Genes for E1, E2, and E3 small nucleolar RNAs.

Abstract

We have found earlier three small nucleolar RNA (snoRNA) species, named El, E2, and E3, that have unique nudeotide sequences and may participate in ribosome formation. The present report shows that there is a monophosphate at the 5' end of each of these three snoRNAs, suggesting that their 5' termini are formed by RNA processing. El, E2, and E3 human genomic sequences were isolated. Apparently, the E2 and E3 loci are genes for the main E2 and E3 RNA species, based on their full homology, while the El locus is a gene for an El RNA sequence variant in HeLa cells. These loci do not have any of the intragenic or flanking sequences known to be functional in other genes. The El gene is located within the first intron of the gene for RCC1, a protein that regulates onset of mitosis. There is subsntial sequence homology between the human E3 gene and flanking regions, and intron 8 and neighboring exons of the gene for mouse translation initiion factor 4AII. Injection of the human El, E2, and E3 genes into Xenopus oocytes generated sequence-specific transcripts of the approximate sizes of the respective snoRNAs. We discus why the available results are compatible with specific transcription and prosing occurring in frog oocytes.Some of the small nuclear RNA genes, such as Ul, U2, U3, U4 and U5, constitute an additional subfamily of genes transcribed by RNA polymerase II, while others, such as U6 and 7SK, represent another class of genes transcribed by RNA polymerase III (1-3). Seven small nucleolar RNAs (snoRNAs) have been described in metazoa (U3, U8, U13, U14, X, Y, and 7-2/MRP) and 12 snoRNAs have been characterized in yeast (U3, U14, snR3, snR4, snR5, snR8, snR9, snR10, snRll, snR30, snR189, and snR190) (4). We recently found three additional snoRNAs in human cells, which were named El, E2, and E3 (5). Their unique sequences imply that they are members of another class of snoRNAs, their 5' termini are not capped, they are present at low levels in vertebrate cells, and they appear to be "housekeeping" RNAs, expressed in all tissues examined (5). They may function in some aspect of ribosome formation, since in addition to being detected only in the nucleolar fraction, they are psoralen-photocrosslinked in vivo to unique segments of pre-rRNA (6). The the snoRNA plasmids when indicated) were injected into the nucleus of oocytes (20 nl per oocyte), which were then incubated at 19°C for 24 hr. When indicated, 2 hr after the plasmid injection [a-32P]GTP was injected into the cytoplasm of half of the oocytes, and then all oocytes were incubated at 19°C for 24 hr. When indicated, the solution containing one or two plasmids also included a-amanitin at 2 or 400 pg/ml ("low" or "high" level, respectively). The deproteinized samples were digested with DNase I [Worthington (code DPFF) or BRL] at 100 pg/ml, with or without RNase A (Sigma) at 40 pg/ml for either 15 min at 22°C or 30 min at 37°C. Nonradioactive RNA was fractionated by 5% (10% for radioactive RNA) polyacrylamide gel electrophoresis and electroblotted to Zeta-Pr...

Characterization of the Intron-Encoded U19 RNA, a New Mammalian Small Nucleolar RNA That Is Not Associated with Fibrillarin

“…Some of these RNAs, e.g., U3, U8, and U13, are transcribed from independent transcription units and contain 5Ј-terminal trimethylguanosine caps. Most snoRNAs, however, are processed from introns of pre-mRNAs (32; reviewed in references 13, 37, and 52) and contain a monophosphate at the 5Ј end (24,42,57), consistent with their processing from longer precursor RNAs.Several snoRNAs have been demonstrated to participate in the processing of pre-rRNA. The U3 snoRNA is involved in the earliest cleavage event, which occurs in the 5Ј external transcribed spacer (19,21,41), and its depletion impairs the accumulation of mature 18S rRNA in the yeast Saccharomyces cerevisiae and vertebrates (19,50).…”

“…Some of these RNAs, e.g., U3, U8, and U13, are transcribed from independent transcription units and contain 5Ј-terminal trimethylguanosine caps. Most snoRNAs, however, are processed from introns of pre-mRNAs (32; reviewed in references 13, 37, and 52) and contain a monophosphate at the 5Ј end (24,42,57), consistent with their processing from longer precursor RNAs.…”

Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns.

“…In contrast to U3, U8, U13, and 7-2/MRP RNAs, most of the other known snoRNAs (U14---U22) are not transcribed from independent genes but are encoded within introns of genes coding for proteins (Liu and Max-well 1990;Leverette et al 1992;Fragapane et al 1993;Kiss and Filipowicz 1993;Prislei et al 1993;Tycowski et al 1993;Cecconi et al 1994;Nicoloso et al 1994;Qu et al 1994;Tycowski et al 1994). Because these snoRNAs are processed from pre-mRNA transcripts, their 5' ends are not capped but, rather, contain a monophosphate group Nag et al 1993;Tycowski et al 1993).…”

Evolutionary patterns of non-coding RNAs

“…blast searches starting from human snoRNAs, for examples, are usually unsuccessful already in non-mammalian vertebrate genomes. As a starting point for investigating the evolution of snoRNAs we have therefore focused on the three snoRNAs that were first discovered [296], since sequences for these examples have been reported from a variety of different vertebrates. All three belong to the H/ACA class and are intron-encoded [369,283].…”