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HIGHLIGHTS
NON-CODING RNA
Getting organized with non-coding RNAs
The nucleus contains several
membraneless structures, known as
non-coding nuclear bodies, but the mechanisms
by which these structures become
RNAs (ncR-
spatially organized in the nucleus
NAs) can drive were unknown. Now, Quinodoz et al.
the organiza- show that non-coding RNAs
tion of nuclear (ncRNAs) can drive the organiza­
tion of nuclear compartments by
compartments recruiting RNA and proteins to
by recruiting specific genomic regions.
RNA and pro- Nuclear bodies include the
teins to spe- nucleolus, which mediates ribosome
biogenesis through the transcription
cific genomic of rRNA genes, and other structures
regions involved in RNA processing and
transcription, such as Cajal bodies,
histone locus bodies and nuclear
speckles. To elucidate the mechan­
isms of their compartmentalization,
the authors used a method called
RD-SPRITE to map RNA–RNA,
RNA–DNA and DNA–DNA
interactions in the nucleus. In this
method, spatially close RNA, DNA
and proteins are crosslinked in situ
before cell lysis and chromatin
fragmentation. RNA and DNA
molecules are tagged using a
split-and-pool strategy to generate
barcodes specific to the nucleic acid
components of each crosslinked
complex. DNA and RNA are then
sequenced, revealing the organization
of specific RNAs in relation to each
other and genomic DNA.
Limited
r Nature
/Springe
Morgan
Credit: P.
NAtuRe Reviews | GeNetics
RD-SPRITE analysis identified
distinct groups of RNAs in which
members were frequently associated
and localized to similar regions of
genomic DNA. These groups — or
‘hubs’ — corresponded with known
types of nuclear bodies. The authors
consistently found strong enrichment
of known diffusible regulatory
ncRNAs at nascent RNAs and
their corresponding genomic
loci. For example, in the
‘nucleolar’ hub, small nucleolar
RNAs (snoRNAs) involved in
rRNA biogenesis were strongly
associated with 45S pre-rRNA
and localized at its genomic locus.
In a Cajal-body-like hub, small
Cajal-body-specific RNAs (scaRNAs)
were highly enriched at genomic
DNA regions encoding their small
nuclear RNA gene targets. In the
spliceosomal hub, the authors
found splicing-related ncRNAs
were enriched in DNA regions near
clusters of actively transcribed RNA
polymerase II (Pol II) genes, rather
than being evenly distributed across
the genome. Inhibition of RNA Pol I
and II with actinomycin D (ActD)
profoundly disrupted snoRNA and
scaRNA localization in the nucleus,
suggesting the presence of nascent
ncRNA acts to recruit diffusible
ncRNAs. Overall, these results show
that spatial organization of diffusible
ncRNAs in relation to genomic DNA
is common to nuclear structures.
Mapping of around 650 long
ncRNAs (lncRNAs) to the genome
showed 93% were strongly enriched
within close proximity of their
transcriptional loci. Contrary
to the data from nuclear bodies
involved in transcriptional regu­
lation, this association was often
stable even after treatment
with a transcriptional inhibitor,
indicating the association of
mature RNAs with these loci.
To study whether lncRNAs
direct protein recruitment to
genomic DNA, the authors used
super-resolution microscopy to
characterize the localization of
SHARP, a protein binding partner
of the lncRNA Xist that is involved
in X chromosome inactivation.
SHARP showed compartmentalized
localization in the nucleus that was
lost on deletion of its RNA binding
domains, indicating that RNA is
required for the spatial localization
of SHARP. By purifying SHARP-
bound RNAs from cells, the authors
identified strong binding between
SHARP and the lncRNA Kcnq1ot1,
which is involved in transcriptional
silencing of a paternally imprinted
gene cluster. RD-SPRITE showed
Kcnq1ot1 strongly localizes within
a topologically associating domain
(TAD) containing its target genes.
Inducing Kcnq1ot1 expression
enriched SHARP at the Kcnq1ot1
locus, indicating that Kcnq1ot1 acts
to recruit SHARP. Furthermore,
both downregulation of Kcnq1ot1
and loss of the SHARP binding site
on Kcnq1ot1 led to upregulation of
its known target genes. These results
suggest that lncRNAs can direct the
localization of proteins to specific
genomic loci and modulate gene
expression.
In summary, the authors
demonstrate a role for both
nascent and mature ncRNAs
as seeds for driving the spatial
localization of diffusible
ncRNAs and protein molecules
in the nucleus. Future work will
investigate further relationships
between the organization and
function of RNA and DNA
structures.
Joseph Willson
Original article Quinodoz, S. A. et al. RNA
promotes the formation of spatial compartments
in the nucleus. Cell 184, 5775–5790 (2021)
volume 23 | JANUARY 2022 | 1