Featured Publications
Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin
Machyna M, Kiefer L, Simon MD. Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nature Structural & Molecular Biology 2020, 27: 297-304. PMID: 32157249, DOI: 10.1038/s41594-020-0390-z.Peer-Reviewed Original ResearchConceptsHybridization capture approachGenome-wide changesLong non-coding RNAsUnfolded protein responseNon-coding RNAsStrand exchange reactionLncRNA localizationIndividual RNAsRNA captureUncharacterized changesX chromosomeProtein responseHeat shockChromatinLncRNAsRNACapture approachBinding sitesNucleic acidsNucleotide chemistryRoX2AutosomesChromosomesRelocalizationSpecies
2019
Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice
Canzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL, Duffy EE, Duffié R, Monahan K, O'Keeffe S, Simon MD, Lomvardas S, Maniatis T. Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice. Cell 2019, 177: 639-653.e15. PMID: 30955885, PMCID: PMC6823843, DOI: 10.1016/j.cell.2019.03.008.Peer-Reviewed Original ResearchConceptsDNA demethylationAntisense promoterPromoter choiceHS5-1 enhancerCTCF binding siteNeural circuit assemblyMouse olfactory neuronsPcdhα genesDemethylation functionLncRNA transcriptionSense promoterAntisense transcriptionProtocadherin (Pcdh) αTET3 overexpressionTranscriptional statesAlternate genesPromoter DNAGene choiceDistal enhancerFirst exonPromoterTranscriptionΓ geneGenesOlfactory neurons
2011
The genomic binding sites of a noncoding RNA
Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. The genomic binding sites of a noncoding RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20497-20502. PMID: 22143764, PMCID: PMC3251105, DOI: 10.1073/pnas.1113536108.Peer-Reviewed Original ResearchConceptsDosage compensationCross-linked chromatin extractsMale-specific lethal (MSL) complexLevel of chromatinSpecific genomic sitesImportant regulatory roleHybridization-based techniquesLethal complexLncRNAs bindWide mappingSites of proteinsGenomic sitesChromatin extractsGenomic targetsEndogenous RNAEndogenous lncRNARNA targetsProtein targetsRegulatory roleHybridization analysisRoX2RNAChromatinProteinBinds