A Novel Brain-specific Box C/D Small Nucleolar RNA Processed from Tandemly Repeated Introns of a Noncoding RNA Gene in Rats

Abstract

Antisense box C/D small nucleolar RNAs (snoRNAs) guide the 2-O-ribose methylations of eukaryotic rRNAs and small nuclear RNAs (snRNAs) through formation of a specific base pairing at each RNA methylation site. By analysis of a box C/D snoRNA cDNA library constructed from rat brain RNAs, we have identified a novel box C/D snoRNA, RBII-36, which is devoid of complementarity to rRNA or an snRNA and exhibits a brain-specific expression pattern. It is uniformly expressed in all major areas of adult rat brain (except for choroid plexus) and throughout rat brain ontogeny but exclusively detected in neurons in which it exhibits a nucleolar localization. In vertebrates, known methylation guide snoRNAs are intron-encoded and processed from transcripts of housekeeping genes. In contrast, RBII-36 snoRNA is intron-encoded in a gene preferentially expressed in the rat central nervous system and not in proliferating cells. Remarkably, this host gene, which encodes a previously reported noncoding RNA, Bsr, spans tandemly repeated 0.9-kilobase units including the snoRNA-containing intron. The novel brain-specific snoRNA appears to result not only from processing of the debranched lariat but also from endonucleolytic cleavages of unspliced Bsr RNA (i.e. an alternative splicing-independent pathway unreported so far for mammalian intronic snoRNAs). Sequences homologous to RBII-36 snoRNA were exclusively detected in the Rattus genus of rodents, suggesting a very recent origin of this brain-specific snoRNA.In eukaryotic cells, ribosome biogenesis takes place mainly in the nucleolus, through a series of intricate steps including (i) rDNA transcription by the cognate RNA polymerase I, (ii) processing of the pre-rRNA transcript by endo-and exonucleases and covalent modification of a subset of pre-rRNA nucleotides, (iii) packaging of pre-rRNA by ribosomal proteins, and (iv) cytoplasmic export of ribosomal subunits. Pre-rRNA maturation involves a large number of small nucleolar ribonucleoprotein particles (snoRNPs), 1 which can be defined as a metabolically stable association between small nucleolar RNA (snoRNA) and a specific set of proteins (1). All snoRNAs to date (except the RNA component for RNase MRP) fall into two major classes, box C/D and box H/ACA snoRNAs, based on the presence of short consensus sequence motifs (2). Whereas a few of them are involved in pre-rRNA nucleolytic cleavages, most box C/D and box H/ACA snoRNAs play a key role in specifying the two major types of rRNA nucleotide modification (2Ј-O-ribose methylations and pseudouridylations, respectively) through formation of a specific RNA duplex at the modification site (3-6). While function(s) of these nucleotide modifications are still elusive they are proposed to fine tune rRNA folding and interactions with ribosomal proteins. Thereby, they could play a role in the biogenesis and activity of mature cytoplasmic ribosomes, particularly with regard to their peptidyl transferase activities (7). Antisense box C/D snoRNAs contain conserved sequence motifs box C (5Ј-RUGAUG...

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

“…4B). In fact, a similar enrichment of ncRNA expression in brain versus other tissues has previously been demonstrated in mouse (Ravasi et al 2006), and several reports on the involvement and relative abundance of ncRNA in human CNS function and development have recently emerged (Cavaille et al 2001;French et al 2001;Pollard et al 2006;Sone et al 2007). Furthermore, an RNAz screen of porcine EST sequences revealed that developmental brain tissue seems to contain more ncRNAs than other tissues (Seemann et al 2007).…”

A new paradigm for developmental biology

“…Moreover, it would be expected that increasing numbers of genes would have evolved solely to express RNA as higher-order regulators in this increasingly complex system. This will have occurred at least in part by gene duplication followed by loss of protein-coding capacity, as appears to have happened in Xist (the ncRNA controlling X chromosome inactivation in female mammals) (Duret et al, 2006) and in many of the non-protein-coding genes that encode snoRNAs or miRNAs in their introns (Cavaille et al, 2001;Mattick and Makunin, 2005;Rodriguez et al, 2004;Tycowski et al, 1996;Ying and Lin, 2005). Interestingly, many ncRNAs are alternatively spliced (Cocquet et al, 2005;Pang et al, 2005), suggesting that there is an operational distinction between RNA sourced from exons and introns.…”

“…A subset of box H/ACA snoRNAs is located in Cajal bodies (a class of small nuclear organelle), and are sometimes called scaRNAs (small Cajal body RNAs) (Meier, 2005), where they modify telomerase RNA in a cell-cycle dependent manner (Jady et al, 2004;Jady et al, 2003). At least some snoRNAs exhibit tissue-specific and developmental regulation and/or imprinting (Cavaille et al, 2000;Cavaille et al, 2002;Cavaille et al, 2001;Rogelj and Giese, 2004), which is indicative of a regulatory function. There are also a number of so-called 'orphan' snoRNAs without known targets (Cavaille et al, 2000;Cavaille et al, 2002;Cavaille et al, 2001;Huttenhofer et al, 2001;Kiss et al, 2004;Vitali et al, 2003), one of which has recently been shown to be involved in the aberrant splicing of the serotonin receptor 5-HT(2C)R gene in Prader-Willi syndrome patients (Cavaille et al, 2000;Kishore and Stamm, 2006).…”

Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays

“…The Snurf-Snrpn domain therefore shares common genomic and epigenetic features with the Dlk1-Dio3 domain (Cavaille et al, 2002;Cavaille et al, 2001;Royo et al, 2007;Royo and Cavaille, 2008) (Fig. 1).…”