@article {49674, title = {Evolutionary dynamics of U12-type spliceosomal introns.}, journal = {BMC Evol Biol}, volume = {10}, year = {2010}, month = {2010}, pages = {47}, abstract = {

BACKGROUND: Many multicellular eukaryotes have two types of spliceosomes for the removal of introns from messenger RNA precursors. The major (U2) spliceosome processes the vast majority of introns, referred to as U2-type introns, while the minor (U12) spliceosome removes a small fraction (less than 0.5\%) of introns, referred to as U12-type introns. U12-type introns have distinct sequence elements and usually occur together in genes with U2-type introns. A phylogenetic distribution of U12-type introns shows that the minor splicing pathway appeared very early in eukaryotic evolution and has been lost repeatedly.

RESULTS: We have investigated the evolution of U12-type introns among eighteen metazoan genomes by analyzing orthologous U12-type intron clusters. Examination of gain, loss, and type switching shows that intron type is remarkably conserved among vertebrates. Among 180 intron clusters, only eight show intron loss in any vertebrate species and only five show conversion between the U12 and the U2-type. Although there are only nineteen U12-type introns in Drosophila melanogaster, we found one case of U2 to U12-type conversion, apparently mediated by the activation of cryptic U12 splice sites early in the dipteran lineage. Overall, loss of U12-type introns is more common than conversion to U2-type and the U12 to U2 conversion occurs more frequently among introns of the GT-AG subtype than among introns of the AT-AC subtype. We also found support for natural U12-type introns with non-canonical terminal dinucleotides (CT-AC, GG-AG, and GA-AG) that have not been previously reported.

CONCLUSIONS: Although complete loss of the U12-type spliceosome has occurred repeatedly, U12 introns are extremely stable in some taxa, including eutheria. Loss of U12 introns or the genes containing them is more common than conversion to the U2-type. The degeneracy of U12-type terminal dinucleotides among natural U12-type introns is higher than previously thought.

}, keywords = {Animals, Arabidopsis, Evolution, Molecular, HUMANS, Introns, RNA, Small Nuclear, Spliceosomes}, issn = {1471-2148}, doi = {10.1186/1471-2148-10-47}, author = {Lin, Chiao-Feng and Mount, Stephen M and Jarmo{\l}owski, Artur and Maka{\l}owski, Wojciech} } @article {49681, title = {Spliceosomal small nuclear RNA genes in 11 insect genomes.}, journal = {RNA}, volume = {13}, year = {2007}, month = {2007 Jan}, pages = {5-14}, abstract = {

The removal of introns from the primary transcripts of protein-coding genes is accomplished by the spliceosome, a large macromolecular complex of which small nuclear RNAs (snRNAs) are crucial components. Following the recent sequencing of the honeybee (Apis mellifera) genome, we used various computational methods, ranging from sequence similarity search to RNA secondary structure prediction, to search for putative snRNA genes (including their promoters) and to examine their pattern of conservation among 11 available insect genomes (A. mellifera, Tribolium castaneum, Bombyx mori, Anopheles gambiae, Aedes aegypti, and six Drosophila species). We identified candidates for all nine spliceosomal snRNA genes in all the analyzed genomes. All the species contain a similar number of snRNA genes, with the exception of A. aegypti, whose genome contains more U1, U2, and U5 genes, and A. mellifera, whose genome contains fewer U2 and U5 genes. We found that snRNA genes are generally more closely related to homologs within the same genus than to those in other genera. Promoter regions for all spliceosomal snRNA genes within each insect species share similar sequence motifs that are likely to correspond to the PSEA (proximal sequence element A), the binding site for snRNA activating protein complex, but these promoter elements vary in sequence among the five insect families surveyed here. In contrast to the other insect species investigated, Dipteran genomes are characterized by a rapid evolution (or loss) of components of the U12 spliceosome and a striking loss of U12-type introns.

