Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches

Transcription and genome architecture are interdependent, but it is still unclear how nucleosomes in the chromatin fiber interact with nascent RNA, and which is the relative nuclear distribution of these RNAs and elongating RNA polymerase II (RNAP II). Using super-resolution (SR) microscopy, we visualized the nascent transcriptome, in both nucleoplasm and nucleolus, with nanoscale resolution. We found that nascent RNAs organize in structures we termed RNA nanodomains, whose characteristics are independent of the number of transcripts produced over time. Dual-color SR imaging of nascent RNAs, together with elongating RNAP II and H2B, shows the physical relation between nucleosome clutches, RNAP II, and RNA nanodomains. The distance between nucleosome clutches and RNA nanodomains is larger than the distance measured between elongating RNAP II and RNA nanodomains. Elongating RNAP II stands between nascent RNAs and the small, transcriptionally active, nucleosome clutches. Moreover, RNA factories are small and largely formed by few RNAP II. Finally, we describe a novel approach to quantify the transcriptional activity at an individual gene locus. By measuring local nascent RNA accumulation upon transcriptional activation at single alleles, we confirm the measurements made at the global nuclear level.Innovative Team Program of Guangzhou Regenerative Medicine and Health Guangdong Laboratory [2018GZR110103001 to M.P.C.]; Guangzhou Key Projects of Brain Science and Brain-Like Intelligence Technology [20200730009 to M.P.C.]; National Natural Science Foundation of China [31971177 to M.P.C.]; Science and Technology Program of Guangzhou, China [202002030146 to M.P.C.]; European Union's Horizon 2020 Research and Innovation Programme [CellViewer No. 686637 to M.P.C. and M.L.]; Ministerio de Ciencia e Innovación [BFU2017-86760-P (AEI/FEDER, UE) to M.P.C.]; AGAUR grant from Secretaria d’Universitats i Recerca del Departament d’Empresa I Coneixement de la Generalitat de Catalunya [2017 SGR 689 to M.P.C.]; Centro de Excelencia Severo Ochoa [2013–2017 to M.P.C.]; CERCA Programme/Generalitat de Catalunya [to M.P.C.]; People Program (Marie Curie Actions) FP7/2007–2013 under REA grant [608959 to M.V.N.]; Spanish Ministry of Science and Innovation to the European Molecular Biology Laboratory (EMBL) partnership [to M.P.C.]; Juan de la Cierva-Incorporación 2017 [to M.V.N.]. Funding for open access charge: National Natural Science Foundation of China (NSFC) grant [31971177 to M.P.C]