RNA as a fundamental component of interphase chromosomes: could repeats prove key?

Hall, Lisa L.; Lawrence, Jeanne B.

doi:10.1016/j.gde.2016.04.005

Cited by 32 publications

(33 citation statements)

References 82 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some are highly abundant long non-coding RNAs (lncRNA) such as NEAT1 or MALAT1 or other diverse lncRNAs including FIRRE, HOTAIR, XIST etc. In contrast to these defined lncRNAs other studies [14,15] have suggested that a large proportion of nuclear RNAs hybridise to a C0t-1 probe, indicating that they are enriched in transcripts derived from a repetitive fraction of the genome. They also showed that these RNAs are quite stable and are turned over relatively slowly.…”

Section: Hnrnasmentioning

confidence: 90%

“…In contrast to defined lncRNAs, it has been shown that repetitive non-coding RNA species, labelled using C0t-1 DNA as a probe, do not migrate far from their site of synthesis [14,33]. To us this suggests that many RNAs produced in the nucleus, unless they are proactively transported, will stay in the vicinity of the site of transcription, it was then suggested that once structural RNAs are embedded with chromatin/scaffold proteins they might become very stable [15]. Few studies have looked at the fate of spliced out introns, although the Lawrence group reported that spliced out introns drift into the nucleoplasm over time [14].…”

Section: Rna Mobilitymentioning

confidence: 99%

“…Our experiments so far have suggested that the SAF-A/RNA mesh does not directly bind to chromatin but inhibits chromatin fibre-fibre interactions, modulating interphase chromatin structure. Hall et al likened the physical presence of the RNA to 'water' than can keep the chromatin/scaffold 'sponge' from shrinking (compacting) [15]. In Drosophila the abundant Df31 protein was identified as interacting with snoRNAs to regulate chromatin structure [38].…”

Section: Rna/protein Nuclear Meshmentioning

confidence: 99%

See 2 more Smart Citations

RNA: Nuclear Glue for Folding the Genome

Nozawa

Gilbert

2019

Trends in Cell Biology

View full text Add to dashboard Cite

A significant amount of RNA is present in the nucleus of mammalian cells but only a small proportion of it is destined for the cytoplasm and subsequent translation, leaving much RNA to associate with chromatin. Historically nuclear RNA was thought to interact with proteins to form a filamentous nuclear matrix, but this idea became less popular as more dynamic models of chromatin behavior became more prevalent. Using new molecular and imaging approaches it is becoming clear that RNA should be considered as an integral component of nuclear organisation; it is transcriptionally responsive and interacts with abundant nuclear RNA binding proteins. We suggest that these protein/RNA structures form a dynamic nuclear mesh that can regulate interphase chromatin structure.

show abstract

Section: Hnrnasmentioning

confidence: 90%

Section: Rna Mobilitymentioning

confidence: 99%

Section: Rna/protein Nuclear Meshmentioning

confidence: 99%

See 1 more Smart Citation

RNA: Nuclear Glue for Folding the Genome

Nozawa

Gilbert

2019

Trends in Cell Biology

View full text Add to dashboard Cite

show abstract

“…Nuclear RNA has long been proposed to play a central role in shaping nuclear structure [13][14][15][16][17][18] . Initial experiments performed more than 30 years ago found that global disruption of RNA (using RNase) leads to large scale morphological deficits in the nucleus 13 .…”

Section: Introductionmentioning

confidence: 99%

RNA promotes the formation of spatial compartments in the nucleus

Quinodoz

Bhat

Ollikainen

et al. 2020

Preprint

View full text Add to dashboard Cite

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.

show abstract

“…Finally, we note that SAF-A and other nuclear matrix proteins, including many reported to associate with XIST RNA, are not restricted to the Xi, but are distributed widely over chromatin. Thus, it is plausible that this repertoire of scaffolding proteins could interact with other nuclear non-coding RNAs to modify chromatin architecture throughout the genome [ 59 , 60 ]. This perspective, together with our interest in ‘junk’ of the genome, led us to explore the possibility that XIST RNA exemplifies a broader paradigm for non-coding RNA function in nuclear organization.…”

Section: Xist Rna and The Debated Concept Of A Complex Non-cmentioning

confidence: 99%

XISTRNA: a window into the broader role of RNA in nuclear chromosome architecture

Creamer¹,

Lawrence²

2017

Phil. Trans. R. Soc. B

View full text Add to dashboard Cite

XIST RNA triggers the transformation of an active X chromosome into a condensed, inactive Barr body and therefore provides a unique window into transitions of higher-order chromosome architecture. Despite recent progress, how XIST RNA localizes and interacts with the X chromosome remains poorly understood. Genetic engineering of XIST into a trisomic autosome demonstrates remarkable capacity of XIST RNA to localize and comprehensively silence that autosome. Thus, XIST does not require X chromosome-specific sequences but operates on mechanisms available genome-wide. Prior results suggested XIST localization is controlled by attachment to the insoluble nuclear scaffold. Our recent work affirms that scaffold attachment factor A (SAF-A) is involved in anchoring XIST, but argues against the view that SAF-A provides a unimolecular bridge between RNA and the chromosome. Rather, we suggest that a complex meshwork of architectural proteins interact with XIST RNA. Parallel work studying the territory of actively transcribed chromosomes suggests that repeat-rich RNA ‘coats’ euchromatin and may impact chromosome architecture in a manner opposite of XIST. A model is discussed whereby RNA may not just recruit histone modifications, but more directly impact higher-order chromatin condensation via interaction with architectural proteins of the nucleus.This article is part of the themed issue ‘X-chromosome inactivation: a tribute to Mary Lyon’.

show abstract

RNA as a fundamental component of interphase chromosomes: could repeats prove key?

Cited by 32 publications

References 82 publications

RNA: Nuclear Glue for Folding the Genome

RNA: Nuclear Glue for Folding the Genome

RNA promotes the formation of spatial compartments in the nucleus

XISTRNA: a window into the broader role of RNA in nuclear chromosome architecture

Contact Info

Product

Resources

About