Gene regulation by non-coding RNAs in the 3D genome architecture
Introduction
In eukaryotes, the genomic DNA is packaged into chromatin, in which the fundamental repeating unit is a nucleosome consisting of 180 bp DNA and four histone proteins, H2A, H2B, H3, and H4 [1]. The array of nucleosomes are folded into multiple layers, from lower to higher order, involving hundreds of kbs of chromatin loops, approximately 1 Mb of TADs (topologically associated domains), mega-bases of A and B compartments, and individual chromosome territories [2, 3, 4, 5, 6, 7, 8]. Chromatin loops contain long-range chromosomal contacts and local chromatin loops, such as in enhancer–promoter interactions. TAD is a self-interacting chromatin region that compartmentalizes genomes. Enhancers can co-regulate genes within the TAD, but not outside of it. Disruption of the TAD boundaries leads to impaired gene expression, and corresponds to certain diseases [9,10]. The A and B compartments are much larger chromatin domains, and roughly correspond to euchromatin with active histone marks and heterochromatin with repressive histone marks, respectively [5,11]. This finding implies that the 3D genome structures originating from chromatin interactions play a key role in the regulation of gene expression.
Over 40 years ago, chromatin was found to cofractionate with RNAs, thus suggesting the presence of chromatin-associated RNAs [12, 13, 14]. More recent experiments with the Drosophila cell line have demonstrated that chromatin is increasingly endonuclease-resistant when cellular RNAs are hydrolyzed with RNaseA [15]. In this case, small nucleolar RNAs bind to chromatin though their associated proteins, and this is responsible for the chromatin inaccessibility. The possible involvement of other less-abundant RNAs remains to be investigated. These indicate that nuclear RNAs may facilitate the formation of an open euchromatin structure, and regulate gene expression under certain circumstances.
Recent high throughput sequence analyses have revealed that the genome is pervasively transcribed [16]. It is estimated that over 100 000 RNAs lacking protein coding potential, referred to as non-coding RNAs (ncRNAs), exist in cells [16]. ncRNAs with lengths longer than 200 nt are long ncRNAs (lncRNAs), and some play key roles in development. One of the best-studied examples is the Xist RNA, which is involved in X-chromosome inactivation (XCI) in mammalian females, as described below. Xist is produced from the unique locus, Xic (X chromosome inactivation center), which contains a cluster of ncRNA genes including RepA, Tsix, Xite, Jpx, Ftx, and Tsx. These ncRNAs are involved in the regulation of Xist expression and function, as well as XCI. This implies that ncRNAs are important cellular regulatory factors.
In this review article, we discuss the recent work on the ncRNAs that are involved in gene regulation, mainly through modulating higher order chromatin structures and epigenetic marks. We also consider the significance of ncRNAs in mammalian development, immunity, and cancer.
Section snippets
Xist functions in X chromosome inactivation during female early embryonic development
During early development in female mammals, one of the two X chromosomes (XX) is silenced as dosage compensation, relative to males with only one X chromosome (XY). This is referred to as X-chromosome inactivation (XCI). The X chromosome carries over 1000 genes essential for development and cell viability, and their overexpression due to XCI failure is potentially harmful [17,18]. The key regulator of XCI is the Xist (X-inactive–specific transcript) RNA, a 17 kb lncRNA expressed from the
Other ncRNAs that recruit repressive and active factors to chromatin
Several genes are expressed from only the maternal or paternal chromosome, in a phenomenon referred to as genomic imprinting. In addition to DNA methylation and histone modifications, ncRNAs are involved in this process. The Airn (Antisense Igf2r RNA non-coding) ncRNA is expressed only from the paternal allele, and required for the paternal-specific silencing of the multiple neighboring imprinted genes, Slc22a3, Slc22a2, and Igf2r, in the mouse placenta [36, 37, 38]. As with Xist, Airn forms an
Firre serves as a platform for trans-chromosomal associations
The long-range chromatin interaction analyses identified a genomic region that interacts with the X-linked macrosatellite region, DXZ4. It is the Firre (Functional intergenic repeating RNA element) locus that abundantly produces the Firre lncRNA, primarily from the active X chromosome [40,41•]. Firre forms RNA clouds in the nucleus, and serves as a platform for trans-chromosomal associations. Firre has 156 nt repeats, termed the repeating RNA domain (RRD), and they bind to the nuclear-matrix
UMLILO primes immune-genes for robust transcription in trained immunity
For an enhanced innate immune response, or trained immunity, immune-related gene promoters are primed for robust transcription. The active histone mark H3K4me3 is accumulated at their promoters, before immune stimulations. IPLs (Immune-gene priming lncRNAs) are a collection of lncRNAs expressed from the TAD containing the TNF (tumor-necrosis factor) responsive genes, and regulate them in cis [43••]. Among them is the UMLILO (Upstream Master LncRNA of the Inflammatory chemokine Locus) lncRNA,
ELEANORS delineate the active TAD and the long-range chromatin interactions in breast cancer recurrence
Gene expression profiles are remodeled in cancers. For example, the ESR1 gene is upregulated when ER (estrogen receptor)-positive breast cancer acquires endocrine therapy resistance. In this recurrence process, estrogen is deprived due to the therapy, and a cluster of lncRNAs, ELEANORS (ESR1 locus enhancing and activating noncoding RNAs), are produced from the TAD including the ESR1 gene, termed the ELEANOR TAD. ELEANORS remain at their own transcription sites, form the RNA cloud, and activate
Conclusion and perspectives
In this review, we have described examples of lncRNAs that are involved in the 3D genome structure and gene regulation. The modes of action for lncRNAs are diverse, and they participate in transcription activation or repression, by recruiting epigenetic modifiers, organizing nuclear substructures, co-regulating multiple genes in the same TAD, and mediating long-range chromatin interactions. LncRNAs are also involved in many different events, including development, immune responses, and
Conflict of interest statement
Nothing declared.
References and recommended reading
Papers of particular interest, published within the period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Acknowledgements
We apologize to authors whose work could not be cited due to space constraints. We would like to thank the members of the Saitoh laboratory (The Cancer Institute of JFCR) for helpful discussions. This work was supported by JSPS KAKENHI Grant Numbers JP17H05013 [to H.T.], JP19K23736 [to T.Y.], JP18H05531 [to N.S.], and JP18K19310 [to N.S.], and by grants from the Takeda Science Foundation [to N.S.], The Vehicle Racing Commemorative Foundation [to N.S.], and a Research Grant of the Princess
References (49)
- et al.
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
Cell
(2014) - et al.
Cause and consequence of tethering a SubTAD to different nuclear compartments
Mol Cell
(2016) - et al.
Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions
Cell
(2015) - et al.
Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin
Mol Cell
(2012) - et al.
The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus
Cell
(1992) - et al.
A 450 kb transgene displays properties of the mammalian X-inactivation center
Cell
(1996) - et al.
Jpx RNA activates Xist by evicting CTCF
Cell
(2013) - et al.
Xist deletional analysis reveals an interdependency between Xist RNA and polycomb complexes for spreading along the inactive X
Mol Cell
(2019) - et al.
PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome inactivation
Science
(2017) - et al.
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
Nat Struct Mol Biol
(2014)
Crystal structure of the nucleosome core particle at 2.8Å resolution
Nature
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
Nat Rev Genet
Capturing chromosome conformation
Science
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Nature
Cell-cycle dynamics of chromosomal organization at single-cell resolution
Nature
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Nature
Disruption of nuclear speckles reduces chromatin interactions in active compartments
Epigenetics Chromatin
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
Science
Molecular complementarity between nuclear DNA and organ-specific chromosomal RNA
Proc Natl Acad Sci U S A
A small chromatin-associated RNA homologous to repetitive DNA sequences
Eur J Biochem
Histone-bound RNA, a component of native nucleohistone
Proc Natl Acad Sci U S A
NONCODE 2016: an informative and valuable data source of long non-coding RNAs
Nucleic Acids Res
Gene action in the X-chromosome of the mouse (Mus musculus L.)
Nature
Forty years of decoding the silence in X-chromosome inactivation
Hum Mol Genet
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2021, Neurobiology of DiseaseCitation Excerpt :Non-coding RNAs are comprised of various regulatory molecules and include lncRNAs and small non-coding RNAs such as microRNAs (miRNAs) among others. LncRNAs are ~200 nucleotides in length and carry out their functions through a number of different mechanisms influencing chromatin modifiers and transcriptional regulation (Brockdorff et al., 2020; Tachiwana et al., 2020; Wang and Chang, 2011). LncRNAs are known to function by organising chromatin in active and inactive domains through interactions with the readers, writers and erasers of histones, and may also direct and determine the location of these modifications (Mondal et al., 2010; Subhash et al., 2018).
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