Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1994 Apr 26;91(9):3607–3611. doi: 10.1073/pnas.91.9.3607

Rodent BC1 RNA gene as a master gene for ID element amplification.

J Kim 1, J A Martignetti 1, M R Shen 1, J Brosius 1, P Deininger 1
PMCID: PMC43629  PMID: 8170955

Abstract

ID elements are short interspersed repetitive DNA elements (SINEs) which have amplified in rodent genomes via retroposition, a process involving an RNA intermediate. BC1, an abundant ID-related transcript, is transcribed from a conserved, single-copy gene in rodents. The gene encoding BC1 RNA represents one of the earliest and possibly the first ID-containing sequence. Comparison of consensus sequences of each rodent ID with its corresponding BC1 RNA gene showed that the variations of BC1 RNA within rodents corresponded to specific changes within the ID consensus sequence for each rodent species. This supports the hypothesis that the BC1 gene is a master gene responsible for the amplification and evolution of ID elements. The rat ID family consists of at least four subfamilies, with the oldest subfamily having been derived from the BC1 RNA. The other three subfamilies appear to have been derived from a new master gene(s), which has been responsible for the large increase in ID element copy number within the rat genome. We have found that the guinea pig genome contains two copies of the BC1 gene, apparently the result of a DNA-mediated duplication event. Both of these guinea pig BC1 genes have a conserved TATA-like element in the 5' flanking region and have contributed to guinea pig ID amplifications.

Full text

PDF
3611

Images in this article

3608Image
on p.3608

Selected References

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

  1. Anzai K., Kobayashi S., Suehiro Y., Goto S. Conservation of the ID sequence and its expression as small RNA in rodent brains: analysis with cDNA for mouse brain-specific small RNA. Brain Res. 1987 Apr;388(1):43–49. doi: 10.1016/0169-328x(87)90019-2. [DOI] [PubMed] [Google Scholar]
  2. Batzer M. A., Kilroy G. E., Richard P. E., Shaikh T. H., Desselle T. D., Hoppens C. L., Deininger P. L. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990 Dec 11;18(23):6793–6798. doi: 10.1093/nar/18.23.6793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brosius J., Gould S. J. On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA". Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10706–10710. doi: 10.1073/pnas.89.22.10706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brosius J. Retroposons--seeds of evolution. Science. 1991 Feb 15;251(4995):753–753. doi: 10.1126/science.1990437. [DOI] [PubMed] [Google Scholar]
  5. Carbon P., Krol A. Transcription of the Xenopus laevis selenocysteine tRNA(Ser)Sec gene: a system that combines an internal B box and upstream elements also found in U6 snRNA genes. EMBO J. 1991 Mar;10(3):599–606. doi: 10.1002/j.1460-2075.1991.tb07987.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dahlberg J. E., Lund E. How does III x II make U6? Science. 1991 Dec 6;254(5037):1462–1463. doi: 10.1126/science.1962205. [DOI] [PubMed] [Google Scholar]
  7. Daniels G. R., Deininger P. L. Characterization of a third major SINE family of repetitive sequences in the galago genome. Nucleic Acids Res. 1991 Apr 11;19(7):1649–1656. doi: 10.1093/nar/19.7.1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Daniels G. R., Deininger P. L. Repeat sequence families derived from mammalian tRNA genes. 1985 Oct 31-Nov 6Nature. 317(6040):819–822. doi: 10.1038/317819a0. [DOI] [PubMed] [Google Scholar]
  9. DeChiara T. M., Brosius J. Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc Natl Acad Sci U S A. 1987 May;84(9):2624–2628. doi: 10.1073/pnas.84.9.2624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Deininger P. L., Batzer M. A., Hutchison C. A., 3rd, Edgell M. H. Master genes in mammalian repetitive DNA amplification. Trends Genet. 1992 Sep;8(9):307–311. doi: 10.1016/0168-9525(92)90262-3. [DOI] [PubMed] [Google Scholar]
  11. Economou E. P., Bergen A. W., Warren A. C., Antonarakis S. E. The polydeoxyadenylate tract of Alu repetitive elements is polymorphic in the human genome. Proc Natl Acad Sci U S A. 1990 Apr;87(8):2951–2954. doi: 10.1073/pnas.87.8.2951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Labuda D., Sinnett D., Richer C., Deragon J. M., Striker G. Evolution of mouse B1 repeats: 7SL RNA folding pattern conserved. J Mol Evol. 1991 May;32(5):405–414. doi: 10.1007/BF02101280. [DOI] [PubMed] [Google Scholar]
  13. Labuda D., Striker G. Sequence conservation in Alu evolution. Nucleic Acids Res. 1989 Apr 11;17(7):2477–2491. doi: 10.1093/nar/17.7.2477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Li W. H., Gojobori T., Nei M. Pseudogenes as a paradigm of neutral evolution. Nature. 1981 Jul 16;292(5820):237–239. doi: 10.1038/292237a0. [DOI] [PubMed] [Google Scholar]
  15. Liu W. M., Leeflang E. P., Schmid C. W. Unusual sequences of two old, inactive human Alu repeats. Biochim Biophys Acta. 1992 Oct 20;1132(3):306–308. doi: 10.1016/0167-4781(92)90165-v. [DOI] [PubMed] [Google Scholar]
  16. Martignetti J. A., Brosius J. Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9698–9702. doi: 10.1073/pnas.90.20.9698. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Matera A. G., Hellmann U., Hintz M. F., Schmid C. W. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 1990 Oct 25;18(20):6019–6023. doi: 10.1093/nar/18.20.6019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. McKinnon R. D., Danielson P., Brow M. A., Bloom F. E., Sutcliffe J. G. Expression of small cytoplasmic transcripts of the rat identifier element in vivo and in cultured cells. Mol Cell Biol. 1987 Jun;7(6):2148–2154. doi: 10.1128/mcb.7.6.2148. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sakamoto K., Okada N. 5-Methylcytidylic modification of in vitro transcript from the rat identifier sequence; evidence that the transcript forms a tRNA-like structure. Nucleic Acids Res. 1985 Oct 25;13(20):7195–7206. doi: 10.1093/nar/13.20.7195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sapienza C., St-Jacques B. 'Brain-specific' transcription and evolution of the identifier sequence. 1986 Jan 30-Feb 5Nature. 319(6052):418–420. doi: 10.1038/319418a0. [DOI] [PubMed] [Google Scholar]
  21. Schmid C., Maraia R. Transcriptional regulation and transpositional selection of active SINE sequences. Curr Opin Genet Dev. 1992 Dec;2(6):874–882. doi: 10.1016/s0959-437x(05)80110-8. [DOI] [PubMed] [Google Scholar]
  22. Sutcliffe J. G., Milner R. J., Gottesfeld J. M., Lerner R. A. Identifier sequences are transcribed specifically in brain. Nature. 1984 Mar 15;308(5956):237–241. doi: 10.1038/308237a0. [DOI] [PubMed] [Google Scholar]
  23. Weiner A. M., Deininger P. L., Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. doi: 10.1146/annurev.bi.55.070186.003215. [DOI] [PubMed] [Google Scholar]
  24. Willis I. M. RNA polymerase III. Genes, factors and transcriptional specificity. Eur J Biochem. 1993 Feb 15;212(1):1–11. doi: 10.1111/j.1432-1033.1993.tb17626.x. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES