SnoRNA U21 is also intron-encoded in Drosophila melanogaster but in a different host-gene as compared to warm-blooded vertebrates

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster

A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome.

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

The exploration of the non-protein-coding RNA (ncRNA) transcriptome is currently focused on profiling of microRNA expression and detection of novel ncRNA transcription units. However, recent studies suggest that RNA processing can be a multi-layer process leading to the generation of ncRNAs of diverse functions from a single primary transcript. Up to date no methodology has been presented to distinguish stable functional RNA species from rapidly degraded side products of nucleases. Thus the correct assessment of widespread RNA processing events is one of the major obstacles in transcriptome research. Here, we present a novel automated computational pipeline, named APART, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data. The major features include efficient handling of non-unique reads, detection of novel stable ncRNA transcripts and processing products and annotation of known transcripts based on multiple sources of information. To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. By employing the APART pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable RNA molecules differentially processed from well known ncRNAs, like rRNAs, tRNAs or snoRNAs, in a stress-dependent manner.

Evolutionary profiling of the U49 snoRNA gene

Small nucleolar RNAs (snoRNAs) are involved in precursor ribosomal RNA (pre-rRNA) processing and rRNA base modifications (2'-O-ribose methylation and pseudouridylation). Their genomic organization show great flexibility: some are individually or polycistronically transcribed, while others are encoded within introns of other genes. Here, we present an evolutionary analysis of the U49 gene in seven species. In all species analyzed, U49 contains the typical hallmarks of C and D box motifs, and a conserved 12-15 nt sequence complementary to rRNA that define them as homologs. In mouse, human, and Drosophila U49 is found encoded within introns of different genes, and in plants it is transcribed polycistronically from four different locations. In addition, U49 has two copies in two different introns of the RpL14 gene in Drosophila. The results indicate a substantial degree of duplication and translocation of the U49 gene in evolution. In light of its variable organization we discuss which of the two proposed mechanisms of rearrangement has acted upon the U49 snoRNA gene: chromosomal duplication or transposition through an RNA intermediate.

The expanding snoRNA world

In eukaryotes, the site-specific formation of the two prevalent types of rRNA modified nucleotides, 2'-O-methylated nucleotides and pseudouridines, is directed by two large families of snoRNAs. These are termed box C/D and H/ACA snoRNAs, respectively, and exert their function through the formation of a canonical guide RNA duplex at the modification site. In each family, one snoRNA acts as a guide for one, or at most two modifications, through a single, or a pair of appropriate antisense elements. The two guide families now appear much larger than anticipated and their role not restricted to ribosome synthesis only. This is reflected by the recent detection of guides that can target other cellular RNAs, including snRNAs, tRNAs and possibly even mRNAs, and by the identification of scores of tissue-specific specimens in mammals. Recent characterization of homologs of eukaryotic modification guide snoRNAs in Archaea reveals the ancient origin of these non-coding RNA families and offers new perspectives as to their range of function.

Non-coding snoRNA host genes in Drosophila: expression strategies for modification guide snoRNAs

Modification guide snoRNAs either are encoded within introns and co-transcribed with the host gene pre-mRNA or are independently transcribed as mono- or polycistronic units. Different eukaryotic kingdoms utilize these coding strategies to various degrees. Intron-encoded and polycistronic snoRNAs are released from primary transcripts as pre-snoRNAs by the spliceosome or by an RNase III-like activity, respectively. In the spliceosomal pathway, the resulting intron lariat is then linearized by a debranching activity. The leader and trailer sequences of pre-snoRNAs are removed by exonucleolytic activities. The majority of snoRNA host genes encode proteins involved in the synthesis, structure or function of the translational apparatus. Several vertebrate snoRNA host genes do not appear to code for functional proteins. We have identified two unusually compact box C/D multi-snoRNA host genes in D. melanogaster, dUHG1 and dUHG2, similar in their organization to the corresponding vertebrate non-protein-coding host genes. In dUHG1 and dUHG2, the snoRNA sequences are located within introns at a conserved distance of about 75 nucleotides upstream of the 3' splice sites. Both genes initiate transcription with TOP-like sequences that share unique features with previously reported Drosophila snoRNA host genes. Although the spliced dUHG RNAs are relatively stable, they exhibit little potential for protein coding.

Evolution of U24 and U36 snoRNAs encoded within introns of vertebrate rpL7a gene homologs: unique features of mammalian U36 variants

U24 and U36 are members of the box C/D-containing group of antisense snoRNAs which possess long (9-21 nucleotide) conserved stretches of sequence complementarity to 18S and 28S rRNA and act as guides for the site-specific ribose methylation of rRNA. Both U24 and two variants of U36 are encoded within introns of the human and chicken rpL7a genes. We now report that an additional U36 variant is encoded within intron 4 of the human rpL7a gene and that murine homologs of the three human U36 variants are encoded within the same adjacent introns (4, 5, and 6) of the mouse rpL7a gene. We also show that, like that of the chicken, the Fugu rubripes rpL7a gene possesses only two U36-like sequences within introns 4 and 5. Whereas the two U36 variants in chicken and Fugu possess stretches of complementarity to both 18S and 28S rRNAs, it is noted that only one mammalian variant (U36b) possesses both. Unusually, the stretch of complementarity to 18S rRNA in the mammalian U36a variants and the stretch of complementarity to 28S rRNA in the mammalian U36c variants are not present, appearing to have diverged extensively from their consensus sequence. Additionally, the mammalian U36 variants show a unique heterogeneity in their potential to form a terminal stembox structure predicted for many other box C/D-containing antisense snoRNAs. Finally, the Saccharomyces cerevisiae small nuclear RNA, snR47, is shown to be homologous to the vertebrate U36 snoRNA.

