè A, Strober B, Zappala Z, Cummings B, Gelfand E, Hadley K, Huang K, Lek M, Li X, Nedzel J, Nguyen D, Noble M, Sullivan T, Tukiainen T, MacArthur D, Getz G, Addington A, Guan P, Koester S, Little A, Lockhart N, Moore H, Rao A, Struewing J, Volpi S, Brigham L, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber W, Lonsdale J, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas J, Walters G, Washington M, Wheeler J, Bridge J, Foster B, Gillard B, Karasik E, Kumar R, Miklos M, Moser M, Jewell S, Montroy R, Rohrer D, Valley D, Mash D, Davis D, Sobin L, Barcus M, Branton P, Abell N, Balliu B, Delaneau O, Frésard L, Gamazon E, Garrido-Martín D, Gewirtz A, Gliner G, Gloudemans M, Han B, He A, Hormozdiari F, Li X, Liu B, Kang E, McDowell I, Ongen H, Palowitch J, Peterson C, Quon G, Ripke S, Saha A, Shabalin A, Shimko T, Sul J, Teran N, Tsang E, Zhang H, Zhou Y, Bustamante C, Cox N, Guigó R, Kellis M, McCarthy M, Conrad D, Eskin E, Li G, Nobel A, Sabatti C, Stranger B, Wen X, Wright F, Ardlie K, Dermitzakis E, Lappalainen T, Aguet F, Ardlie K, Cummings B, Gelfand E, Getz G, Hadley K, Handsaker R, Huang K, Kashin S, Karczewski K, Lek M, Li X, MacArthur D, Nedzel J, Nguyen D, Noble M, Segrè A, Trowbridge C, Tukiainen T, Abell N, Balliu B, Barshir R, Basha O, Battle A, Bogu G, Brown A, Brown C, Castel S, Chen L, Chiang C, Conrad D, Cox N, Damani F, Davis J, Delaneau O, Dermitzakis E, Engelhardt B, Eskin E, Ferreira P, Frésard L, Gamazon E, Garrido-Martín D, Gewirtz A, Gliner G, Gloudemans M, Guigo R, Hall I, Han B, He Y, Hormozdiari F, Howald C, Kyung Im H, Jo B, Yong Kang E, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy M, McDowell I, Mohammadi P, Monlong J, Montgomery S, Muñoz-Aguirre M, Ndungu A, Nicolae D, Nobel A, Oliva M, Ongen H, Palowitch J, Panousis N, Papasaikas P, Park Y, Parsana P, Payne A, Peterson C, Quan J, Reverter F, Sabatti C, Saha A, Sammeth M, Scott A, Shabalin A, Sodaei R, Stephens M, Stranger B, Strober B, Sul J, Tsang E, Urbut S, van de Bunt M, Wang G, Wen X, Wright F, Xi H, Yeger-Lotem E, Zappala Z, Zaugg J, Zhou Y, Akey J, Bates D, Chan J, Chen L, Claussnitzer M, Demanelis K, Diegel M, Doherty J, Feinberg A, Fernando M, Halow J, Hansen K, Haugen E, Hickey P, Hou L, Jasmine F, Jian R, Jiang L, Johnson A, Kaul R, Kellis M, Kibriya M, Lee K, Billy Li J, Li Q, Li X, Lin J, Lin S, Linder S, Linke C, Liu Y, Maurano M, Molinie B, Montgomery S, Nelson J, Neri F, Oliva M, Park Y, Pierce B, Rinaldi N, Rizzardi L, Sandstrom R, Skol A, Smith K, Snyder M, Stamatoyannopoulos J, Stranger B, Tang H, Tsang E, Wang L, Wang M, Van Wittenberghe N, Wu F, Zhang R, Nierras C, Branton P, Carithers L, Guan P, Moore H, Rao A, Vaught J, Gould S, Lockart N, Martin C, Struewing J, Volpi S, Addington A, Koester S, Little A, Brigham L, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber W, Lonsdale J, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas J, Walters G, Washington M, Wheeler J, Bridge J, Foster B, Gillard B, Karasik E, Kumar R, Miklos M, Moser M, Jewell S, Montroy R, Rohrer D, Valley D, Davis D, Mash D, Undale A, Smith A, Tabor D, Roche N, McLean J, Vatanian N, Robinson K, Sobin L, Barcus M, Valentino K, Qi L, Hunter S, Hariharan P, Singh S, Um K, Matose T, Tomaszewski M, Barker L, Mosavel M, Siminoff L, Traino H, Flicek P, Juettemann T, Ruffier M, Sheppard D, Taylor K, Trevanion S, Zerbino D, Craft B, Goldman M, Haeussler M, Kent W, Lee C, Paten B, Rosenbloom K, Vivian J, Zhu J. Genetic effects on gene expression across human tissues. Nature 2017, 550: 204-213. PMID: 29022597, PMCID: PMC5776756, DOI: 10.1038/nature24277.Peer-Reviewed Original ResearchConceptsGene expression levelsGenetic effectsExpression levelsGenotype-Tissue Expression (GTEx) projectLocal genetic variationMajority of genesHuman genetic traitsDisease-associated variationMolecular functionsGene regulationHuman genomeHuman tissuesExpression projectGenetic variationGenetic basisDiverse tissuesGene expressionTissue specificityGenetic traitsCellular mechanismsGenesFunctional propertiesGenomeTissueLociUnderstanding 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 targetsTranscription
