Alternative titles; symbols
HGNC Approved Gene Symbol: RNU2-1
Cytogenetic location: 17q21.31 Genomic coordinates (GRCh38): 17:43,233,790-43,233,977 (from NCBI)
Westin et al. (1984) found that genes for human nuclear RNA U2 are present within 6.2-kb-long tandem repeats. The haploid human genome contains about 20 such repeats, organized in 1 or a few large clusters. Like U1 snRNA (180680), U2 snRNA is thought to be involved in RNA processing.
As reviewed by Sharp (1987), the splicing of nuclear mRNA precursors involves the formation of a multicomponent complex, the spliceosome. This splicing body contains at least 3 different small nuclear ribonucleoprotein particles (snRNPs), U2, U5 (see 180691), and U4 plus U6 (see 180692). A complex containing precursor RNA and the U2 snRNP particle is a likely intermediate in the formation of the spliceosome.
Valadkhan and Manley (2001) demonstrated that a protein-free complex of 2 snRNAs, U2 and U6, can bind and position a small RNA containing the sequence of the intron branch site, and activate the branch adenosine to attack a catalytically critical domain of U6 in a reaction that is related to the first step of splicing. Valadkhan and Manley (2001) concluded that their data provide direct evidence for the catalytic potential of spliceosomal snRNAs.
Transcription, 5-prime capping, 3-prime polyadenylation, and splicing of pre-mRNA are coupled in vivo. Kyburz et al. (2006) found that proteins of the U2 snRNP were associated with CPSF (see CPSF1; 606027). CPSF was necessary for efficient splicing activity in coupled assays, and mutations in the pre-mRNA binding site of the U2 snRNP resulted in impaired splicing and reduced cleavage efficiency. Efficient cleavage required the presence of U2 snRNA in coupled assays. Kyburz et al. (2006) concluded that interaction between CPSF and U2 snRNP contributes to the coupling of splicing and 3-prime end formation.
Chen et al. (2020) found that internal levels of N6,2-prime-O-dimethyladenosine (m6Am) in total RNA were significantly reduced in METTL4 (619626)-knockout human cells, and that m6Am levels could be rescued by reexpression of wildtype METTL4. Further analysis demonstrated that U2 snRNA was a substrate of METTL4, with METTL4 mediating methylation on m6Am of U2 snRNA at position 30, with a preferred sequence motif of AAG and a requirement for predeposited 2-prime-O-methylation. RNA-sequencing analysis suggested that METTL4 was involved in RNA splicing regulation by mediating internal m6Am methylation of U2 small nuclear RNA.
Independently, Goh et al. (2020) found that METTL4 was necessary for formation of m6Am within U2 snRNA, as m6Am of U2 snRNA was absent in METTL4-knockout HEK293T cells. In vitro analysis with purified recombinant proteins revealed that METTL4 directly catalyzed N6 methylation of internal Am at position 30 of U2 snRNA to m6Am, and that the reaction required the METTL4 DPPW catalytic motif. METTL4 could also N6-methylate A into m6A, but it preferred Am over A, with A in the middle of CAAGUG in U2 snRNA as the target substrate sequence for METTL4. In vivo, METTL4 directly catalyzed N6 methylation of U2 snRNA Am and rescued loss of m6Am in U2 snRNA of METTL4-knockout cells. Overexpression of METTL4 showed that HMAGKD (with H = A/C/U, M = A/C, K = G/U, D = A/G/U, and A as the methylation site) was the preferred target sequence motif of METTL4, with cis- or trans-acting elements associated with the coding sequence helping guide methylation by METTL4. N6 methylation of U2 snRNA regulated pre-mRNA splicing, as METTL4 knockout repressed splicing and increased cassette exon inclusion or splicing of retained introns, with exhibition of features like splice-site weakness and short introns.
By in situ hybridization, Lindgren et al. (1984) assigned the RNU2 genes to chromosome 17q21-q22. Whereas the U1 genes are loosely clustered in chromosomal band 1p36 with intergenic distances exceeding 44 kb, the 10 to 20 U2 genes are clustered tightly in a virtually perfect tandem array (Lindgren et al., 1985).
Liao et al. (1997) stated that the U2 locus consists of 6 to more than 30 tandem repeats spanning from 37 to more than 200 kb. They examined individual U2 tandem arrays from 8 diverse populations, and found that the arrays are homogeneous for each polymorphic marker examined, although the alleles can occur in any combination and undergo random assortment on an evolutionary time scale. Furthermore, there is no exchange of flanking markers, which led Liao et al. (1997) to suggest that the primary driving force for the observed concerted evolution is gene conversion and/or sister chromatid exchange.
