RNA promotes the formation of spatial compartments in the nucleus

Abstract

The nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D structures. To address this, we developed RNA & DNA SPRITE (RD-SPRITE) to comprehensively map the location of all RNAs relative to DNA and other RNAs. Using this approach, we identify many RNAs that are localized near their transcriptional loci (RNA-DNA) together with other diffusible ncRNAs (RNA-RNA) within higher-order DNA structures (DNA-DNA). These RNA-chromatin compartments span three major classes of nuclear functions: RNA processing (including ribosome biogenesis, mRNA splicing, snRNA biogenesis, and histone mRNA processing), heterochromatin assembly, and gene regulation. More generally, we identify hundreds of ncRNAs that form stable nuclear compartments in spatial proximity to their transcriptional loci. We find that dozens of nuclear compartments require RNA to guide protein regulators into these 3D structures, and focusing on several ncRNAs, we show that these ncRNAs specifically regulate heterochromatin assembly and the expression of genes contained within these compartments. Together, our results demonstrate a unique mechanism by which RNA acts to shape nuclear structure by forming high concentration territories immediately upon transcription, binding to diffusible regulators, and guiding them into spatial compartments to regulate a wide range of essential nuclear functions.

MeCP2: The Genetic Driver of Rett Syndrome Epigenetics

“…Further research of their interactions with MeCP2 are integral to understanding how they may relate to RTT. Of note, RNA has been shown to promote the formation of spatial compartments in the nucleus ( Quinodoz et al, 2020 ), and might assist MeCP2 in its formation of heterochromatin condensates ( Sheikh et al, 2016 ; Li et al, 2020 ).…”

Compartmap enables inference of higher-order chromatin structure in individual cells from scRNA-seq and scATAC-seq

“…Recently, Quinodoz et al demonstrated this with a proximity-ligation independent technique (RD-SPRITE) that readily captures and characterizes RNA and DNA interactions within the context of chromatin domains 27,[81][82][83][84][85] . An intriguing finding is that noncoding RNA species (ncRNA) tend to spatially localize to their own sites of transcription, likely to modulate transcription through physical means 27 . One example of lncRNA-mediated spatial control of DNA and multi-locus gene expression regulation is the RNA-DNA interaction of Xist in X-chromosome inactivation of embryonic stem cells 27 .…”

“…Yet others, such as the massive Mediator and Integrator complexes, span both roles [12][13][14][15][16][17][18][19][20] . Recent work in developmental and cancer biology has revealed that alterations in structural complexes can impact transcription in ways unrelated to genome integrity, causing developmental abnormalities and premalignant conditions [21][22][23][24][25][26][27][28][29][30][31] . In otherwise healthy organisms, viral transcriptional read-through can remodel the physical arrangement of surrounding DNA.…”

Understanding and Engineering Chromatin as a Dynamical System across Length and Timescales

“…Although 3C-based methods are widely used to probe 3D genome organization, the proximity ligation step required in 3C-derivatives may miss important interactions that do not occur close enough for molecules to proximity ligate to one another (Beagrie et al, 2017;Quinodoz et al, 2018Quinodoz et al, , 2020. Thus, nonproximity methods may enable mapping of structures beyond this limit.…”

“…Specifically, SPRITE crosslinks RNA and DNA within the nucleus together, fragments it, then uses a ''split-pool tagging'' process to uniquely barcode each crosslinked fragment. This split-pool barcoding approach allows both RNA and DNA to be directly read, enabling the simultaneous identification of DNA-DNA, RNA-DNA, and RNA-RNA interactions (Quinodoz et al, 2018(Quinodoz et al, , 2020. Average 3D chromatin structures are similarly recapitulated by Hi-C, GAM, and SPRITE methods (Fiorillo et al, 2020).…”