2023
Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq
Patel S, Sexton A, Strine M, Wilen C, Simon M, Pyle A. Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nature Communications 2023, 14: 3426. PMID: 37296103, PMCID: PMC10255950, DOI: 10.1038/s41467-023-38623-1.Peer-Reviewed Original Research
2018
Carbodiimide reagents for the chemical probing of RNA structure in cells
Wang PY, Sexton AN, Culligan WJ, Simon MD. Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA 2018, 25: 135-146. PMID: 30389828, PMCID: PMC6298570, DOI: 10.1261/rna.067561.118.Peer-Reviewed Original ResearchConceptsConformation of RNAU nucleotidesIntact cellsChemical probesDimethyl sulfateNucleotides of RNASingle-stranded nucleotidesXist lncRNACellular contextNoncoding RNAsRNA elementsSHAPE reagentsAccessible nucleotidesRNA conformationRNA structureBiological contextChemical probingWatson-Crick faceCellular environmentFunctional roleCarbodiimide reagentRNA nucleotidesRNANucleotidesStructured regions
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