Cloning and characterization of rat 4.5S RNAI genes

4.5SI RNA genes and the role of their 5'-flanking sequences in the gene transcription

4.5S(I) RNA is a small nuclear RNA synthesized by RNA polymerase III and detected in rodents of only four families. Hundreds of copies of this RNA retropseudogenes are interspersed throughout the mouse (Mus musculus) and rat (Rattus norvegicus) genomes. We found a single locus containing 4.5S(I) RNA genes in the genomes of these rodents. The locus harbors three genes and occupies 80 kb on M. musculus chromosome 6 and 44 kb on R. norvegicus chromosome 4. Two long duplications seem to have taken place during evolution of this locus. Two mouse 4.5S(I) RNA genes were used for a study of the role of 5'-flanking sequences in transcription in vitro and ex vivo. We found that removal of these DNA sequences resulted in a dramatic reduction of transcription though an internal promoter for RNA polymerase III was preserved in 4.5S(I) RNA genes. Thus, 5'-flanking sequences (from -1 to -90) containing conserved regions are important for 4.5S(I) RNA gene expression.

Evolutionary history of 4.5SH RNA

4.5SH RNA is a 94-nt small RNA with unknown function. This RNA is known to be present in the mouse, rat, and hamster cells; however, it is not found in human, rabbit, and chicken. In the mouse genome, the 4.5SH RNA gene is a part of a long (4.2 kb) tandem repeat ( approximately 800 copies) unit. Here, we found that 4.5SH RNA genes are present only in rodents of six families that comprise the Myodonta clade: Muridae, Cricetidae, Spalacidae, Rhizomyidae, Zapodidae, and Dipodidae. The analysis of complementary DNA derived from the rodents of these families showed general evolutionary conservation of 4.5SH RNA and some intraspecific heterogeneity of these RNA molecules. 4.5SH RNA genes in the Norway rat, mole rat, hamster and jerboa genomes are included in the repeated sequences. In the jerboa genome these repeats are 4.0-kb long and arranged tandemly, similar to the corresponding arrangements in the mouse and rat genomic DNA. Sequencing of the rat and jerboa DNA repeats containing 4.5SH RNA genes showed fast evolution of the gene-flanking sequences. The repeat sequences of the distantly related rodents (mouse and rat vs. jerboa) have no apparent similarity except for the 4.5SH RNA gene itself. Conservation of the 4.5SH RNA gene nucleotide sequence indicates that this RNA is likely to be under selection pressure and, thus, may have a function. The repeats from the different rodents have similar lengths and contain many simple short repeats. The data obtained suggest that long insertions, deletions, and simple sequence amplifications significantly contribute in the evolution of the repeats containing 4.5SH RNA genes. The 4.5SH RNA gene seems to have originated 50-85 MYA in a Myodonta ancestor from a copy of the B1 short interspersed element. The amplification of the gene with the flanking sequences could result from the supposed cellular requirement of the intensive synthesis of 4.5SH RNA. Further Myodonta evolution led to dramatic changes of the repeat sequences in every lineage with the conservation of the 4.5SH RNA genes only. This gene, like some other relatively recently originated genes, could be a useful model for studying generation and evolution of non-protein-coding genes.

Complete genomic sequence and analysis of the prion protein gene region from three mammalian species

The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we sequenced 10(5) bp of DNA from clones containing human, sheep, and mouse PrP genes isolated in cosmids or lambda phage. Our findings are as follows: (1) Although the human PrP transcript does not include the untranslated exon 2 found in its mouse and sheep counterparts, the large intron of the human PrP gene contains an exon 2-like sequence flanked by consensus splice acceptor and donor sites. (2) The mouse Prnpa but not the Prnpb allele found in 44 inbred lines contains a 6593 nucleotide retroviral genome inserted into the anticoding strand of intron 2. This intracisternal A-particle element is flanked by duplications of an AAGGCT nucleotide motif. (3) We found that the PrP gene regions contain from 40% to 57% genome-wide repetitive elements that independently increased the size of the locus in all three species by numerous mutations. The unusually long sheep PrP 3'-untranslated region contains a "fossil" 1.2-kb mariner transposable element. (4) We identified sequences in noncoding DNA that are conserved between the three species and may represent biologically functional sites.

A family of U1 pseudogenes in Bombyx mori may be derived from an ancestral pseudogene

Seven EMBL-4 lambda clones containing U1 small nuclear RNA sequences were isolated from a Bombyx mori genomic library. Six of the seven represent unique sequences. The six unique U1 sequences exhibit fixed point 3'-end truncation. Five out of the six clones share immediate 3'-end flanking sequences while two share 5'-end flanking sequences. Fixed point 3'-end truncation and a hierarchy of shared to unique diagnostic mutations may suggest a family of U1 pseudogenes generated from a reverse-transcribed class II pseudogene in B. mori. An ancestral 'master' U1 pseudogene capable of RNA- and/or DNA-mediated transposition may give rise to generations of U1 pseudogenes that include the original pseudogene's flanking sequences. Identical 3'-end truncation in some of these U1 sequences can be explained by RNA self-priming due to intra-strand binding prior to reverse transcription.

