2024
Autonomous transposons tune their sequences to ensure somatic suppression
Ilık İ, Glažar P, Tse K, Brändl B, Meierhofer D, Müller F, Smith Z, Aktaş T. Autonomous transposons tune their sequences to ensure somatic suppression. Nature 2024, 626: 1116-1124. PMID: 38355802, PMCID: PMC10901741, DOI: 10.1038/s41586-024-07081-0.Peer-Reviewed Original ResearchConceptsTransposable elementsSAFB proteinsPiwi-interacting RNA pathwayRNA-basedIntronic transposed elementsRNA processing signalsPre-mRNA processingIntronic spaceNested genesPostmeiotic spermatidsAutonomous transposonsDNA transposonsRNA pathwaysCassette exonsSplicing codeSplicing eventsGenome integrityTE exonizationHuman genesL1 elementsRNA synthesisHost genesTissue-specificSAFBSomatic cells
2021
Smart-RRBS for single-cell methylome and transcriptome analysis
Gu H, Raman AT, Wang X, Gaiti F, Chaligne R, Mohammad AW, Arczewska A, Smith ZD, Landau DA, Aryee MJ, Meissner A, Gnirke A. Smart-RRBS for single-cell methylome and transcriptome analysis. Nature Protocols 2021, 16: 4004-4030. PMID: 34244697, PMCID: PMC8672372, DOI: 10.1038/s41596-021-00571-9.Peer-Reviewed Original ResearchConceptsSingle cellsProtein-coding genesSingle-cell methylomesSame single cellMulti-omics approachRare cell populationsSmart-seq2Transcriptional statesDNA methylomeTranscriptome analysisImportant mechanistic insightsEpigenetic modificationsDNA methylationDissected tissue samplesGenomic DNAHundreds of cellsCellular heterogeneityFlow sortingRegulatory consequencesMethylomeEpigenetic promoterMechanistic insightsCell populationsCellsTypical single cell
2019
Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression
Tsankov AM, Wadsworth MH, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A. Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. Development 2019, 146: dev174722. PMID: 31515224, PMCID: PMC6803377, DOI: 10.1242/dev.174722.Peer-Reviewed Original ResearchMeSH KeywordsCell CycleCell DifferentiationDNA (Cytosine-5-)-Methyltransferase 1DNA (Cytosine-5-)-MethyltransferasesDNA MethylationDNA Methyltransferase 3AEnhancer Elements, GeneticEntropyGene Expression Regulation, DevelopmentalHuman Embryonic Stem CellsHumansMaleRepressor ProteinsRNA, MessengerTranscription, GeneticConceptsGlobal methylation levelsTranscriptional repressionSingle-cell RNA-sequencing dataMethylation levelsNew cell fatesMaintenance of pluripotencyHuman embryonic stem cellsMethylation of cytosineRNA-sequencing dataCell-cell variabilityStem cellsEmbryonic stem cellsHuman pluripotent stem cellsDNA methyltransferase activityMRNA expression dataPluripotent stem cellsTranscriptional variabilityMethyltransferases Dnmt3aCell fateEpigenetic regulatorsMethyltransferase DNMT3AExtrinsic signalsHigh-resolution viewMethyltransferase activityProper differentiation
2010
Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA
Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ. Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA. Cell Stem Cell 2010, 7: 618-630. PMID: 20888316, PMCID: PMC3656821, DOI: 10.1016/j.stem.2010.08.012.Peer-Reviewed Original ResearchMeSH KeywordsCell DifferentiationCell LineageCells, CulturedCellular ReprogrammingHumansInduced Pluripotent Stem CellsRNA, MessengerConceptsInduced pluripotent stem cellsPluripotent stem cellsCell fateMultiple human cell typesSomatic cell reprogrammingCell typesUseful cell typesStem cellsHuman cell typesPatient-specific induced pluripotent stem cellsCell reprogrammingCellular reprogrammingInnate antiviral responseDirected DifferentiationIPSC derivationHuman cellsMyogenic cellsSynthetic mRNAAntiviral responseDisease modelingReprogrammingModified mRNARegenerative medicineFateMRNA