Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1986 Mar 11;14(5):2109–2122. doi: 10.1093/nar/14.5.2109

Sequence characterization of Tetrahymena macronuclear DNA ends.

R Yokoyama, M C Yao
PMCID: PMC339646  PMID: 3008087

Abstract

Tetrahymena is a ciliated protozoan which has two nuclei: a micronucleus, which maintains the genetic continuity of the cell, and the macronucleus which is derived from the micronucleus after sexual conjugation. A macronuclear DNA library was constructed to contain DNA ends. A probe containing C4A2 repeats which are known to be present at macronuclear DNA ends (1) was used to screen the library. Three clones were characterized by sequencing, restriction enzyme mapping and Bal 31 digestion. The data indicate that these three clones represent macronuclear DNA ends which were generated by DNA fragmentation during macronuclear formation. The sequencing data at the C4A2 repeat junction show a conserved sequence of five nucleotides, TTATT. Sequences further away show no obvious homologies except that they are highly enriched in AT. This structure is quite different from the subtelomeric sequences of other organisms.

Full text

PDF
2109

Images in this article

2114Image
on p.2114
2116Image
on p.2116

Selected References

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

  1. Altschuler M. I., Yao M. C. Macronuclear DNA of Tetrahymena thermophila exists as defined subchromosomal-sized molecules. Nucleic Acids Res. 1985 Aug 26;13(16):5817–5831. doi: 10.1093/nar/13.16.5817. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bahl C. P., Marians K. J., Wu R. A general method for inserting specific DNA sequences into cloning vehicles. Gene. 1976;1(1):81–92. doi: 10.1016/0378-1119(76)90008-1. [DOI] [PubMed] [Google Scholar]
  3. Bedbrook J. R., Jones J., O'Dell M., Thompson R. D., Flavell R. B. A molecular description of telometic heterochromatin in secale species. Cell. 1980 Feb;19(2):545–560. doi: 10.1016/0092-8674(80)90529-2. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. Bergold P. J., Campbell G. R., Littau V. C., Johnson E. M. Sequence and hairpin structure of an inverted repeat series at termini of the Physarum extrachromosomal rDNA molecule. Cell. 1983 Apr;32(4):1287–1299. doi: 10.1016/0092-8674(83)90310-0. [DOI] [PubMed] [Google Scholar]
  6. Blackburn E. H., Gall J. G. A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena. J Mol Biol. 1978 Mar 25;120(1):33–53. doi: 10.1016/0022-2836(78)90294-2. [DOI] [PubMed] [Google Scholar]
  7. Blackburn E. H. Telomeres: do the ends justify the means? Cell. 1984 May;37(1):7–8. doi: 10.1016/0092-8674(84)90295-2. [DOI] [PubMed] [Google Scholar]
  8. Chan C. S., Tye B. K. Organization of DNA sequences and replication origins at yeast telomeres. Cell. 1983 Jun;33(2):563–573. doi: 10.1016/0092-8674(83)90437-3. [DOI] [PubMed] [Google Scholar]
  9. Denhardt D. T. A membrane-filter technique for the detection of complementary DNA. Biochem Biophys Res Commun. 1966 Jun 13;23(5):641–646. doi: 10.1016/0006-291x(66)90447-5. [DOI] [PubMed] [Google Scholar]
  10. Dente L., Cesareni G., Cortese R. pEMBL: a new family of single stranded plasmids. Nucleic Acids Res. 1983 Mar 25;11(6):1645–1655. doi: 10.1093/nar/11.6.1645. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Emery H. S., Weiner A. M. An irregular satellite sequence is found at the termini of the linear extrachromosomal rDNA in Dictyostelium discoideum. Cell. 1981 Nov;26(3 Pt 1):411–419. doi: 10.1016/0092-8674(81)90210-5. [DOI] [PubMed] [Google Scholar]
