Polypurine-repeat-containing RNAs: a novel class of long non-coding RNA in mammalian cells

Abstract

SummaryIn higher eukaryotic cells, long non-protein-coding RNAs (lncRNAs) have been implicated in a wide array of cellular functions. Cellor tissue-specific expression of lncRNA genes encoded in the mammalian genome is thought to contribute to the complex gene networks needed to regulate cellular function. Here, we have identified a novel species of polypurine triplet repeat-rich lncRNAs, designated as GAA repeat-containing RNAs (GRC-RNAs), that localize to numerous punctate foci in the mammalian interphase nuclei. GRC-RNAs consist of a heterogeneous population of RNAs, ranging in size from ~1.5 kb to ~4 kb and localize to subnuclear domains, several of which associate with GAA.TTC-repeat-containing genomic regions. GRC-RNAs are components of the nuclear matrix and interact with various nuclear matrix-associated proteins. In mitotic cells, GRC-RNAs form distinct cytoplasmic foci and, in telophase and G1 cells, localize to the midbody, a structure involved in accurate cell division. Differentiation of tissue culture cells leads to a decrease in the number of GRC-RNA nuclear foci, albeit with an increase in size as compared with proliferating cells. Conversely, the number of GRC-RNA foci increases during cellular transformation. We propose that nuclear GRC-RNAs represent a novel family of mammalian lncRNAs that might play crucial roles in the cell nucleus.Key words: Non-coding RNAs, Nuclear domains, Nuclear matrix, Triplex repeats, Midbody Journal of Cell ScienceRNAs) that are distributed throughout the nucleus in a micropunctate pattern. GRC-RNAs primarily consist of polypurine repeats and are heterogeneous in size, ranging from 1.5-4 kb. GRC-RNAs associate with the nuclear matrix and interact with several bona fide nuclear matrix proteins. Our studies further indicate that the nuclear GRC-RNA foci is altered in cells that either are highly proliferating or are cell-cycle-arrested owing to serum deprivation. We propose that GRC-RNAs are novel members of the nrRNA family of RNAs that interact with components of the nuclear matrix and play crucial structural roles in the maintenance of the nuclear matrix and/or regulate gene expression. Results GRC-RNAs are members of the nrRNA family of lncRNAsRNA in situ hybridization studies have previously cataloged~850 lncRNAs that are expressed in specific cell types or in specific subcellular compartments within the adult mouse brain (Lein et al., 2007;Mercer et al., 2008). To gain further insight into the cellular function of these novel ncRNAs, we analyzed their distribution in various mammalian cell lines by RNA-FISH (fluorescent in situ hybridization). One of these ncRNAs (EST clone AK082015; ~2.2 kb) showed a punctate distribution in the nucleus of mouse NIH-3T3 cells (Fig. 1A). In most of the cells, apart from numerous nuclear foci, 2-5 distinct brightly labeled GRC-RNA-positive foci were also observed in the cytoplasm (see arrows in Fig. 1A; supplementary material Fig. S1B,C). To identify the minimal region of the cDNA probe that hybridized to the nuclear foci-associa...

AAGAG repeat RNA is an essential component of nuclear matrix inDrosophila

“…Recently, GAA-repeat containing RNA was found in the nuclear matrix of mammalian cells. 54 Although functional significance of this RNA was not investigated, it was shown to interact with multiple nuclear matrix proteins and associate with the midbody during cell division. NuMat has been shown earlier to be dependent on RNA component but molecular nature of these RNAs has not been reported.…”

Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data

“…By default, Triplexator ignores low-complexity regions. It should be kept in mind that such regions can resemble valid triplex features (Zheng et al 2010;Buske et al 2011), and the user may consider disabling repeat filtering.…”

Potential in vivo roles of nucleic acid triple-helices

“…110 The formation of H-DNA provides contact points that may participate in chromatin organization possibly through ncRNAs, which in turn may interact with the nuclear matrix or nuclear matrix-associated proteins. 10 Repeat regions in particular SRF and ELK-1. Hence, these proteins might be able to perform their function in the vicinity of the targeted locus such as modifying the epigenetic landscape or altering gene transcription.…”

“…Important pieces to the puzzle have been added by recent work on new methods for triplex detection, 4 the discovery of new triplex-unwinding helicases, 5 as well as the increasingly apparent biological roles played by non-coding RNAs 6 that suggest the involvement of triple-helices. [7][8][9][10] With the advent of high-throughput sequencing of RNA and DNA we now have the technology to map the genomic locations of RNA-DNA triplexes and to begin unraveling their functions. The ability of double-stranded DNA to form a triple-helical structure by hydrogen bonding with a third strand is well established, but the biological functions of these structures remain largely unknown.…”