Differential contribution of steady‐state
            <scp>RNA</scp>
            and active transcription in chromatin organization

Barutcu, A. Rasim; Blencowe, Benjamin J.; Rinn, John L.

doi:10.15252/embr.201948068

Cited by 71 publications

(75 citation statements)

References 84 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Previous studies have shown that global disruption of RNA by RNase A leads to disruption of HP1 localization at chromocenters 91 . However, RNAse A is not specific and can impact several structures in the nucleus, including nucleoli 93 . Because major and minor satellite-derived ncRNAs localize exclusively within centromere-proximal structures, we hypothesized that these ncRNAs might be important for HP1 localization.…”

Section: Satellite-derived Ncrnas Organize Hp1 Localization At Inter-mentioning

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

Section: Satellite-derived Ncrnas Organize Hp1 Localization At Inter-mentioning

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

show abstract

“…Previous reports have proposed that actively transcribed genes may play such a role. First, Transcriptional Start Sites (TSSs) of housekeeping genes are enriched at TAD borders (8,35) and, second, the act of transcription can affect 3D genome structure independently of CTCF (36)(37)(38). However, whether an actively transcribed gene can behave as a boundary, in a similar manner to a CTCF element, has not been previously tested in mammalian systems.…”

Section: Gene Expression Throughout Development and Differentiation Imentioning

confidence: 99%

A functional overlap between actively transcribed genes and chromatin boundary elements

Harrold

Gosden

Hanssen

et al. 2020

Preprint

View full text Add to dashboard Cite

AbstractMammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ∼70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.Significance StatementMammalian genomes are complex, organised 3D structures, partitioned into Topologically Associating Domains (TADs): chromatin regions that preferentially self-interact. These chromatin interactions are thought to be driven by a mechanism that continuously extrudes chromatin loops, forming structures delimited by chromatin boundary elements and reflecting the activity of enhancers and promoters. Boundary elements bind architectural proteins such as CCCTC-binding factor (CTCF). Previously, an overlap between the functional roles of enhancers and promoters has been shown. However, whether there is overlap between enhancers/promoters and boundary elements is not known. Here, we show that actively transcribed genes can also behave as boundary elements, similar to CTCF boundaries. In both cases, multi-protein complexes bound to these regions may stall the process of chromatin loop extrusion.

show abstract

“…D) Cytological visualization of NPM1 under indicated conditions. nization such as topologically associated domains (TADs) remain unaffected, a subtle change in long-range interactions within heterochromatic, gene-poor, and silent genomic compartments is observed upon RNA depletion (Barutcu et al, 2019). However, the low resolution of both cytology and Hi-C methods limits their use in deciphering the involvement of RNA in chromatin structure.…”

Section: Introductionmentioning

confidence: 99%

Architectural RNA is required for heterochromatin organization

Thakur

Llagas

et al. 2019

Preprint

View full text Add to dashboard Cite

In addition to its known roles in protein synthesis and enzyme catalysis, RNA has been proposed to stabilize higher-order chromatin structure. To distinguish presumed architectural roles of RNA from other functions, we applied a ribonuclease digestion strategy to our CUT&RUN in situ chromatin profiling method (CUT&RUN.RNase). We find that depletion of RNA compromises association of the murine nucleolar protein Nucleophosmin with pericentric heterochromatin and alters the chromatin environment of CCCTC-binding factor (CTCF) bound regions. Strikingly, we find that RNA maintains the integrity of both constitutive (H3K9me3 marked) and facultative (H3K27me3 marked) heterochromatic regions as compact domains, but only moderately stabilizes euchromatin. To establish the specificity of heterochromatin stabilization by RNA, we performed CUT&RUN on cells deleted for the Firre long non-coding RNA and observed disruption of H3K27me3 domains on several chromosomes. We conclude that RNA maintains local and global chromatin organization by acting as a structural scaffold for heterochromatic domains.1

show abstract

Differential contribution of steady‐state RNA and active transcription in chromatin organization

Cited by 71 publications

References 84 publications

RNA promotes the formation of spatial compartments in the nucleus

RNA promotes the formation of spatial compartments in the nucleus

A functional overlap between actively transcribed genes and chromatin boundary elements

Architectural RNA is required for heterochromatin organization

Contact Info

Product

Resources

About