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
2019
Differential regulation of OCT4 targets facilitates reacquisition of pluripotency
Thakurela S, Sindhu C, Yurkovsky E, Riemenschneider C, Smith ZD, Nachman I, Meissner A. Differential regulation of OCT4 targets facilitates reacquisition of pluripotency. Nature Communications 2019, 10: 4444. PMID: 31570708, PMCID: PMC6768871, DOI: 10.1038/s41467-019-11741-5.Peer-Reviewed Original ResearchConceptsEctopic transcription factorsReacquisition of pluripotencySomatic cell reprogrammingCis-regulatory elementsTranscription factor expressionExact molecular mechanismsOCT4 targetsPluripotent stem cellsPluripotency inductionCell reprogrammingTranscription factorsSomatic cellsMolecular mechanismsDifferential regulationPluripotencyStem cellsVivo differentiationPrimary targetCellsFactor expressionFinal stepExperimental systemReprogrammingTargetDifferentiation
2016
Molecular features of cellular reprogramming and development
Smith ZD, Sindhu C, Meissner A. Molecular features of cellular reprogramming and development. Nature Reviews Molecular Cell Biology 2016, 17: 139-154. PMID: 26883001, DOI: 10.1038/nrm.2016.6.Peer-Reviewed Original ResearchConceptsKrüppel-like factor 4Pluripotent stateSRY-box 2Somatic cellsDirect reprogrammingInduced pluripotent stem cell generationDifferentiated cellsPluripotent stem cell generationCis-regulatory elementsStem cell generationAdditional molecular featuresMolecular featuresPluripotent stem cellsChromatin remodellersBivalent chromatinEpigenetic barriersDevelopmental genesCellular identityCellular reprogrammingGenetic modulesEpigenetic regulationCompact chromatinTranscriptional inductionEpigenetic repressorEpigenetic modifiers
2015
Epigenetic predisposition to reprogramming fates in somatic cells
Pour M, Pilzer I, Rosner R, Smith ZD, Meissner A, Nachman I. Epigenetic predisposition to reprogramming fates in somatic cells. EMBO Reports 2015, 16: 370-378. PMID: 25600117, PMCID: PMC4364876, DOI: 10.15252/embr.201439264.Peer-Reviewed Original ResearchConceptsSomatic cellsFactor inductionLive-cell imagingPluripotent stem cellsEpigenetic stateCell identitySuccessful reprogrammingEpigenetic heterogeneityDaughter cellsSister cellsCell lineagesCellular responsesLineagesEZH2 inhibitorsLow-efficiency processColony formationStem cellsEpigenetic predispositionReprogramPopulation levelCellsNovel statistical approachSomatic populationInductionFate
2012
A unique regulatory phase of DNA methylation in the early mammalian embryo
Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 2012, 484: 339-344. PMID: 22456710, PMCID: PMC3331945, DOI: 10.1038/nature10960.Peer-Reviewed Original ResearchConceptsDNA methylationGenome-scale DNA methylation mapsLong terminal repeat (LTR) retroelementsDNA methylation mapsBase-resolution mapsEarly mammalian embryoCpG island promotersBlastocyst stageMammalian embryogenesisMethylation mapsPaternal genomeMammalian embryosEpigenetic modificationsEarly embryosSomatic cellsGlobal hypomethylationSomatic patternMouse gametesElement 1MethylationEmbryosMethylation valuesRegulatory phaseGametesZygotes
2011
Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling
Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling. Cell Stem Cell 2011, 8: 96-105. PMID: 21211784, PMCID: PMC3220622, DOI: 10.1016/j.stem.2010.12.001.Peer-Reviewed Original ResearchConceptsPluripotent stem cell stateEuchromatic histone modificationsRepressive H3K27me3 modificationGenome-wide changesStem cell stateChromatin remodelingH3K4 methylationHistone modificationsH3K27me3 modificationEpigenetic responsesTranscriptional changesSomatic cellsRegulatory eventsGene promoterEpigenetic changesCell statesCorresponding lociSomatic identityMechanistic questionsFactor inductionEarly eventsLociH3K4me2ReprogrammingRapid progress