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. 1984 Oct 11;12(19):7411–7421. doi: 10.1093/nar/12.19.7411

Three linked chicken U1 RNA genes have limited flanking DNA sequence homologies that reveal potential regulatory signals.

J M Earley 3rd, K A Roebuck, W E Stumph
PMCID: PMC320171  PMID: 6208531

Abstract

We have isolated and characterized a cluster of three closely linked chicken U1 RNA genes from a lambda genomic library. These genes, which are completely collinear and homologous in sequence to chicken U1 RNA, are spaced about 1.8 kilobase pairs (kb) apart in the chicken genome. However, they are not tandemly repeated in that one of the genes has an inverse transcriptional orientation relative to the other two genes which are adjacent in the cluster. A comparison of sequences flanking the 5' ends of these genes reveals that homology is generally limited to a region around position -200 and to the region from -59 to -1. None of the genes possess a "TATA" box near the -25 position. The chicken sequences were compared to various mammalian snRNA genes and significant homology was observed around positions -200, -55 and -20. These data suggest that U1 RNA genes utilize an unusual RNA polymerase II promoter signal and that potential regulatory sequences are located as far as 200 bp upstream from the mature U1 RNA cap site.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Azorin F., Nordheim A., Rich A. Formation of Z-DNA in negatively supercoiled plasmids is sensitive to small changes in salt concentration within the physiological range. EMBO J. 1983;2(5):649–655. doi: 10.1002/j.1460-2075.1983.tb01479.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Beck E., Jorcano J. L., Alonso A. Drosophila melanogaster U1 and U2 small nuclear RNA genes contain common flanking sequences. J Mol Biol. 1984 Mar 15;173(4):539–542. doi: 10.1016/0022-2836(84)90397-8. [DOI] [PubMed] [Google Scholar]
  3. Branlant C., Krol A., Ebel J. P., Lazar E., Gallinaro H., Jacob M., Sri-Widada J., Jeanteur P. Nucleotide sequences of nuclear U1A RNAs from chicken, rat and man. Nucleic Acids Res. 1980 Sep 25;8(18):4143–4154. doi: 10.1093/nar/8.18.4143. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Card C. O., Morris G. F., Brown D. T., Marzluff W. F. Sea urchin small nuclear RNA genes are organized in distinct tandemly repeating units. Nucleic Acids Res. 1982 Dec 11;10(23):7677–7688. doi: 10.1093/nar/10.23.7677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Denison R. A., Weiner A. M. Human U1 RNA pseudogenes may be generated by both DNA- and RNA-mediated mechanisms. Mol Cell Biol. 1982 Jul;2(7):815–828. doi: 10.1128/mcb.2.7.815. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Eliceiri G. L. Formation of low molecular weight RNA species in HeLa cells. J Cell Physiol. 1980 Feb;102(2):199–207. doi: 10.1002/jcp.1041020211. [DOI] [PubMed] [Google Scholar]
  7. Eliceiri G. L., Smith J. H. Sensitivity to UV radiation of small nuclear RNA synthesis in mammalian cells. Mol Cell Biol. 1983 Dec;3(12):2151–2155. doi: 10.1128/mcb.3.12.2151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Frederiksen S., Hellung-Larsen P., Gram Jensen E. The differential inhibitory effect of alpha-amanitin on the synthesis of low molecular weight RNA components in BHK cells. FEBS Lett. 1978 Mar 15;87(2):227–231. doi: 10.1016/0014-5793(78)80338-x. [DOI] [PubMed] [Google Scholar]
  9. Hernandez N., Keller W. Splicing of in vitro synthesized messenger RNA precursors in HeLa cell extracts. Cell. 1983 Nov;35(1):89–99. doi: 10.1016/0092-8674(83)90211-8. [DOI] [PubMed] [Google Scholar]
  10. Jensen E. G., Hellung-Larsen P., Frederiksen S. Synthesis of low molecular weight RNA components A, C and D by polymerase II in alpha-amanitin-resistant hamster cells. Nucleic Acids Res. 1979 Jan;6(1):321–330. doi: 10.1093/nar/6.1.321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kristo P., Tsai M. J., O'Malley B. W. Characterization of three chicken pseudogenes for U1 RNA. DNA. 1984 Aug;3(4):281–286. doi: 10.1089/dna.1.1984.3.281. [DOI] [PubMed] [Google Scholar]
  12. Lerner M. R., Boyle J. A., Mount S. M., Wolin S. L., Steitz J. A. Are snRNPs involved in splicing? Nature. 1980 Jan 10;283(5743):220–224. doi: 10.1038/283220a0. [DOI] [PubMed] [Google Scholar]