Differentially expressed snoRNAs in Bungarus multicinctus (Taiwan banded krait)

Twenty novel snoRNAs forming extensive sequence complementarities to mature 5S rRNA were identified from Bungarus multicinctus by reverse transcription-polymerase chain reaction. It was found that the snoRNA species were differentially transcribed in different tissues as evidenced by single stranded conformational polymorphism analysis and direct nucleotide sequence analysis. Although the diversity in the sequences of snoRNAs is observed, comparison of these snoRNA genes reveals that the regions involved in binding to 5S rRNA are highly conserved and form two 12-nt-15-nt tracts of complementarity to phylogenetically invariant sequences in eukaryotic 5S rRNAs. Nevertheless, the lower conservation of box C/D or box H/ACA in these snoRNAs was observed. Likewise, the sequences in several fish and human genes forming perfect duplexes with 5S rRNA also did not highly retain these box elements. These results may infer that the box elements are dispensable for the function of snoRNA species identified in the present study. Moreover, the novel finding of the differentially expressed snoRNA variants in B. multicinctus suggests that the snoRNA genes are selectively processed in different tissues and are likely associated with tissue-specific regulation of their host gene transcripts.

Genomic structures of cardiotoxin 4 and cobrotoxin from Naja naja atra (Taiwan cobra)

Two genomic DNAs with the size of 2.3 kb and 2.4 kb, which were isolated from the liver of Naja naja atra (Taiwan cobra), encoded the precursors of cardiotoxin 4 and cobrotoxin, respectively. Both genes shared virtually identical overall organization with three exons separated by two introns, which were inserted in the similar positions of the gene's coding regions. Moreover, their nucleotide sequences shared approximately 84.2% identity. This result reveals the evolutionary relationship between cardiotoxin and cobrotoxin. The exon/intron structures of cardiotoxin 4 and cobrotoxin genes were similar to that reported for erabutoxin c gene, a neurotoxin genomic DNA from a sea snake (Laticauda semifasciata). However, in contrast to the finding that the intron 2 of these genes had a similar size, a notable variation with the size of intron 1 was observed (1233 bp, 1269 bp and 197 bp for cardiotoxin 4, cobrotoxin and erabutoxin c genes, respectively). The different size with intron 1 is due to the middle region at the first intron of cardiotoxin 4 and cobrotoxin genes, which encoded small nucleolar RNA (snoRNA), being absent in that of erabutoxin c gene. These results, together with the finding of the potential mobility of snoRNA genes during evolution, suggest that intron insertions or deletions of snoRNA genes occur with the evolutionary divergence of snake neurotoxins and cardiotoxins.

Novel SnoRNAs from Naja naja atra (Taiwan cobra) and Bungarus multicinctus (Taiwan banded krait), form extended sequence complementarity to 5S rRNA

During the mapping and sequencing of Naja naja atra cobrotoxin and cardiotoxin 4 genes, we have found that novel small nucleolar RNAs (snoRNAs) are encoded in the first intron of the two genes. The snoRNAs in Naja naja atra were amplified from the venom glands cDNA mixtures of Naja naja atra by reverse transcription-polymerase chain reaction using the primers designed from the first intronic sequences of cobrotoxin and cardiotoxin 4 genes. Likewise, the snoRNAs in Bungarus multicinctus were also amplified by the same primers. Comparison of these snoRNA genes reveals that the regions involved in binding to 5S rRNA are highly conserved among these genes, and form 12-nt and 15-nt tracts of complementarity to phylogenetically invariant sequences in eukaryotic 5S rRNAs. The box C sequence in these snoRNAs is consensus, however, variations with the sequence of box D motif are observed. The present study is the first case of intron-encoded snoRNAs contain extended regions of perfect complementarity to mature 5S rRNA.

Small RNA database

The small RNA database is a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondrial small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses. Currently, about 600 small RNA sequences are in our database. It also gives the sources of individual RNAs and their GenBank accession numbers. The small RNA database can be accessed through WWW(World Wide Web). Our WWW URL address is: http://mbcr.bcm.tmc.edu/smallRNA/smallrna. html . The new small RNA sequences published since our last compilation are listed in this paper.

Processing of fibrillarin-associated snoRNAs from pre-mRNA introns: an exonucleolytic process exclusively directed by the common stem-box terminal structure

Nucleoli contain complex populations of small nucleolar RNAs (snoRNAs) likely to be involved in pre-rRNA processing and ribosome biogenesis. A growing family of snoRNAs which interacts with nucleolar protein fibrillarin is structurally related by the presence of long complementarities to rRNA (12 to 21 nucleotides) and of a pair of common sequence motifs, termed boxes C and D. All are encoded in introns and produced by processing of intronic RNA. We have analysed the mechanism of processing of one of these snoRNAs, U20, by transfection in mouse cells. We show here that the cis-acting signals for its processing are restricted to a minor portion of the mature snoRNA sequence. A terminal structure in which the two box motifs are brought in close vicinity by the pairing of the 5' and 3' terminal nucleotides is sufficient to direct faithful processing. Particularly, the key role of the terminal stem shared by most snoRNAs of this family is demonstrated by the effect of compensatory mutations. Our results also indicate that faithful processing at both ends of the snoRNA can be uncoupled and that it is not strictly dependent on pre-mRNA splicing. Finally, our data point to the exclusive involvement of 5'-->3' and 3'-->5' exonucleolytic activities in the processing of intronic snoRNAs of this family.