2023
linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells
Tornini V, Miao L, Lee H, Gerson T, Dube S, Schmidt V, Kroll F, Tang Y, Du K, Kuchroo M, Vejnar C, Bazzini A, Krishnaswamy S, Rihel J, Giraldez A. linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. ELife 2023, 12: e82249. PMID: 37191016, PMCID: PMC10188112, DOI: 10.7554/elife.82249.Peer-Reviewed Original ResearchConceptsCell typesIntergenic non-coding RNAsChromatin architectural proteinCryptic open reading frameGene regulatory networksOpen reading frameNon-coding RNAsNew cell typesNeural cell typesBrain cell typesPutative lincRNAsVertebrate genomesArchitectural proteinsChromatin disruptionChromatin accessibilityRegulatory networksGenetic basisCell developmentMicropeptidesBrain cell developmentReceptor-mediated pathwaySystematic identificationLincRNAsNeural cellsCerebellar cells
2022
Systematic identification of biomarker-driven drug combinations to overcome resistance
Rees M, Brenan L, do Carmo M, Duggan P, Bajrami B, Arciprete M, Boghossian A, Vaimberg E, Ferrara S, Lewis T, Rosenberg D, Sangpo T, Roth J, Kaushik V, Piccioni F, Doench J, Root D, Johannessen C. Systematic identification of biomarker-driven drug combinations to overcome resistance. Nature Chemical Biology 2022, 18: 615-624. PMID: 35332332, DOI: 10.1038/s41589-022-00996-7.Peer-Reviewed Original ResearchConceptsSmall molecule responsesCell linesGSK-J4Gene expression featuresMonoacylglycerol lipaseGene knockoutSerine hydrolaseCancer cell linesSystematic identificationCell viability profileInsensitive cell linesNovel relationshipSmall moleculesMechanism of actionEnzymatic modificationSpecific mechanismsViability profileIntrinsic resistanceVariable responseMechanistic studiesRational candidatesMechanism
2018
High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development
Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Reports 2018, 23: 1581-1597. PMID: 29719267, PMCID: PMC5965702, DOI: 10.1016/j.celrep.2018.03.129.Peer-Reviewed Original ResearchConceptsRegulatory sequencesEmbryonic developmentEmbryonic craniofacial developmentEmbryonic craniofacial tissueGene regulatory programsNormal facial variationHuman embryonic developmentCraniofacial abnormalitiesEpigenomic annotationsEpigenomic atlasCraniofacial developmentIntronic sequencesCraniofacial tissuesRegulatory programsCraniofacial researchersMultiple tissuesCell typesSignificant enrichmentSystematic identificationCommon variantsCausal regionOrofacial cleftingEmbryonic periodSequenceCraniofacial complex
2014
A Functional Screen Identifies miRs That Induce Radioresistance in Glioblastomas
Moskwa P, Zinn PO, Choi YE, Shukla SA, Fendler W, Chen CC, Lu J, Golub TR, Hjelmeland A, Chowdhury D. A Functional Screen Identifies miRs That Induce Radioresistance in Glioblastomas. Molecular Cancer Research 2014, 12: 1767-1778. PMID: 25256711, PMCID: PMC4386891, DOI: 10.1158/1541-7786.mcr-14-0268.Peer-Reviewed Original ResearchConceptsCell cycle checkpoint responsesFunctional screen identifiesTGFβ receptor inhibitorUnbiased functional screenCheckpoint responseScreen identifiesCancer Genome AtlasFunctional screenGlioblastoma patient specimensMolecular networksGlioblastoma datasetGlioblastoma cellsGenome AtlasSystematic identificationGlioblastoma radioresistanceTherapeutic resistanceMiR125aRadioresistanceTGFβNew roleTGFβ inhibitorsTherapeutic applicationsGlioblastomaMIR1MiR150
2004
Integrative Analysis of the Mitochondrial Proteome in Yeast
Prokisch H, Scharfe C, Camp DG, Xiao W, David L, Andreoli C, Monroe ME, Moore RJ, Gritsenko MA, Kozany C, Hixson KK, Mottaz HM, Zischka H, Ueffing M, Herman ZS, Davis RW, Meitinger T, Oefner PJ, Smith RD, Steinmetz LM. Integrative Analysis of the Mitochondrial Proteome in Yeast. PLOS Biology 2004, 2: e160. PMID: 15208715, PMCID: PMC423137, DOI: 10.1371/journal.pbio.0020160.Peer-Reviewed Original ResearchConceptsMitochondrial proteomeGenomic approachesPhenotype screeningGenome-wide approachesSubcellular localization studiesComplex mitochondrial disordersDifferent genomic approachesProtein interaction analysisYeast mitochondriaMitochondrial proteinsMitochondrial organellesProteomic approachProteome studiesAbundant proteinsExpression analysisCandidate genesExpression profilingIntegrative analysisMitochondrial functionLocalization studiesOrganellesMitochondrial disordersProteinSystematic identificationMass spectrometry
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