2012
Mitochondrial Stress Engages E2F1 Apoptotic Signaling to Cause Deafness
Raimundo N, Song L, Shutt TE, McKay SE, Cotney J, Guan MX, Gilliland TC, Hohuan D, Santos-Sacchi J, Shadel GS. Mitochondrial Stress Engages E2F1 Apoptotic Signaling to Cause Deafness. Cell 2012, 148: 716-726. PMID: 22341444, PMCID: PMC3285425, DOI: 10.1016/j.cell.2011.12.027.Peer-Reviewed Original ResearchConceptsAltered reactive oxygen speciesReactive oxygen speciesMitochondrial ribosome functionMitochondrial disease modelTranscription factor E2F1Tissue-specific pathologyROS-dependent activationRibosome functionRRNA methylationMitochondrial stressApoptotic signalingTissue specificityMtDNA mutationsMetabolic signalingAMP kinaseMultiple tissuesMitochondrial dysfunctionOxygen speciesE2F1MethylationSignalingG cellsEnvironmental factorsApoptosisMice exhibit
2009
Diferentially expressed adenylyl cyclase isoforms mediate secretory functions in cholangiocyte subpopulation
Strazzabosco M, Fiorotto R, Melero S, Glaser S, Francis H, Spirli C, Alpini G. Diferentially expressed adenylyl cyclase isoforms mediate secretory functions in cholangiocyte subpopulation. Hepatology 2009, 50: 244-252. PMID: 19444869, PMCID: PMC2738985, DOI: 10.1002/hep.22926.Peer-Reviewed Original ResearchConceptsSoluble adenylyl cyclaseAdenylyl cyclasesGene expressionAC isoformsCyclic adenosine monophosphateAC gene expressionDifferent tissue specificitiesGroup of enzymesAdenylyl cyclase isoformsTissue specificityCholangiocyte secretionCyclase isoformsIsoformsSAC inhibitorIsohydric changesAdenylyl cyclaseIsoform expressionSACS geneReal-time polymerase chain reactionGenesAdenosine monophosphateAC8ExpressionCAMP levelsCAMP production
2008
Specific Induction of Tumor Neovasculature Death by Modified Murine PPE-1 Promoter Armed with HSV-TK
Varda-Bloom N, Hodish I, Shaish A, Greenberger S, Tal R, Feder B, Roitelman J, Breitbart E, Bangio L, Barshack I, Pfeffer R, Harats D. Specific Induction of Tumor Neovasculature Death by Modified Murine PPE-1 Promoter Armed with HSV-TK. Pathobiology 2008, 75: 346-355. PMID: 19096230, DOI: 10.1159/000164219.Peer-Reviewed Original ResearchConceptsHSV-TKSimplex virus thymidine kinaseHSV-TK geneTherapeutic genesVirus thymidine kinaseGene therapyMurine preproendothelin-1 promoterAdenoviral vectorPreproendothelin-1 promoterReporter geneTissue specificityTumor neovasculaturePromoterSpecific inductionGenesHigh expressionTumor angiogenesisMetastasis developmentExpressionNeovasculatureMouse modelKinaseSelectivityEfficiencySpecificity
2007
Differential Cell-Specific Modulation of HOXA10 by Estrogen and Specificity Protein 1 Response Elements
