Architecture of the U5 small nuclear RNA

We have used comparative sequence analysis and deletion analysis to examine the secondary structure of the U5 small nuclear RNA (snRNA), an essential component of the pre-mRNA splicing apparatus. The secondary structure of Saccharomyces cerevisiae U5 snRNA was studied in detail, while sequences from six other fungal species were included in the phylogenetic analysis. Our results indicate that fungal U5 snRNAs, like their counterparts from other taxa, can be folded into a secondary structure characterized by a highly conserved stem-loop (stem-loop 1) that is flanked by a moderately conserved internal loop (internal loop 1). In addition, several of the fungal U5 snRNAs include a novel stem-loop structure (ca. 30 nucleotides) that is adjacent to stem-loop 1. By deletion analysis of the S. cerevisiae snRNA, we have demonstrated that the minimal U5 snRNA that can complement the lethal phenotype of a U5 gene disruption consists of (i) stem-loop 1, (ii) internal loop 1, (iii) a stem-closing internal loop 1, and (iv) the conserved Sm protein binding site. Remarkably, all essential, U5-specific primary sequence elements are encoded by a 39-nucleotide domain consisting of stem-loop 1 and internal loop 1. This domain must, therefore, contain all U5-specific sequences that are essential for splicing activity, including binding sites for U5-specific proteins.

Small nuclear RNAs from budding yeasts: phylogenetic comparisons reveal extensive size variation

Homologues of each of the five metazoan snRNAs required for pre-mRNA splicing have recently been identified in the budding yeast Saccharomyces cerevisiae on the basis of shared structural elements and evidence of similar roles during splicing. However, the spliceosomal snRNAs in this yeast are up to six times larger than their mammalian counterparts, suggesting that they may perform additional, perhaps species-specific, functions in the pre-mRNA processing pathway. We have undertaken a survey of 23 other budding yeasts to determine whether increased snRNA size is unique to Sacch. cerevisiae and, if not, to look for common structural motifs among homologous snRNAs. Our studies reveal that the spliceosomal snRNAs exhibit a surprising degree of size variation among these species. Furthermore, partial sequence analysis has identified a specific domain in the U6 snRNA which accounts for the observed size polymorphisms.

P element insertions and rearrangements at the singed locus of Drosophila melanogaster

DNA from the singed gene of Drosophila melanogaster was isolated using an inversion between a previously cloned P element at cytological location 17C and the hypermutable allele singed-weak. Five out of nine singed mutants examined have alterations in their DNA maps in this region. The singed locus is a hotspot for mutation during P-M hybrid dysgenesis, and we have analyzed 22 mutations induced by P-M hybrid dysgenesis. All 22 have a P element inserted within a 700-bp region. The precise positions of 10 P element insertions were determined and they define 4 sites within a 100-bp interval. During P-M hybrid dysgenesis, the singed-weak allele is destabilized, producing two classes of phenotypically altered derivatives at high frequency. In singed-weak, two defective P elements are present in a "head-to-head" or inverse tandem arrangement. Excision of one element results in a more extreme singed bristle phenotype while excision of the other leads to a wild-type bristle phenotype.

An essential snRNA from S. cerevisiae has properties predicted for U4, including interaction with a U6-like snRNA

Three yeast snRNAs (snR20, snR7, and snR14) have been implicated in pre-mRNA splicing. snR20 and snR7 contain domains of homology to U2 and U5, respectively, and each is required for viability. These RNAs are found associated with the spliceosome, as is snR14. We show here that snR14 is also an essential gene product. Sequence analysis reveals that, like snR7 and snR20, snR14 contains a consensus binding site for the Sm antigen, a feature common to all mammalian snRNAs involved in splicing. Moreover, snR14 exhibits several blocks of sequence and structural homology to U4, which in metazoans is found in association with U6. Native gel electrophoresis demonstrates that snR14 is in fact base-paired with another yeast snRNA, designated snR6, which has primary sequence homology to U6. We conclude that snR14 is the yeast analog of U4.

Site specific insertion of a type I rDNA element into a unique sequence in the Drosophila melanogaster genome

We describe a cloned segment of unique DNA from the Oregon R strain of Drosophila melanogaster that contains a short type I insertion of the kind principally found within rDNA. The predominant type I rDNA insertion is 5kb in length, but there are also a co-terminal sub-set of shorter type I elements that share a common right hand junction with the rDNA. The insertion that we now describe is another member of this sub-set. The right hand junction of the type I sequence with the unique DNA is identical to the right hand junction of the type I sequences with rDNA. There is no significant feature within the insertion sequence that could have determined the position of the left junction with the sequence into which it is inserted. Like the corresponding short type I insertions in rDNA, the insertion into the unique DNA is flanked on both sides by a duplicated sequence, which in this case is 10 base pairs long. The cloning of a sequence corresponding to the uninterrupted unique location was facilitated by the observation that the Karsnas strain of D. melanogaster contains only uninterrupted sequences of this kind. The duplicated sequence at the target site for the insertion is only present as a single copy in the uninterrupted DNA. The sequence of the target site for the insertion (ACTGTTCT) in the unique segment shows a striking homology to the target in rDNA (ACTGTCCC).

Widely differing degrees of sequence conservation of the two types of rDNA insertion within the melanogaster species sub-group of Drosophila

We have examined the distribution of sequences homologous to the type I and type II rDNA insertions of Drosophila melanogaster in its sibling species. Each of the six species we have examined has sequences homologous to the type I insertion, which have undergone extensive divergence by the criterion of their EcoRI, BstI and HindIII restriction patterns. We have isolated cosmid clones containing type I sequences from D. simulans and D. mauritiana, the two species most closely related to D. melanogaster. Southern hybridisation analysis of these clones indicates that, as in D. melanogaster, the type I sequences can exist independently of rDNA and can also dissociate to give sub-components homologous to the right hand segment of the D. melanogaster type I insertion. The type II sequences, on the other hand are present in five out of the six species, but their restriction endonuclease cleavage profile is highly conserved. The differences in the degree of conservation of the two types of insertion sequence are discussed.

Duplicated rDNA sequences of variable lengths flanking the short type I insertions in the rDNA of Drosophila melanogaster

We describe cloned segments of rDNA that contain short type I insertions of differing lengths. These insertions represent a coterminal subset of sequences from the right hand side of the major 5kb type I insertion. Three of these shorter insertions are flanked on both sides by a short sequence present as a single copy in uninterrupted rDNA units. The duplicated segment is 7, 14 and 15 nucleotides in the different clones. In this respect, the insertions differ from the 5kb type I insertion, where the corresponding sequence is found only at the right hand junction and where at the left hand side there is a deletion of 9 nucleotides of rDNA (Roiha et al.,1981). One clone is unusual in that it contains two type I insertions, one of which is flanked by a 14 nucleotide repeat. The left hand junction of the second insertion occurs 380 nucleotides downstream in the rDNA unit from the first. It has an identical right hand junction to the other elements and the 380 nucleotide rDNA sequence is repeated on both sides of the insertion. We discuss the variety of sequence rearrangements of the rDNA which flank type I insertions.