Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs

A spliceosomal intron binding protein, IBP160, links position-dependent assembly of intron-encoded box C/D snoRNP to pre-mRNA splicing

Pre-mRNA splicing in vertebrates is molecularly linked to other processes. We previously reported that splicing is required for efficient assembly of intron-encoded box C/D small nucleolar ribonucleoprotein (snoRNP). In the spliceosomal C1 complex, snoRNP proteins efficiently assemble onto snoRNA sequences if they are located about 50 nt upstream of the intron branchpoint. Here, we identify the splicing factor responsible for coupling snoRNP assembly to intron excision. Intron binding protein (IBP) 160, a helicase-like protein previously detected in the spliceosomal C1 complex, binds the pre-mRNA in a sequence-independent manner, contacting nucleotides 33-40 upstream of the intron branch site, regardless of whether a snoRNA is present. Depletion of IBP160 abrogates snoRNP assembly in vitro. IBP160 binding directly to a snoRNA located too close to the intron branch site interferes with snoRNP assembly. Thus, IBP160 is the key factor linking snoRNP biogenesis and perhaps other postsplicing events to pre-mRNA splicing.

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome

Small nucleolar RNAs (snoRNAs) represent an abundant group of non-coding RNAs in eukaryotes. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Current snoRNA-searching programs, which are essentially based on sequence complementarity to rRNAs or snRNAs, exist only for the screening of guide snoRNAs. In this study, we have developed an advanced computational package, snoSeeker, which includes CDseeker and ACAseeker programs, for the highly efficient and specific screening of both guide and orphan snoRNA genes in mammalian genomes. By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern. The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.

Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact

Ribosomal RNA from all organisms contains post-transcriptionally modified nucleotides whose function is far from clear. To gain insight into the molecular interactions of modified nucleotides, we investigated the modification status of Thermus thermophilus 5 S and 23 S ribosomal RNA by mass spectrometry and chemical derivatization/primer extension. A total of eleven modified nucleotides was found in 23 S rRNA, of which eight were singly methylated nucleotides and three were pseudouridines. These modified nucleotides were mapped into the published three-dimensional ribosome structure. Seven of the modified nucleotides located to domain IV, and four modified nucleotides located to domain V of the 23 S rRNA. All posttranscriptionally modified nucleotides map in the center of the ribosome, and none of them are in contact with ribosomal proteins. All except one of the modified nucleotides were found in secondary structure elements of the 23 S ribosomal RNA that contact either 16 S ribosomal RNA or transfer RNA, with five of these nucleotides physically involved in intermolecular RNA-RNA bridges. These findings strongly suggest that the post-transcriptional modifications play a role in modulating intermolecular RNA-RNA contacts, which is the first suggestion on a specific function of endogenous ribosomal RNA modifications.

Characterization and differential nuclear localization of Nopp140 and a novel Nopp140-like protein in trypanosomes

Trypanosomatids possess two homologues of Nopp140: a canonical Nopp140 and a Nopp140-like protein (TbNoLP) in which a GAR domain replaces the C-terminal SRP40 domain. Both are phosphorylated and coimmunoprecipitate with RNA polymerase I. Each paralogue has a distinct subnuclear localization, and depletion of TbNoLP produces an enlarged nucleolus in which TbNopp140-containing regions disperse. The restricted occurrence pattern of NoLP proteins reflects an intriguing convergence in evolution, suggestive of a function in nucleoplasmic small nucleolar ribonucleoprotein shuttling.

A novel experimental approach for systematic identification of box H/ACA snoRNAs from eukaryotes

Box H/ACA snoRNAs represent an abundant group of small non-coding RNAs mainly involved in the pseudouridylation of rRNAs and/or snRNAs in eukaryotes and Archaea. In this study, we describe a novel experimental method for systematic identification of box H/ACA snoRNAs from eukaryotes. In the specialized cDNA libraries constructed by this method with total cellular RNAs from human blood cells, the high efficiency of cloning for diverse box H/ACA snoRNAs was achieved and seven novel species of this snoRNA family were identified from human for the first time. Furthermore, the novel method has been successfully applied for the identification of the box H/ACA snoRNAs from Drosophila and the fission yeast, demonstrating a powerful ability for systematic analysis of box H/ACA snoRNAs in a broad spectrum of eukaryotes.

Maintaining a conserved methylation in plant and insect U2 snRNA through compensatory mutation by nucleotide insertion

The extensive post-transcriptional modification of U2 snRNA is required for spliceosome assembly and pre-mRNA splicing in vertebrates. However, the rare modification of U2 snRNA in yeast implies a different mechanism for regulating spliceosome biogenesis in single-celled eukaryotes. To understand the evolutionary pattern of U2 snRNA methylation, we determined for the first time, the 2'-O-methylations of U2 snRNA in Oryza sativa, Arabidopsis thaliana and Drosophila melanogaster, and revealed two methylations which are conserved in a crucial region of U2 snRNA in plants. Interestingly, one of the methylations, U2-Cm29 is also methylated in D. melanogaster, but not in vertebrates. According to the methylation of U2-C29, computational analysis of databases identified three canonical box C/D snoRNAs, named OsmgU2-29, AtmgU2-29 and DmmgU2-28, as small methylation guides of U2 snRNA from O. sativa, A. thaliana and D. melanogaster, respectively. Although very divergent in their sequence, the three snoRNAs exhibit in common an 11 nucleotide-long sequence complementarity to corresponding U2 snRNA, implying a functional constraint on the modification during evolution. Interestingly, a nucleotide is found to be inserted both in U2 snRNA and DmmgU2-28 and maintains a perfect match of duplex specifying the methylation of C28 in Drosophila U2 snRNA. This is the first time a new model is being provided for compensatory mutations between a small guide RNA and its target by nucleotide insertion, instead of the known nucleotide substitution. In contrast to small Cajal body-specific RNAs (scaRNAs), the snoRNAs are similar to the reported singlet guide RNAs and are known to localize in nucleolus.