Martin R, Taylor MB, Krikun G, Lockwood C, Akbas GE, Taylor HS. Differential Cell-Specific Modulation of HOXA10 by Estrogen and Specificity Protein 1 Response Elements. The Journal Of Clinical Endocrinology & Metabolism 2007, 92: 1920-1926. PMID: 17311863, DOI: 10.1210/jc.2006-1694.Peer-Reviewed Original ResearchMeSH KeywordsBreastCells, CulturedElectrophoretic Mobility Shift AssayEstrogensFemaleGenes, ReporterHomeobox A10 ProteinsHomeodomain ProteinsHumansImmunohistochemistryLuciferasesPlasmidsReceptors, EstrogenResponse ElementsReverse Transcriptase Polymerase Chain ReactionSp1 Transcription FactorTransfectionUterusConceptsEstrogen response elementHOXA10 estrogen response elementResponse elementSp1 sitesShift assaysStage-specific expression patternsTissue specificityElectrophoretic mobility shift assaysCell typesSpecificity protein 1Mobility shift assaysAdult reproductive tractGel shift assaysDifferential cellular expressionDistinct differential expressionHox genesSp1 proteinCell-specific modulationTranscription factorsEmbryonic developmentRegulatory elementsExpression patternsReporter assaysBreast MCF-7 cellsDifferential expression
2005
The origin and evolution of human pathogens
Groisman EA, Casadesús J. The origin and evolution of human pathogens. Molecular Microbiology 2005, 56: 1-7. PMID: 15773974, DOI: 10.1111/j.1365-2958.2005.04564.x.Peer-Reviewed Original ResearchConceptsCreation of genesNon-host environmentsHuman pathogensRelated bacterial speciesCertain pathogensORFan genesHomologous genesCell surface modificationExpression of productsHousekeeping functionsRelated membersHost rangeColonization processTissue specificityPathogenicity islandSequence databasesCertain lociBacterial speciesGenesCell surfaceDisparate regulationGenetic originBacterial pathogensNew functionsGene variation
2003
The hedgehog pathway and developmental disorders
Bale A. The hedgehog pathway and developmental disorders. 2003, 258-272. DOI: 10.4324/9780203450420-14.Peer-Reviewed Original ResearchHedgehog signal transduction pathwaySignal transduction pathwaysDrosophila melanogasterDevelopmental biologistsN-terminal fragmentTransduction pathwaysActive N-terminal fragmentFruit flyTissue specificityAutocatalytic cleavageHuman diseasesWnt pathwayHedgehog pathwayDownstream membersPathwayHedgehogTwo-hit modelVariety of tumorsMutationsGermline mutationsAutosomal dominant disorderBirth defectsMelanogasterDominant disorderEmbryogenesis
2002
Dcas Is Required for importin-α3 Nuclear Export and Mechano-Sensory Organ Cell Fate Specification in Drosophila
Tekotte H, Berdnik D, Török T, Buszczak M, Jones LM, Cooley L, Knoblich JA, Davis I. Dcas Is Required for importin-α3 Nuclear Export and Mechano-Sensory Organ Cell Fate Specification in Drosophila. Developmental Biology 2002, 244: 396-406. PMID: 11944946, DOI: 10.1006/dbio.2002.0612.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell Nucleusalpha KaryopherinsAnimalsApoptosisCellular Apoptosis Susceptibility ProteinDNA HelicasesDrosophila melanogasterDrosophila ProteinsEmbryo, NonmammalianGene Expression Regulation, DevelopmentalIn Situ HybridizationMechanoreceptorsMorphogenesisPhylogenyRNA, MessengerSense OrgansConceptsNuclear exportEmbryonic central nervous systemNuclear protein importCell fate specificationSpecific developmental phenotypesHuman genetic disordersProtein importDrosophila orthologImportin alphaFate specificationExport receptorCell identityDevelopmental phenotypesHypomorphic alleleEmbryonic cellsVivo functionNotch pathwayTissue specificityCytoplasmic distributionEpidermal cellsDifferent tissuesCharacteristics of mutationsGenetic disordersMutationsPhenotype
2000
Candidate Taste Receptors in Drosophila
