Caroline Hoppe, PhD
Postdoctoral FellowAbout
Research
Publications
2021
Scalable inference of transcriptional kinetic parameters from MS2 time series data
Bowles J, Hoppe C, Ashe H, Rattray M. Scalable inference of transcriptional kinetic parameters from MS2 time series data. Bioinformatics 2021, 38: 1030-1036. PMID: 34788793, PMCID: PMC8796374, DOI: 10.1093/bioinformatics/btab765.Peer-Reviewed Original ResearchLive and fixed imaging of translation sites at single mRNA resolution in the Drosophila embryo
Vinter D, Hoppe C, Ashe H. Live and fixed imaging of translation sites at single mRNA resolution in the Drosophila embryo. STAR Protocols 2021, 2: 100812. PMID: 34585149, PMCID: PMC8450298, DOI: 10.1016/j.xpro.2021.100812.Peer-Reviewed Original ResearchDynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo
Vinter DJ, Hoppe C, Minchington TG, Sutcliffe C, Ashe HL. Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. Development 2021, 148: dev196121. PMID: 33722899, PMCID: PMC8077512, DOI: 10.1242/dev.196121.Peer-Reviewed Original ResearchConceptsSingle mRNA resolutionDrosophila embryosHb mRNAMRNA translationAnterior-posterior patterningLive embryosSingle-molecule imagingTissue culture cellsTranslational repressionDevelopmental patterningSpatiotemporal regulationTranslational regulationExpression domainsSunTag systemTranscription factorsExpression boundariesTranslation dynamicsEmbryosCulture cellsMRNARepressionRegulationPatterningDrosophilaTranslationLive imaging and quantitation of nascent transcription using the MS2/MCP system in the Drosophila embryo
Hoppe C, Ashe HL. Live imaging and quantitation of nascent transcription using the MS2/MCP system in the Drosophila embryo. STAR Protocols 2021, 2: 100379. PMID: 33778778, PMCID: PMC7982776, DOI: 10.1016/j.xpro.2021.100379.Peer-Reviewed Original ResearchCRISPR-Cas9 strategies to insert MS2 stem-loops into endogenous loci in Drosophila embryos
Hoppe C, Ashe HL. CRISPR-Cas9 strategies to insert MS2 stem-loops into endogenous loci in Drosophila embryos. STAR Protocols 2021, 2: 100380. PMID: 33786461, PMCID: PMC7988240, DOI: 10.1016/j.xpro.2021.100380.Peer-Reviewed Original Research
2020
Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo
Hoppe C, Bowles JR, Minchington TG, Sutcliffe C, Upadhyai P, Rattray M, Ashe HL. Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo. Developmental Cell 2020, 54: 727-741.e7. PMID: 32758422, PMCID: PMC7527239, DOI: 10.1016/j.devcel.2020.07.007.Peer-Reviewed Original ResearchConceptsDrosophila embryosCell fate decisionsMorphogen gradient interpretationTarget gene transcriptsSingle-cell resolutionBMP gradientMRNA outputAxis patterningCell fateExpression domainsTranscriptional responsePromoter sequencesGene transcriptsProtein gradientGradient interpretationBurst kineticsBMPEmbryosEnhancerClassic exampleCellsActivation rateMorphogensTranscriptsGeneral features
2016
The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non‐coding RNA and synonymous mutations
Diederichs S, Bartsch L, Berkmann JC, Fröse K, Heitmann J, Hoppe C, Iggena D, Jazmati D, Karschnia P, Linsenmeier M, Maulhardt T, Möhrmann L, Morstein J, Paffenholz SV, Röpenack P, Rückert T, Sandig L, Schell M, Steinmann A, Voss G, Wasmuth J, Weinberger ME, Wullenkord R. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non‐coding RNA and synonymous mutations. EMBO Molecular Medicine 2016, 8: 442-457. PMID: 26992833, PMCID: PMC5126213, DOI: 10.15252/emmm.201506055.Peer-Reviewed Original ResearchConceptsCancer genomesSynonymous mutationsProtein-coding sequencesNon-coding sequencesNon-coding RNANon-coding RNAsDeep sequencing studiesTumor suppressor geneTP53/p53Gene regulationSplicing patternsRegulatory elementsProtein sequencesMRNA stabilityGenetic elementsGenomeUntranslated regionSequencing studiesSplice siteSplice site mutationSuppressor geneOncogene activationFunctional studiesSite mutationNovel mechanism
2013
The NHR-8 Nuclear Receptor Regulates Cholesterol and Bile Acid Homeostasis in C. elegans
Magner DB, Wollam J, Shen Y, Hoppe C, Li D, Latza C, Rottiers V, Hutter H, Antebi A. The NHR-8 Nuclear Receptor Regulates Cholesterol and Bile Acid Homeostasis in C. elegans. Cell Metabolism 2013, 18: 212-224. PMID: 23931753, PMCID: PMC3909615, DOI: 10.1016/j.cmet.2013.07.007.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsApolipoproteinsBile Acids and SaltsBiological TransportCaenorhabditis elegansCaenorhabditis elegans ProteinsCholestenesCholesterolFatty AcidsFertilityForkhead Transcription FactorsGene Expression RegulationHomeostasisLipid MetabolismLongevityMolecular Sequence DataOxygenasesReceptors, Cytoplasmic and NuclearSequence AlignmentSignal TransductionTranscription FactorsConceptsNuclear receptorsDAF-16/FOXOFatty acid desaturationCholesterol balanceDauer stageNHR-8Dafachronic acidTranscriptional regulatorsDevelopmental arrestNuclear receptor controlLiver XAcid homeostasisAcid metabolismUnregulated growthVitamin D receptorCholesterol availabilityReceptor controlEndocrine networkHomeostasisLife spanReproductionMetabolismBile acid homeostasisApolipoprotein productionImportant insights