2022
Functional elements of the cis-regulatory lincRNA-p21
Winkler L, Jimenez M, Zimmer JT, Williams A, Simon MD, Dimitrova N. Functional elements of the cis-regulatory lincRNA-p21. Cell Reports 2022, 39: 110687. PMID: 35443176, PMCID: PMC9118141, DOI: 10.1016/j.celrep.2022.110687.Peer-Reviewed Original ResearchConceptsGene expression controlFull-length transcriptionDNA regulatory elementsCell cycle genesCDKN1A/p21P53-dependent expressionFunctional elementsChromatin organizationLncRNA lociNascent transcriptionRegulatory lociExpression controlCycle genesLncRNA transcriptsRegulatory elementsMolecular mechanismsTranscriptionExon 1LincRNA-p21LociP21 expressionGenetic modelsAccumulationExpressionSplicing
2021
Noncoding RNAs: biology and applications—a Keystone Symposia report
Cable J, Heard E, Hirose T, Prasanth KV, Chen L, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen C, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications—a Keystone Symposia report. Annals Of The New York Academy Of Sciences 2021, 1506: 118-141. PMID: 34791665, PMCID: PMC9808899, DOI: 10.1111/nyas.14713.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsKeystone Symposia reportPotential drug targetsRNA biologyHuman transcriptomeEpigenetic modificationsKeystone eSymposiumNoncoding RNAsCell signalingBasic biologyDrug targetsRNABiologyDisease mechanismsNucleotidesSpeciesTranscriptomeImportant roleRNAsTranscriptionSymposium reportSignalingTranslationRoleTarget
2020
Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor
Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chemical Biology 2020, 28: 463-474.e7. PMID: 33357462, PMCID: PMC8052284, DOI: 10.1016/j.chembiol.2020.12.003.Peer-Reviewed Original ResearchConceptsRNA decayEnzyme DCP2P-bodiesDCP2Genetic approachesRNA substratesBicyclic peptide inhibitorsHuman RNAExpression changesCellular substratesPhage display selectionSelective chemical inhibitorsChemical inhibitorsHuman cellsGenetic ablationBicyclic peptide ligandsPeptide inhibitorCP21Display selectionPeptide ligandsHigh affinityRegulomeTranscriptionInhibitorsPowerful tool
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
2014
The Properties of Long Noncoding RNAs that Regulate Chromatin
Rutenberg-Schoenberg M, Sexton A, Simon M. The Properties of Long Noncoding RNAs that Regulate Chromatin. Annual Review Of Genomics And Human Genetics 2014, 17: 1-26. DOI: 10.1146/annurev-genom-090314-024939.Peer-Reviewed Original ResearchChromatin-based processesLong noncoding RNAMechanisms of lncRNAsChromatin biologyChromatin structureLncRNA functionsNuclear roleHuman lncRNAsPosttranscriptional regulationNoncoding RNAsRNA moleculesGene expressionFinal online publication dateBiochemical mechanismsBroader roleRNAUpstream roleLncRNAsOnline publication dateHuman physiologyChromatinGenomicsTranscriptionBiologyMechanism