Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1982 Aug 11;10(15):4627–4640. doi: 10.1093/nar/10.15.4627

Mouse DNA sequences complementary to small nuclear RNA U1.

M Piechaczyk, M N Lelay-Taha, J Sri-Widada, C Brunel, J P Liautard, P Jeanteur
PMCID: PMC321117  PMID: 6182525

Abstract

A mouse genomic library was screened for sequences complementary to U1 nuclear RNA. Out of the eight clones tested, none contained more than one copy of U1. Six of them were identical and one of those (clone 0U1-XIII) was further analyzed. This latter clone contained no other gene for discrete species of small size RNA in the 8 Kb EcoRI fragment encoding U1. A 248 bp Bg1II fragment from 0U1-XIII encompassing the full length of U1 as well as flanking regions on both sides has been subcloned and sequenced in M13 phage. Although the coding region was 96.5% homologous to rat U1a RNA, there is no direct evidence that this clone is a true gene. 3' and 5' flanking sequences of this as well as other published clones have been searched for homologies and the results of this search are discussed.

Full text

PDF
4627

Images in this article

Selected References

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

  1. Alonso A., Krieg L., Winter H., Sekeris C. E. The synthesis of a cDNA copy complementary to two snRNAs and the localization of their genes in the rat genome. Biochem Biophys Res Commun. 1980 Jul 16;95(1):148–155. doi: 10.1016/0006-291x(80)90716-0. [DOI] [PubMed] [Google Scholar]
  2. Bolivar F. Construction and characterization of new cloning vehicles. III. Derivatives of plasmid pBR322 carrying unique Eco RI sites for selection of Eco RI generated recombinant DNA molecules. Gene. 1978 Oct;4(2):121–136. doi: 10.1016/0378-1119(78)90025-2. [DOI] [PubMed] [Google Scholar]
  3. Bozzoni I., Beccari E., Luo Z. X., Amaldi F. Xenopus laevis ribosomal protein genes: isolation of recombinant cDNA clones and study of the genomic organization. Nucleic Acids Res. 1981 Mar 11;9(5):1069–1086. doi: 10.1093/nar/9.5.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. Brown S. D., Dover G. Organization and evolutionary progress of a dispersed repetitive family of sequences in widely separated rodent genomes. J Mol Biol. 1981 Aug 25;150(4):441–466. doi: 10.1016/0022-2836(81)90374-0. [DOI] [PubMed] [Google Scholar]
  6. Chaconas G., van de Sande J. H. 5'-32P labeling of RNA and DNA restriction fragments. Methods Enzymol. 1980;65(1):75–85. doi: 10.1016/s0076-6879(80)65012-5. [DOI] [PubMed] [Google Scholar]
  7. Denison R. A., Van Arsdell S. W., Bernstein L. B., Weiner A. M. Abundant pseudogenes for small nuclear RNAs are dispersed in the human genome. Proc Natl Acad Sci U S A. 1981 Feb;78(2):810–814. doi: 10.1073/pnas.78.2.810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Ducamp C., Jeanteur P. Characterization of nuclear RNP particles from Hela cells. Analysis of protein and RNA constituents. Presence of poly (A). Biochimie. 1973;55(10):1235–1243. doi: 10.1016/s0300-9084(74)80328-7. [DOI] [PubMed] [Google Scholar]
  9. Eliceiri G. L. Sensitivity of low molecular weight RNA synthesis to UV radiation. Nature. 1979 May 3;279(5708):80–81. doi: 10.1038/279080a0. [DOI] [PubMed] [Google Scholar]
  10. Hayashi K. Organization of sequences related to U6 RNA in the human genome. Nucleic Acids Res. 1981 Jul 24;9(14):3379–3388. doi: 10.1093/nar/9.14.3379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hörz W., Altenburger W. Nucleotide sequence of mouse satellite DNA. Nucleic Acids Res. 1981 Feb 11;9(3):683–696. doi: 10.1093/nar/9.3.683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Jelinek W. R., Toomey T. P., Leinwand L., Duncan C. H., Biro P. A., Choudary P. V., Weissman S. M., Rubin C. M., Houck C. M., Deininger P. L. Ubiquitous, interspersed repeated sequences in mammalian genomes. Proc Natl Acad Sci U S A. 1980 Mar;77(3):1398–1402. doi: 10.1073/pnas.77.3.1398. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kenter A. L., Birshtein B. K. Chi, a promoter of generalized recombination in lambda phage, is present in immunoglobulin genes. Nature. 1981 Oct 1;293(5831):402–404. doi: 10.1038/293402a0. [DOI] [PubMed] [Google Scholar]
  14. Kramerov D. A., Grigoryan A. A., Ryskov A. P., Georgiev G. P. Long double-stranded sequences (dsRNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. Nucleic Acids Res. 1979 Feb;6(2):697–713. doi: 10.1093/nar/6.2.697. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Krayev A. S., Kramerov D. A., Skryabin K. G., Ryskov A. P., Bayev A. A., Georgiev G. P. The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res. 1980 Mar 25;8(6):1201–1215. doi: 10.1093/nar/8.6.1201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Larsen C. J., Galibert F., Lelong J. C., Boiron M. Caractérisation dans la fraction nucléaire de cellules KB d'un ARN métaboliquement stable de faible poids moléculaire. C R Acad Sci Hebd Seances Acad Sci D. 1967 Mar 13;264(11):1523–1526. [PubMed] [Google Scholar]