}, keywords = {Animals, Base Sequence, Bees, Computational Biology, Diptera, Evolution, Molecular, Genes, Insect, Genome, Insect, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, Promoter Regions, Genetic, RNA Splicing, RNA, Small Nuclear, Sequence Analysis, RNA, Spliceosomes}, issn = {1355-8382}, doi = {10.1261/rna.259207}, author = {Mount, Stephen M and Gotea, Valer and Lin, Chiao-Feng and Hernandez, Kristina and Makalowski, Wojciech} } @article {49695, title = {AT-AC introns: an ATtACk on dogma.}, journal = {Science}, volume = {271}, year = {1996}, month = {1996 Mar 22}, pages = {1690-2}, keywords = {Animals, Base Composition, Base Sequence, Consensus Sequence, HUMANS, Introns, Molecular Sequence Data, Mutation, RNA Precursors, RNA Splicing, RNA, Small Nuclear, Spliceosomes}, issn = {0036-8075}, author = {Mount, S M} } @article {49698, title = {Suppressor U1 snRNAs in Drosophila.}, journal = {Genetics}, volume = {138}, year = {1994}, month = {1994 Oct}, pages = {365-78}, abstract = {

Although the role of U1 small nuclear RNAs (snRNAs) in 5{\textquoteright} splice site recognition is well established, suppressor U1 snRNAs active in intact multicellular animals have been lacking. Here we describe suppression of a 5{\textquoteright} splice site mutation in the Drosophila melanogaster white gene (wDR18) by compensatory changes in U1 snRNA. Mutation of positions -1 and +6 of the 5{\textquoteright} splice site of the second intron (ACG[GTGAGT to ACC]GTGAGC) results in the accumulation of RNA retaining this 74-nucleotide intron in both transfected cells and transgenic flies. U1-3G, a suppressor U1 snRNA which restores base-pairing at position +6 of the mutant intron, increases the ratio of spliced to unspliced wDR18 RNA up to fivefold in transfected Schneider cells and increases eye pigmentation in wDR18 flies. U1-9G, which targets position -1, suppresses wDR18 in transfected cells less well. U1-3G,9G has the same effect as U1-3G although it accumulates to lower levels. Suppression of wDR18 has revealed that the U1b embryonic variant (G134 to U) is active in Schneider cells and pupal eye discs. However, the combination of 9G with 134U leads to reduced accumulation of both U1b-9G and U1b-3G,9G, possibly because nucleotides 9 and 134 both participate in a potential long-range intramolecular base-pairing interaction. High levels of functional U1-3G suppressor reduce both viability and fertility in transformed flies. These results show that, despite the difficulties inherent in stably altering splice site selection in multicellular organisms, it is possible to obtain suppressor U1 snRNAs in flies.

}, keywords = {Alternative Splicing, Animals, Base Sequence, Cell Line, Cell Nucleus, DNA Primers, Drosophila melanogaster, Female, Genes, Suppressor, Genetic Variation, GENOTYPE, Introns, Male, Molecular Sequence Data, Mutagenesis, Site-Directed, Nucleic Acid Conformation, Oligodeoxyribonucleotides, PHENOTYPE, Recombinant Proteins, Ribonucleoprotein, U1 Small Nuclear, RNA, Small Nuclear, Transfection, Transformation, Genetic}, issn = {0016-6731}, author = {Lo, P C and Roy, D and Mount, S M} } @article {49704, title = {Drosophila melanogaster genes for U1 snRNA variants and their expression during development.}, journal = {Nucleic Acids Res}, volume = {18}, year = {1990}, month = {1990 Dec 11}, pages = {6971-9}, abstract = {

We have cloned and characterized a complete set of seven U1-related sequences from Drosophila melanogaster. These sequences are located at the three cytogenetic loci 21D, 82E, and 95C. Three of these sequences have been previously studied: one U1 gene at 21D which encodes the prototype U1 sequence (U1a), one U1 gene at 82E which encodes a U1 variant with a single nucleotide substitution (U1b), and a pseudogene at 82E. The four previously uncharacterized genes are another U1b gene at 82E, two additional U1a genes at 95C, and a U1 gene at 95C which encodes a new variant (U1c) with a distinct single nucleotide change relative to U1a. Three blocks of 5{\textquoteright} flanking sequence similarity are common to all six full length genes. Using specific primer extension assays, we have observed that the U1b RNA is expressed in Drosophila Kc cells and is associated with snRNP proteins, suggesting that the U1b-containing snRNP particles are able to participate in the process of pre-mRNA splicing. We have also examined the expression throughout Drosophila development of the two U1 variants relative to the prototype sequence. The U1c variant is undetectable by our methods, while the U1b variant exhibits a primarily embryonic pattern reminiscent of the expression of certain U1 variants in sea urchin, Xenopus, and mouse.