  13. Lund E., Bostock C., Robertson M., Christie S., Mitchen J. L., Dahlberg J. E. U1 small nuclear RNA genes are located on human chromosome 1 and are expressed in mouse-human hybrid cells. Mol Cell Biol. 1983 Dec;3(12):2211–2220. doi: 10.1128/mcb.3.12.2211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Lund E., Dahlberg J. E. True genes for human U1 small nuclear RNA. Copy number, polymorphism, and methylation. J Biol Chem. 1984 Feb 10;259(3):2013–2021. [PubMed] [Google Scholar]
  15. Lund E., Dahlberg J. E. True genes for human U1 small nuclear RNA. Copy number, polymorphism, and methylation. J Biol Chem. 1984 Feb 10;259(3):2013–2021. [PubMed] [Google Scholar]
  16. Manser T., Gesteland R. F. Characterization of small nuclear RNA U1 gene candidates and pseudogenes from the human genome. J Mol Appl Genet. 1981;1(2):117–125. [PubMed] [Google Scholar]
  17. Manser T., Gesteland R. F. Human U1 loci: genes for human U1 RNA have dramatically similar genomic environments. Cell. 1982 May;29(1):257–264. doi: 10.1016/0092-8674(82)90110-6. [DOI] [PubMed] [Google Scholar]
  18. Marzluff W. F., Brown D. T., Lobo S., Wang S. S. Isolation and characterization of two linked mouse U1b small nuclear RNA genes. Nucleic Acids Res. 1983 Sep 24;11(18):6255–6270. doi: 10.1093/nar/11.18.6255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mattaj I. W., Zeller R. Xenopus laevis U2 snRNA genes: tandemly repeated transcription units sharing 5' and 3' flanking homology with other RNA polymerase II transcribed genes. EMBO J. 1983;2(11):1883–1891. doi: 10.1002/j.1460-2075.1983.tb01675.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  21. Murphy J. T., Burgess R. R., Dahlberg J. E., Lund E. Transcription of a gene for human U1 small nuclear RNA. Cell. 1982 May;29(1):265–274. doi: 10.1016/0092-8674(82)90111-8. [DOI] [PubMed] [Google Scholar]
  22. Nojima H., Kornberg R. D. Genes and pseudogenes for mouse U1 and U2 small nuclear RNAs. J Biol Chem. 1983 Jul 10;258(13):8151–8155. [PubMed] [Google Scholar]
  23. Nordheim A., Rich A. Negatively supercoiled simian virus 40 DNA contains Z-DNA segments within transcriptional enhancer sequences. Nature. 1983 Jun 23;303(5919):674–679. doi: 10.1038/303674a0. [DOI] [PubMed] [Google Scholar]
  24. Padgett R. A., Mount S. M., Steitz J. A., Sharp P. A. Splicing of messenger RNA precursors is inhibited by antisera to small nuclear ribonucleoprotein. Cell. 1983 Nov;35(1):101–107. doi: 10.1016/0092-8674(83)90212-x. [DOI] [PubMed] [Google Scholar]
  25. Rogers J., Wall R. A mechanism for RNA splicing. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1877–1879. doi: 10.1073/pnas.77.4.1877. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Roop D. R., Kristo P., Stumph W. E., Tsai M. J., O'Malley B. W. Structure and expression of a chicken gene coding for U1 RNA. Cell. 1981 Mar;23(3):671–680. doi: 10.1016/0092-8674(81)90430-x. [DOI] [PubMed] [Google Scholar]
  27. Saluz H. P., Schmidt T., Dudler R., Altwegg M., Stumm-Zollinger E., Kubli E., Chen P. S. The genes coding for 4 snRNAs of Drosophila melanogaster: localization and determination of gene numbers. Nucleic Acids Res. 1983 Jan 11;11(1):77–90. doi: 10.1093/nar/11.1.77. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  29. Tani T., Watanabe-Nagasu N., Okada N., Ohshima Y. Molecular cloning and characterization of a gene for rat U2 small nuclear RNA. J Mol Biol. 1983 Aug 15;168(3):579–594. doi: 10.1016/s0022-2836(83)80303-9. [DOI] [PubMed] [Google Scholar]
  30. Van Arsdell S. W., Weiner A. M. Human genes for U2 small nuclear RNA are tandemly repeated. Mol Cell Biol. 1984 Mar;4(3):492–499. doi: 10.1128/mcb.4.3.492. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Watanabe-Nagasu N., Itoh Y., Tani T., Okano K., Koga N., Okada N., Ohshima Y. Structural analysis of gene loci for rat U1 small nuclear RNA. Nucleic Acids Res. 1983 Mar 25;11(6):1791–1801. doi: 10.1093/nar/11.6.1791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Yang V. W., Lerner M. R., Steitz J. A., Flint S. J. A small nuclear ribonucleoprotein is required for splicing of adenoviral early RNA sequences. Proc Natl Acad Sci U S A. 1981 Mar;78(3):1371–1375. doi: 10.1073/pnas.78.3.1371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Zeller R., Carri M. T., Mattaj I. W., De Robertis E. M. Xenopus laevis U1 snRNA genes: characterisation of transcriptionally active genes reveals major and minor repeated gene families. EMBO J. 1984 May;3(5):1075–1081. doi: 10.1002/j.1460-2075.1984.tb01931.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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