  17. Lelay M. N., Brunel C., Jeanteur P. Peptide mapping of in vivo and in vitro phosphorylated sites of proteins from HeLa hnRNP. FEBS Lett. 1978 Jun 1;90(1):54–56. doi: 10.1016/0014-5793(78)80296-8. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. Lerner M. R., Steitz J. A. Antibodies to small nuclear RNAs complexed with proteins are produced by patients with systemic lupus erythematosus. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5495–5499. doi: 10.1073/pnas.76.11.5495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Mandel M., Higa A. Calcium-dependent bacteriophage DNA infection. J Mol Biol. 1970 Oct 14;53(1):159–162. doi: 10.1016/0022-2836(70)90051-3. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. 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]
  23. Messing J., Crea R., Seeburg P. H. A system for shotgun DNA sequencing. Nucleic Acids Res. 1981 Jan 24;9(2):309–321. doi: 10.1093/nar/9.2.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Messing J., Gronenborn B., Müller-Hill B., Hans Hopschneider P. Filamentous coliphage M13 as a cloning vehicle: insertion of a HindII fragment of the lac regulatory region in M13 replicative form in vitro. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3642–3646. doi: 10.1073/pnas.74.9.3642. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mount S. M., Steitz J. A. Sequence of U1 RNA from Drosophila melanogaster: implications for U1 secondary structure and possible involvement in splicing. Nucleic Acids Res. 1981 Dec 11;9(23):6351–6368. doi: 10.1093/nar/9.23.6351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. Murray V., Holliday R. Mechanism for RNA splicing of gene transcripts. FEBS Lett. 1979 Oct 1;106(1):5–7. doi: 10.1016/0014-5793(79)80682-1. [DOI] [PubMed] [Google Scholar]
  28. Ohshima Y., Okada N., Tani T., Itoh Y., Itoh M. Nucleotide sequences of mouse genomic loci including a gene or pseudogene for U6 (4.8S) nuclear RNA. Nucleic Acids Res. 1981 Oct 10;9(19):5145–5158. doi: 10.1093/nar/9.19.5145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. 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]
  30. 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]
  31. Sanger F., Coulson A. R. The use of thin acrylamide gels for DNA sequencing. FEBS Lett. 1978 Mar 1;87(1):107–110. doi: 10.1016/0014-5793(78)80145-8. [DOI] [PubMed] [Google Scholar]
  32. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Schreier P. H., Cortese R. A fast and simple method for sequencing DNA cloned in the single-stranded bacteriophage M13. J Mol Biol. 1979 Mar 25;129(1):169–172. doi: 10.1016/0022-2836(79)90068-8. [DOI] [PubMed] [Google Scholar]
  34. Smith G. E., Summers M. D. The bidirectional transfer of DNA and RNA to nitrocellulose or diazobenzyloxymethyl-paper. Anal Biochem. 1980 Nov 15;109(1):123–129. doi: 10.1016/0003-2697(80)90019-6. [DOI] [PubMed] [Google Scholar]
  35. Smith G. R., Kunes S. M., Schultz D. W., Taylor A., Triman K. L. Structure of chi hotspots of generalized recombination. Cell. 1981 May;24(2):429–436. doi: 10.1016/0092-8674(81)90333-0. [DOI] [PubMed] [Google Scholar]
  36. 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]
  37. Udvardy A., Seifart K. H. Transcription of specific genes in isolated nuclei from HeLa cells in vitro. Eur J Biochem. 1976 Feb 16;62(2):353–363. doi: 10.1111/j.1432-1033.1976.tb10167.x. [DOI] [PubMed] [Google Scholar]
  38. Van Arsdell S. W., Denison R. A., Bernstein L. B., Weiner A. M., Manser T., Gesteland R. F. Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell. 1981 Oct;26(1 Pt 1):11–17. doi: 10.1016/0092-8674(81)90028-3. [DOI] [PubMed] [Google Scholar]
  39. Westin G., Monstein H. J., Zabielski J., Philipson L., Pettersson U. Human DNA sequences complementary to the small nuclear RNA U2. Nucleic Acids Res. 1981 Dec 11;9(23):6323–6338. doi: 10.1093/nar/9.23.6323. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wise J. A., Weiner A. M. Dictyostelium small nuclear RNA D2 is homologous to rat nucleolar RNA U3 and is encoded by a dispersed multigene family. Cell. 1980 Nov;22(1 Pt 1):109–118. doi: 10.1016/0092-8674(80)90159-2. [DOI] [PubMed] [Google Scholar]
  41. Woo S. L. A sensitive and rapid method for recombinant phage screening. Methods Enzymol. 1979;68:389–395. doi: 10.1016/0076-6879(79)68028-x. [DOI] [PubMed] [Google Scholar]
  42. Yamamoto K. R., Alberts B. M., Benzinger R., Lawhorne L., Treiber G. Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification. Virology. 1970 Mar;40(3):734–744. doi: 10.1016/0042-6822(70)90218-7. [DOI] [PubMed] [Google Scholar]
  43. Zieve G., Benecke B. J., Penman S. Synthesis of two classes of small RNA species in vivo and in vitro. Biochemistry. 1977 Oct 4;16(20):4520–4525. doi: 10.1021/bi00639a029. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES