Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome.

Abstract

We have cloned and partially characterized 24 loci from the human genome which are complementary to U1, U2, or U3, the three major species of small nuclear RNA (snRNA) in HeLa cells. When compared to the known Ul (human) and U2 (rat) snRNA sequences, the DNA sequences we report here for the complementary regions from two of the clones, Ul Among the various classes of molecules found in all eukaryotic cells, the small nuclear RNAs (snRNAs) have received relatively little attention until recently. The sequences of eight of these small homogeneous RNA species from mammalian cells (Ul, U2, U3A, U3B, U4, U5, U6, and 4.5S RNA) have been determined (1-6). U3 snRNA is found in the nucleolus, and other snRNA species are associated with either the nucleoskeleton or the nucleoplasm (7). At least three of the snRNAs are subject to considerable evolutionary conservation: Ul and U2 snRNA from chicken, rat, mouse, and human cells yield identical ribonuclease Ti fingerprints (1,8,9), and the RNA sequences of U1 from HeLa cells and Ula from rat Novikoff hepatoma differ in only 2 of 165 positions (1). We have also shown that a snRNA from the lower eukaryotic cellular slime mold Dictyostelium discoideum is over 40% homologous to U3 snRNA from the rat (10).Two recent developments have prompted new interest in the intracellular packaging and function of the snRNAs. First, antibodies produced by patients with the autoimmune disease systemic lupus erythematosus have been shown to recognize discrete cellular components that contain snRNAs complexed with a defined set of proteins (8), thus opening the way for detailed structural studies of small nuclear ribonucleoprotein particles. Second, Lerner et al. (9) (kb) (17).We originally decided to clone the genes encoding snRNAs in the hope that a systematic investigation of their organization and expression would also open up new avenues for understanding the function of the snRNAs themselves. We report here the surprising result that most, if not all, of the genomic loci complementary to snRNAs U1, U2, and U3 that we have examined contain divergent, and in some cases truncated, gene copies when compared with the corresponding HeLa cell snRNA species. MATERIALS AND METHODSA library of 15-kb partial EcoRI fragments of human placental DNA in the A vector Charon 4A (18) was kindly supplied by A. Biro, P. V. Choudary, J. T. Elder, and S. M. Weissman. Plaques were screened by the method of Benton and Davis (19); we used as probes U1, U2, and U3 snRNAs isolated from HeLa cells and labeled in vitro at the 3' end with 5'-32P-labeled pCp and T4 RNA ligase as described (14). As little as 106 cpm of snRNA at a specific activity of 106 cpm/,ug was sufficient to screen six 140-mm nitrocellulose filters, each bearing 8000 plaques. With each probe, 0. 1% of the plaques were scored as positive and repurified for further study. Small quantities of recombinant DNA were prepared from 4-ml NZY cultures (20); larger quantities were prepared from recombinant phage grown and purified as described (18)....

The trypanosome spliced leader small RNA gene family: stage-specific modification of one of several similar dispersed genes

“…The most well-studied orphons, aside from those presented here, are those of the histone gene family of the sea urchin (1), those of a gene cluster which encodes six tRNAs in X. laevis (2), and those of the U small nuclear (sn) RNA gene families of man (4,34,35,36 The phylogeny of the orphon flanking regions parallels that of the SL reiteration unit. Despite the fact that trypanosomatids as diverse as L. collosoma, a parasite of insects, and T. brucei, possess sequences homologous to the SL organized in tandem arrays and orphon elements (6), the reiteration unit in which the SL resides is species-specific (40).…”

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

“…In particular in mammals, the analysis is complicated by high copy number of snRNAs of the major spliceosome and an associated large number of pseudogenes [13]. We focus here on four questions: (1) Is there evidence for discernible paralog groups of snRNAs in some clades?…”

Human genes for U2 small nuclear RNA are tandemly repeated.

“…U2 RNA, as well as the snRNAs Ul, U4, U5, and U6 exist as components of small nuclear ribonucleoprotein particles (13,14,17). Indirect evidence suggests that Ul small nuclear ribonucleoproteins play a role in the nuclear splicing of mRNA precursors (16,23), and a similar role for U2 small nuclear ribonucleoproteins has been proposed (28; but see reference 4).The initial characterization of the multigene families for human Ul, U2, U3, U4, and U6 snRNAs has established that most of the human chromosomal loci complementary to these snRNAs are actually defective gene copies, or pseudogenes, which appear to be dispersed in the genome (2,8,9,11,12,19,22,36,41 Fig. 2A and C) was labeled in vitro with [c-32P]dATP by primed synthesis of the complementary strand.…”