Clyne P, Warr C, Carlson J. Candidate Taste Receptors in Drosophila. Science 2000, 287: 1830-1834. PMID: 10710312, DOI: 10.1126/science.287.5459.1830.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAlternative SplicingAmino Acid SequenceAnimalsChemoreceptor CellsDrosophila melanogasterDrosophila ProteinsExonsGene ExpressionGenes, InsectIn Situ HybridizationInsect ProteinsMembrane ProteinsMolecular Sequence DataMultigene FamilyNeurons, AfferentOrgan SpecificityProtein Structure, TertiaryReceptors, Cell SurfaceReverse Transcriptase Polymerase Chain ReactionSense OrgansSequence AlignmentTasteConceptsDrosophila genome databaseTransmembrane domain proteinCandidate taste receptorsDomain proteinsDrosophila mutantsDivergent familiesGenome databaseTaste receptorsTissue specificityMolecular mechanismsDiverse familyGustatory organsGenesStructural similarityLabellumBasis of structureTaste signalingProteinTaste neuronsInitial eventFamilyExpressionDrosophilaMutantsReceptors
1998
Functional implications of the structure of the murine parvovirus, minute virus of mice
Agbandje-McKenna M, Llamas-Saiz A, Wang F, Tattersall P, Rossmann M. Functional implications of the structure of the murine parvovirus, minute virus of mice. Structure 1998, 6: 1369-1381. PMID: 9817841, DOI: 10.1016/s0969-2126(98)00137-3.Peer-Reviewed Original ResearchConceptsAmino acidsUnique N-terminal regionThree-dimensional structure determinationC-terminal regionDNA recognition siteN-terminal regionGlycine-rich sequenceMinute virusTissue tropismHost cell factorsCanine parvovirusDNA packagingIcosahedral asymmetric unitN-terminal peptideN-terminusMurine parvovirusTissue specificityStructural proteinsPolypeptide chainFivefold channelCapsid proteinViral genomeFunctional implicationsRecognition sitesVirus structure
1996
Other transgenic mutation assays: Tissue specificity of spontaneous point mutations in λsupF transgenic mice
Leach E, Narayanan L, Havre P, Gunther E, Yeasky T, Glazer P. Other transgenic mutation assays: Tissue specificity of spontaneous point mutations in λsupF transgenic mice. Environmental And Molecular Mutagenesis 1996, 28: 459-464. PMID: 8991078, DOI: 10.1002/(sici)1098-2280(1996)28:4<459::aid-em23>3.0.co;2-d.Peer-Reviewed Original Research
1990
The mouse albumin enhancer contains a negative regulatory element that interacts with a novel DNA-binding protein.
Herbst RS, Boczko EM, Darnell JE, Babiss LE. The mouse albumin enhancer contains a negative regulatory element that interacts with a novel DNA-binding protein. Molecular And Cellular Biology 1990, 10: 3896-3905. PMID: 2370857, PMCID: PMC360900, DOI: 10.1128/mcb.10.8.3896.Peer-Reviewed Original ResearchConceptsDNA-binding sitesMouse albumin enhancerNovel DNA-binding proteinAlbumin enhancerNegative regulatory domainDNA-binding proteinsNegative regulatory regionDNA-binding activityNegative regulatory elementPositive-acting elementsOrientation-independent fashionRegulatory domainRegulatory regionsAlbumin gene transcriptionGene transcriptionRegulatory elementsEnhancer functionNew proteinsCap siteTissue specificityAlbumin geneCell typesProteinNonhepatic cellsEnhancerThe Mouse Albumin Enhancer Contains a Negative Regulatory Element That Interacts with a Novel DNA-Binding Protein
Herbst R, Boczko E, Darnell J, Babiss L. The Mouse Albumin Enhancer Contains a Negative Regulatory Element That Interacts with a Novel DNA-Binding Protein. Molecular And Cellular Biology 1990, 10: 3896-3905. DOI: 10.1128/mcb.10.8.3896-3905.1990.Peer-Reviewed Original ResearchDNA-binding sitesMouse albumin enhancerNovel DNA binding proteinAlbumin enhancerNegative regulatory domainDNA binding proteinNegative regulatory regionDNA-binding activityNegative regulatory elementPositive-acting elementsOrientation-independent fashionRegulatory domainRegulatory regionsAlbumin gene transcriptionGene transcriptionRegulatory elementsEnhancer functionNew proteinsCap siteTissue specificityAlbumin geneCell typesProteinNonhepatic cellsEnhancer
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