Featured Publications
STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts
Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD. STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Molecular Cell 2021, 81: 4398-4412.e7. PMID: 34520723, PMCID: PMC9020433, DOI: 10.1016/j.molcel.2021.08.019.Peer-Reviewed Original ResearchConceptsPause releaseRNA polymerase II transcriptsRNA polymerase II moleculesCis-acting DNA elementsTATA box-containing promotersPolymerase II transcriptsPromoter-proximal pausingCritical regulatory functionsTranscriptional regulationRNA turnoverTranscriptional controlDNA elementsTranscriptional shutdownPause sitesHyperosmotic stressRegulatory mechanismsRegulatory functionsPrinciples of regulationHormonal stimuliPausingPremature terminationTranscriptsRegulation
2015
Probing Xist RNA Structure in Cells Using Targeted Structure-Seq
Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. PLOS Genetics 2015, 11: e1005668. PMID: 26646615, PMCID: PMC4672913, DOI: 10.1371/journal.pgen.1005668.Peer-Reviewed Original ResearchConceptsStructure-seqRNA structureRNA conformationNon-coding RNA XISTLong non-coding RNA XISTX-chromosome inactivationSecondary structure mappingRNA of interestXist lncRNAMolecular evolutionC-repeatLncRNA functionsHigher-order structureXist functionRNA functionMammalian cellsMaster regulatorXISTSequencing readsChemical probingParallel sequencingTarget RNARNA XISTRNA basesRNA