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. 1986 Feb 25;14(4):1643–1656. doi: 10.1093/nar/14.4.1643

Cloning and characterization of rat 4.5S RNAI genes.

Y Takeuchi, F Harada
PMCID: PMC339545  PMID: 3951992

Abstract

Genomic clones containing genes for 4.5S RNAI, which is an abundant small nuclear RNA found in rodent cells, were obtained from a rat genomic library. Thirty-four clones that formed RNase A resistant hybrids with 3'-end-labeled 4.5S RNAI were isolated, and seven of them (clones lambda I39, lambda I41, lambda I42, lambda I51, lambda I106, lambda I123 and lambda I154) were characterized by sequencing and in vitro transcription. Clones lambda I41 and lambda I123 carry one and two genes, respectively, with identical sequences to that of 4.5S RNAI and are actively transcribed in vitro. However, the other five clones contain sequences that seem to be pseudogenes for 4.5S RNAI, since they have nucleotide substitutions or deletions in the sequence corresponding to 4.5S RNAI or are not transcribed. Four clones (lambda I39, lambda I42, lambda I106 and lambda I154) were found to have 13-18 nucleotide-long direct repeats flanking the 4.5S RNAI sequences. The genomic organization of the genes and their related sequences is discussed.

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Selected References

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

  1. Benton W. D., Davis R. W. Screening lambdagt recombinant clones by hybridization to single plaques in situ. Science. 1977 Apr 8;196(4286):180–182. doi: 10.1126/science.322279. [DOI] [PubMed] [Google Scholar]
  2. Bruce A. G., Uhlenbeck O. C. Reactions at the termini of tRNA with T4 RNA ligase. Nucleic Acids Res. 1978 Oct;5(10):3665–3677. doi: 10.1093/nar/5.10.3665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Busch H., Reddy R., Rothblum L., Choi Y. C. SnRNAs, SnRNPs, and RNA processing. Annu Rev Biochem. 1982;51:617–654. doi: 10.1146/annurev.bi.51.070182.003153. [DOI] [PubMed] [Google Scholar]
  4. Fowlkes D. M., Shenk T. Transcriptional control regions of the adenovirus VAI RNA gene. Cell. 1980 Nov;22(2 Pt 2):405–413. doi: 10.1016/0092-8674(80)90351-7. [DOI] [PubMed] [Google Scholar]
  5. Galli G., Hofstetter H., Birnstiel M. L. Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature. 1981 Dec 17;294(5842):626–631. doi: 10.1038/294626a0. [DOI] [PubMed] [Google Scholar]
  6. Harada F., Ikawa Y. A new series of RNAs associated with the genome of spleen focus forming virus (SFFV) and poly(A)-containing RNA from SFFV-infected cells. Nucleic Acids Res. 1979 Oct 25;7(4):895–908. doi: 10.1093/nar/7.4.895. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Harada F., Kato N. Nucleotide sequences of 4.5S RNAs associated with poly(A)-containing RNAs of mouse and hamster cells. Nucleic Acids Res. 1980 Mar 25;8(6):1273–1285. doi: 10.1093/nar/8.6.1273. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Harada F., Peters G. G., Dahlberg J. E. The primer tRNA for Moloney murine leukemia virus DNA synthesis. Nucleotide sequence and aminoacylation of tRNAPro. J Biol Chem. 1979 Nov 10;254(21):10979–10985. [PubMed] [Google Scholar]
  9. Hayashi K. A cloning vehicle suitable for strand separation. Gene. 1980 Oct;11(1-2):109–115. doi: 10.1016/0378-1119(80)90091-8. [DOI] [PubMed] [Google Scholar]
  10. Haynes S. R., Jelinek W. R. Low molecular weight RNAs transcribed in vitro by RNA polymerase III from Alu-type dispersed repeats in Chinese hamster DNA are also found in vivo. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6130–6134. doi: 10.1073/pnas.78.10.6130. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hendrick J. P., Wolin S. L., Rinke J., Lerner M. R., Steitz J. A. Ro small cytoplasmic ribonucleoproteins are a subclass of La ribonucleoproteins: further characterization of the Ro and La small ribonucleoproteins from uninfected mammalian cells. Mol Cell Biol. 1981 Dec;1(12):1138–1149. doi: 10.1128/mcb.1.12.1138. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Higashi K., Narayanan K. S., Adams H. R., Busch H. Utilization of the citric acid procedure and zonal ultracentrifugation for mass isolation of nuclear RNA from Walker 256 carcinosarcoma. Cancer Res. 1966 Jul;26(7):1582–1590. [PubMed] [Google Scholar]
  13. Ikemura T., Dahlberg J. E. Small ribonucleic acids of Escherichia coli. I. Characterization by polyacrylamide gel electrophoresis and fingerprint analysis. J Biol Chem. 1973 Jul 25;248(14):5024–5032. [PubMed] [Google Scholar]
  14. Ikemura T., Shimura Y., Sakano H., Ozeki H. Precursor molecules of Escherichia coli transfer RNAs accumulated in a temperature-sensitive mutant. J Mol Biol. 1975 Jul 25;96(1):69–86. doi: 10.1016/0022-2836(75)90182-5. [DOI] [PubMed] [Google Scholar]
  15. Jelinek W. R., Schmid C. W. Repetitive sequences in eukaryotic DNA and their expression. Annu Rev Biochem. 1982;51:813–844. doi: 10.1146/annurev.bi.51.070182.004121. [DOI] [PubMed] [Google Scholar]
  16. Krayev A. S., Markusheva T. V., Kramerov D. A., Ryskov A. P., Skryabin K. G., Bayev A. A., Georgiev G. P. Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing. Nucleic Acids Res. 1982 Dec 11;10(23):7461–7475. doi: 10.1093/nar/10.23.7461. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Manley J. L., Fire A., Cano A., Sharp P. A., Gefter M. L. DNA-dependent transcription of adenovirus genes in a soluble whole-cell extract. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3855–3859. doi: 10.1073/pnas.77.7.3855. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Reddy R., Busch H. Small nuclear RNAs and RNA processing. Prog Nucleic Acid Res Mol Biol. 1983;30:127–162. doi: 10.1016/s0079-6603(08)60685-6. [DOI] [PubMed] [Google Scholar]
  19. Ro-Choi T. S., Redy R., Henning D., Takano T., Taylor C. W., Busch H. Nucleotide sequence of 4.5 S ribonucleic acid of Novikoff hepatoma cell nuclei. J Biol Chem. 1972 May 25;247(10):3205–3222. [PubMed] [Google Scholar]
  20. Saba J. A., Busch H., Reddy R. A new moderately repetitive rat DNA sequence detected by a cloned 4.5 SI DNA. J Biol Chem. 1985 Feb 10;260(3):1354–1357. [PubMed] [Google Scholar]
  21. Singer M. F. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell. 1982 Mar;28(3):433–434. doi: 10.1016/0092-8674(82)90194-5. [DOI] [PubMed] [Google Scholar]
  22. Soeiro R., Darnell J. E. Competition hybridization by "pre-saturation" of HeLa cell DNA. J Mol Biol. 1969 Sep 28;44(3):551–562. doi: 10.1016/0022-2836(69)90379-9. [DOI] [PubMed] [Google Scholar]
  23. 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]

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