Promoter region of the rat gene encoding ornithine aminotransferase: transcriptional activity, sequence, and DNase-I-hypersensitive sites

In the rat, the gene (rOAT) encoding ornithine aminotransferase (OAT) is expressed in all cell types examined; however, regulation of rOAT expression is complex and cell-type specific. Various regions of the rOAT 5' flanking domain were cloned upstream from the cat reporter gene, and the expression of these OAT::cat fusions was examined following transfection into rat kidney epithelial cells (NRK-52E), human embryonic kidney cells (293), and rat hepatoma cells (H-4-II-E). Although these experiments suggested the presence of one or more positive regulatory elements between nucleotides -661 and -158, and one or more negative elements upstream from nt -897, none of these putative elements appeared to function in a cell-type-specific manner. The nt sequence of 2531 bp of the rOAT domain flanking the promoter revealed several putative promoter/enhancer elements in positions analogous to the human OAT gene, numerous AGGTCA-like motifs related to the binding sites for the estrogen and thyroid hormone receptors, and multiple motifs resembling a putative regulatory element associated with genes encoding enzymes of the urea cycle. Finally, sensitivity of the 5' end of rOAT to cleavage by DNase I was examined, as DNase-I-hypersensitive sites (DHS) are often found in association with cis-acting regulatory elements. Two DHS were identified; one DHS approximately 140 bp upstream, and the second DHS approximately 300 bp downstream, of the transcription start point (tsp). These data provide the foundation upon which to base future studies aimed at elucidating the molecular mechanisms through which rOAT expression is regulated in a cell-type specific manner.

Evidence for a relationship between the Bombyx mori middle repetitive Bm1 sequence family and U1 snRNA

Several genomic library equivalents of Bombyx mori were constructed in the EMBL-4 lambda derivative. The genomic bank was screened with purified Bombyx mori U1 RNA and twenty positive clones for the U1 gene were isolated. Three U1-related sequences were subcloned and sequenced. Two of the sequences are U1 pseudogenes while a third sequence represents a member of the Bm 1 family of repetitive elements of B.mori with significant sequence similarity to U1 small nuclear RNA. The U1-related Bm1 element exhibits 82% sequence similarity with the Bm1 consensus sequence and, under less stringent computer comparison parameters, 60% similarity with a composite B.mori/Drosophila melanogaster U1 gene. The Bm1 family consensus sequence exhibits 53% sequence similarity with the composite U1 gene. The two pseudogenes possess highly conserved sequences with the B.mori U1 gene only for the first 101 nucleotides. These findings are indicative of at least two different categories of U1-related sequences in B.mori, one with a possible evolutionary relationship to the Bm1 family of repetitive elements and the other representing characteristic processed pseudogenes with retroposon mode of dispersion and target selection for the TTTA hotspot. In addition, the U1-related Bm1 element may demonstrate for the first time that a family of retroposons is ultimately derived from a U snRNA.

Small B2 RNAs in mouse oocytes, embryos, and somatic tissues

RNAs of full-grown mouse oocytes, ovulated eggs, embryos, and somatic tissues have been analyzed on Northern blots for the presence of small transcripts homologous to the B2 element, a repetitive 180-nucleotide (N) sequence in the genome, using a single stranded RNA probe. In addition to the heterogeneous 200- to 600-N polyadenylated group reported by others, cytoplasmic RNA contains discrete nonadenylated species of B2-related RNA, approximately 100, 120, 155, and 180 N in length. During meiotic maturation of oocytes, the 200- to 600-N group declines and the 155-N species becomes more prominent. Upon hybridization to oligo(dT) and cleavage with RNase H to remove poly(A) regions, the 200- to 600-N group is removed, the 180-N species increased greatly, and the 155-N species increased slightly. Essentially all of the 200- to 600-N species bind to poly(U) sepharose. We conclude that polyadenylation rather than run-on transcription of B2 elements accounts for most of the heterogeneity of the 200- to 600-N group and that some deadenylation and cleavage take place during maturation. Small B2 RNAs make up 0.04% of total RNA in oocytes and eggs, 6- to 9-fold more than in brain. For comparison, a known small RNA, 4.5 S RNA, is relatively sparse in oocytes and almost absent in eggs. The 100-N B2-related species has been tentatively identified as 4.5 SI RNA; relative to total RNA, it remains approximately constant in oocytes and somatic tissues. During development to the blastocyst stage, small B2 RNAs per embryo increase severalfold, but decline as a fraction of total RNA. In postimplantation development, they continue to decline toward the level found in brain. Expression of B2 transcripts in hnRNA rises around 10 days of development to the level found in brain. The time course of expression of small B2 RNAs suggests an important role in development.

Metabolism of U6 RNA species in nonirradiated and UV-irradiated mammalian cells

We observed a series of rapidly labeled U6 RNA bands, which were hybrid selected with U6 DNA, in nonirradiated human cells. The electrophoretic mobility of these bands in denaturing gels was lower than that of the known mature U6 RNA species, and was equivalent to transcripts up to approximately 7 nucleotides longer. These multiple U6 RNA species lost their label during a chase without a proportional increase in radioactivity in the known mature U6 RNA, which suggests that a substantial fraction is not processed into the major mature U6 RNA. During a label chase, the multiple U6 RNA bands appeared first in the cytoplasmic fraction and later in nuclei. One of the major rapidly labeled U6 RNA bands had the electrophoretic mobility of an RNA species one nucleotide shorter than the known mature U6 RNA. UV light induced a UV dose-dependent, preferential disappearance of recently synthesized molecules of the U6 RNA species of higher gel electrophoretic mobility, including the known mature U6 RNA. Since this effect was seen in cells pulse-labeled immediately before or after irradiation, it suggests that UV radiation induces the specific degradation of the electrophoretically faster moving species of U6 RNA, which are apparently shorter chains. The effect of UV light was RNA species-specific, was not seen in molecules synthesized long (e.g., 22 hr) before irradiation, and occurred in human and mouse cells.