}, keywords = {Animals, Base Sequence, Blotting, Southern, Cloning, Molecular, Drosophila melanogaster, Gene Expression Regulation, genes, Genetic Variation, Molecular Sequence Data, Nucleic Acid Conformation, Pseudogenes, Restriction Mapping, RNA, Small Nuclear}, issn = {0305-1048}, author = {Lo, P C and Mount, S M} } @article {49715, title = {Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites.}, journal = {Cell}, volume = {32}, year = {1983}, month = {1983 Feb}, pages = {461-72}, abstract = {

We find that both human and rat U3 snRNA can function as self-priming templates for AMV reverse transcriptase in vitro. The 74 base cDNA is primed by the 3{\textquoteright} end of intact U3 snRNA, and spans the characteristically truncated 69 or 70 base U3 sequence found in four different human U3 pseudogenes. The ability of human and rat U3 snRNA to self-prime is consistent with a U3 secondary structure model derived by a comparison between rat U3 snRNA and the homologous D2 snRNA from Dictyostelium discoideum. We propose that U3 pseudogenes are generated in vivo by integration of a self-primed cDNA copy of U3 snRNA at new chromosomal sites. We also consider the possibility that the same cDNA mediates gene conversion at the 5{\textquoteright} end of bona fide U3 genes where, over the entire region spanned by the U3 cDNA, the two rat U3 sequence variants U3A and U3B are identical.

}, keywords = {Animals, Base Sequence, DNA, genes, HUMANS, Nucleic Acid Conformation, Rats, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, RNA, RNA, Small Nuclear, RNA-Directed DNA Polymerase, Templates, Genetic, Transcription, Genetic}, issn = {0092-8674}, author = {Bernstein, L B and Mount, S M and Weiner, A M} } @article {49719, title = {Sequence of U1 RNA from Drosophila melanogaster: implications for U1 secondary structure and possible involvement in splicing.}, journal = {Nucleic Acids Res}, volume = {9}, year = {1981}, month = {1981 Dec 11}, pages = {6351-68}, abstract = {

U1 RNA from cultured Drosophila melanogaster cells (Kc) was identified by its ability to be recognized, as an RNP, by anti-(U1)RNP antibodies from human lupus patients. Its sequence was deduced largely from direct analysis of the RNA molecule and then confirmed by DNA sequence determinations on a genomic clone isolated by hybridization to Drosophila U1 RNA. The Drosophila U1 RNA sequence exhibits 72\% agreement with human U1 RNA. Nucleotides 3-11, which are complementary to the entire consensus sequence for donor (5{\textquoteright}) splice junctions in hnRNA, and to part of the acceptor (3{\textquoteright}) consensus, are exactly conserved. However, nucleotides 14-21, postulated to interact only with acceptor junctions, differ. Comparison of the Drosophila U1 sequence with vertebrate U1 sequences allows a particular secondary structure model to be preferred over others. These results are consistent with the hypothesis that U1 snRNPs are involved in splicing, but suggest specific modifications of the model detailing molecular interactions between U1 RNA and hnRNA during the splicing reaction.

}, keywords = {Animals, Antibodies, Autoimmune Diseases, Base Sequence, Cells, Cultured, Cloning, Molecular, Drosophila melanogaster, HUMANS, Lupus Erythematosus, Systemic, Nucleic Acid Conformation, Nucleic Acid Hybridization, Ribonuclease T1, Ribonucleoproteins, RNA, RNA, Small Nuclear}, issn = {0305-1048}, author = {Mount, S M and Steitz, J A} }