The small nuclear ribonucleoprotein E protein gene contains four introns and has upstream similarities to genes for ribosomal proteins

Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns

Two types of eukaryotic nuclear introns are known: the common U2-dependent class with /GU and AG/ terminal intron dinucleotides, and the rare U12-dependent class with /AU and AC/ termini. Here we show that the U12-dependent splicing system can splice introns with /GU and AG/ termini and that such introns occur naturally. Further, U2-dependent introns with /AU and AC/termini also occur naturally and are evolutionarily conserved. Thus, the sequence of the terminal dinucleotides does not determine which spliceosomal system removes an intron. Rather, the four classes of introns described here can be sorted into two mechanistic classes (U2- or U12-dependent) by inspection of the complete set of conserved splice site sequences.

B-raf oncogene: activation by rearrangements and assignment to human chromosome 7

cDNA clones presumably containing a transforming gene were isolated from transformed NIH3T3 cells, which were obtained by the transfection of DNA from peripheral blood lymphocytes of a familial adenomatous polyposis patient. Sequence analysis of the cDNA clones showed that the gene contained an activated B-raf, the 5' half of which was replaced by the human small nuclear ribonucleoprotein E protein gene and an unknown gene. A partial genomic physical map of the transforming gene was made on the basis of the physical map of the cDNA clones, indicating that rearrangements had occurred during the transfection. The human B-raf gene was shown to be located on chromosome 7 by Southern blotting analysis of rodent-human somatic cell hybrid DNA using the B-raf cDNA as a probe.

Conservation of coding and transcriptional control sequences within the snRNP E protein gene

The snRNP E protein is one of several proteins associated with the U family of small nuclear RNAs that are involved in RNA processing. Isolation and characterization of the snRNP E protein cDNA sequences from mouse and chicken revealed a 100% conservation of the predicted amino acid sequence when compared to that of the human homologue. Further characterization of a genomic clone for the mouse snRNP E protein gene revealed that the 5' untranslated region and the immediate 5' upstream region have also been highly conserved: 72 and 70%, respectively. Conserved 5' regions include multiple copies of the CTTCCG hexamer sequence which are involved in regulating transcription of the human snRNP E protein gene. Mobility shift assays using corresponding DNA fragments from both human and mouse reveal that both fragments can compete for binding of at least one common transcription factor. These studies demonstrate that along with the amino acid sequence conservation between human and mouse, the snRNP E protein gene has also maintained a high DNA sequence conservation within its basal promoter structure.

Structure, chromosomal localization and evolutionary conservation of the gene encoding human U1 snRNP-specific A protein

Three specific proteins, called A, 70K and C, are present in the U1 small nuclear ribonucleoprotein (snRNP) particle, in addition to the common proteins. The human U1 snRNP-specific A protein is, apart from a proline-rich region, highly similar to the U2 snRNP-specific protein B". To examine the homologous regions at the genomic level, we isolated and characterized the human U1-A gene. The human U1-A protein appears to be encoded by a single-copy gene and its locus has been mapped to the q arm of chromosome 19. The gene, about 14-16 kb in length, consists of six exons. The regions homologous to the U2-B" gene are not limited to single exons and are mostly not confined by exon-exon junctions in the corresponding U1-A mRNA. However, the proline-rich region of U1-A, absent in U2-B", is encoded by a single exon, suggesting a specific function for this domain of U1-A. The region of the cap site and upstream sequences contain interesting similarities to the promoter region of other snRNP protein-encoding genes and several housekeeping genes, in particular the vertebrate ribosomal protein-encoding genes. Hybridization experiments with various vertebrate genomic DNAs revealed that U1-A sequences are evolutionarily conserved in all tested vertebrate genomes, except for chicken, duck and pigeon. The divergence of these avian genomes is probably typical for the class of birds.

The snRNP E protein multigene family contains five pseudogenes with common mutations

Sequence data from three previously-uncharacterized members of the snRNP E protein multigene family suggest that each is a non-transcribed processed pseudogene, even though one clone has the potential to code for a full-length protein with greater than 90% similarity to previously-characterized E protein cDNAs. Each of the newly-analyzed family members is without introns, contains a tract of polyadenylic acid residues, and is flanked by short direct repeats. In addition, the three sequences all contain point mutations that distinguish them from the E protein coding sequence. Seven point mutations are common to the three sequences described here and to two previously-described E protein pseudogenes. Although all of these mutations are transitions, only 5 of 7 could have been generated by deamination of methylated cytosines in inactive genes. Thus, the common mutations in the pseudogenes suggest an origin other than the expressed gene that we have described. Allelic variants for two of the pseudogenes were detected and repetitive elements are located near four of the five E protein pseudogenes that have been characterized.

Assignment of the gene for the small nuclear ribonucleoprotein E (SNRPE) to human chromosome 1q25-q43

Small nuclear ribonucleoproteins (snRNPs), which are composed of various U RNAs and several proteins, are components of the mRNA splicing apparatus. The snRNP protein E is encoded by a multigene family which consists of a single expressed gene and several processed pseudogenes. We have used somatic cell hybridization, in situ hybridization, and linkage analysis to both physically and genetically map the expressed E protein gene to human chromosome 1q25-43, with the most probable location being band 1q32. In addition to the snRNP E protein gene, two other snRNP components--the U1 RNA true multigene family and a group of class I U1 pseudogenes--are located on human chromosome 1.