Lindgren et al. (1985) pointed out that the U2 genes map to chromosome 17q21-q22, 1 of 3 major adenovirus-12 modification sites that undergo chromosome decondensation in permissive human cells infected by highly oncogenic strains of adenovirus. The 2 other major modification sites, 1p36 and 1q21, coincide with the locations of U1 genes and class I U1 pseudogenes, respectively. Thus, Lindgren et al. (1985) suggested that snRNA genes are the major targets of viral chromosome modification.
Using in situ hybridization, Durnam et al. (1988) found that the RNU2 gene cluster maps very close to, and is frequently disrupted by, the gaps and breaks induced in 17q21-q22 by adenovirus-12. Restriction mapping showed no structural alterations in the U2 gene locus as a result of adenovirus-12 infection; moreover, no alterations in the level of U2 RNA were detected as a result of infection.
Gargano et al. (1995) stated that a fourth chromosomal region (that of the 5S rRNAs at 1q42-q43; 180420) is affected by adenovirus-12. The ability of adenovirus-12 to induce fragile sites requires expression of viral proteins, but not viral integration. Using U2 constructs integrated at various sites in the genome of human cells, Gargano et al. (1995) found that a transcriptionally competent U2 gene is necessary and sufficient for virus-induced fragility.
Chen, H., Gu, L., Orellana, E. A., Wang, Y., Guo, J., Lui, Q., Wang, L., Shen, Z., Wu, H., Gregory, R. I., Xing, Y., Shi, Y. METTL4 is an snRNA m6Am methyltransferase that regulates RNA splicing. Cell Res. 30: 544-547, 2020. [PubMed: 31913360] [Full Text: https://doi.org/10.1038/s41422-019-0270-4]
Durnam, D. M., Menninger, J. C., Chandler, S. H., Smith, P. P., McDougall, J. K. A fragile site in the human U2 small nuclear RNA gene cluster is revealed by adenovirus type 12 infection. Molec. Cell. Biol. 8: 1863-1867, 1988. [PubMed: 3386628] [Full Text: https://doi.org/10.1128/mcb.8.5.1863-1867.1988]
Gargano, S., Wang, P., Rusanganwa, E., Bacchetti, S. The transcriptionally competent U2 gene is necessary and sufficient for adenovirus type 12 induction of the fragile site at 17q21-22. Molec. Cell. Biol. 15: 6256-6261, 1995. [PubMed: 7565778] [Full Text: https://doi.org/10.1128/MCB.15.11.6256]
Goh, Y. T., Koh, C. W. Q., Sim, D. Y., Roca, X., Goh, W. S. S. METTL4 catalyzes m6Am methylation in U2 snRNA to regulate pre-mRNA splicing. Nucleic Acids Res. 48: 9250-9261, 2020. [PubMed: 32813009] [Full Text: https://doi.org/10.1093/nar/gkaa684]
Kyburz, A., Friedlein, A., Langen, H., Keller, W. Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3-prime end processing and splicing. Molec. Cell 23: 195-205, 2006. [PubMed: 16857586] [Full Text: https://doi.org/10.1016/j.molcel.2006.05.037]
Liao, D., Pavelitz, T., Kidd, J. R., Kidd, K. K., Weiner, A. M. Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion. EMBO J. 16: 588-598, 1997. [PubMed: 9034341] [Full Text: https://doi.org/10.1093/emboj/16.3.588]
Lindgren, V., Ares, M., Bernstein, L. B., Weiner, A. M., Francke, U. Mapping of human small nuclear RNA genes by in situ hybridization. (Abstract) Am. J. Hum. Genet. 36: 101S only, 1984.
Lindgren, V., Ares, M., Jr., Weiner, A. M., Francke, U. Human genes for U2 small nuclear RNA map to a major adenovirus 12 modification site on chromosome 17. Nature 314: 115-116, 1985. [PubMed: 2579339] [Full Text: https://doi.org/10.1038/314115a0]
Lindgren, V., Bernstein, L. B., Weiner, A. M., Francke, U. Human U1 small nuclear RNA pseudogenes are clustered in 1q12-q22, a region distinct from the site of the U1 genes. (Abstract) Cytogenet. Cell Genet. 40: 680-681, 1985.
Sharp, P. A. Splicing of messenger RNA precursors. Science 235: 766-771, 1987. Note: Erratum: Science 237: 964 only, 1987. [PubMed: 3544217] [Full Text: https://doi.org/10.1126/science.3544217]
Valadkhan, S., Manley, J. L. Splicing-related catalysis by protein-free snRNAs. Nature 413: 701-707, 2001. [PubMed: 11607023] [Full Text: https://doi.org/10.1038/35099500]
Westin, G., Zabielski, J., Hammarstrom, K., Monstein, H.-J., Bark, C., Pettersson, U. Clustered genes for human U2 RNA. Proc. Nat. Acad. Sci. 81: 3811-3815, 1984. [PubMed: 6203126] [Full Text: https://doi.org/10.1073/pnas.81.12.3811]