  12. Engberg J., Andersson P., Leick V., Collins J. Free ribosomal DNA molecules from Tetrahymena pyriformis GL are giant palindromes. J Mol Biol. 1976 Jun 25;104(2):455–470. doi: 10.1016/0022-2836(76)90281-3. [DOI] [PubMed] [Google Scholar]
  13. Gorovsky M. A., Yao M. C., Keevert J. B., Pleger G. L. Isolation of micro- and macronuclei of Tetrahymena pyriformis. Methods Cell Biol. 1975;9(0):311–327. doi: 10.1016/s0091-679x(08)60080-1. [DOI] [PubMed] [Google Scholar]
  14. Gray H. B., Jr, Ostrander D. A., Hodnett J. L., Legerski R. J., Robberson D. L. Extracellular nucleases of Pseudomonas BAL 31. I. Characterization of single strand-specific deoxyriboendonuclease and double-strand deoxyriboexonuclease activities. Nucleic Acids Res. 1975 Sep;2(9):1459–1492. doi: 10.1093/nar/2.9.1459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Helling R. B., Goodman H. M., Boyer H. W. Analysis of endonuclease R-EcoRI fragments of DNA from lambdoid bacteriophages and other viruses by agarose-gel electrophoresis. J Virol. 1974 Nov;14(5):1235–1244. doi: 10.1128/jvi.14.5.1235-1244.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hohn B. In vitro packaging of lambda and cosmid DNA. Methods Enzymol. 1979;68:299–309. doi: 10.1016/0076-6879(79)68021-7. [DOI] [PubMed] [Google Scholar]
  17. Horowitz H., Haber J. E. Subtelomeric regions of yeast chromosomes contain a 36 base-pair tandemly repeated sequence. Nucleic Acids Res. 1984 Sep 25;12(18):7105–7121. doi: 10.1093/nar/12.18.7105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jones J. D., Flavell R. B. Chromosomal structure and arrangement of repeated DNA sequences in the telomeric heterochromatin of Secale cereale and its relatives. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1209–1213. doi: 10.1101/sqb.1983.047.01.136. [DOI] [PubMed] [Google Scholar]
  19. Karrer K. M., Gall J. G. The macronuclear ribosomal DNA of Tetrahymena pyriformis is a palindrome. J Mol Biol. 1976 Jun 25;104(2):421–453. doi: 10.1016/0022-2836(76)90280-1. [DOI] [PubMed] [Google Scholar]
  20. King B. O., Yao M. C. Tandemly repeated hexanucleotide at Tetrahymena rDNA free end is generated from a single copy during development. Cell. 1982 Nov;31(1):177–182. doi: 10.1016/0092-8674(82)90417-2. [DOI] [PubMed] [Google Scholar]
  21. Kiss G. B., Amin A. A., Pearlman R. E. Two separate regions of the extrachromosomal ribosomal deoxyribonucleic acid of Tetrahymena thermophila enable autonomous replication of plasmids in Saccharomyces cerevisiae. Mol Cell Biol. 1981 Jun;1(6):535–543. doi: 10.1128/mcb.1.6.535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Klobutcher L. A., Jahn C. L., Prescott D. M. Internal sequences are eliminated from genes during macronuclear development in the ciliated protozoan Oxytricha nova. Cell. 1984 Apr;36(4):1045–1055. doi: 10.1016/0092-8674(84)90054-0. [DOI] [PubMed] [Google Scholar]
  23. Klobutcher L. A., Swanton M. T., Donini P., Prescott D. M. All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3' terminus. Proc Natl Acad Sci U S A. 1981 May;78(5):3015–3019. doi: 10.1073/pnas.78.5.3015. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lis J. T. Fractionation of DNA fragments by polyethylene glycol induced precipitation. Methods Enzymol. 1980;65(1):347–353. doi: 10.1016/s0076-6879(80)65044-7. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Oka Y., Honjo T. Common terminal repeats of the macronuclear DNA are absent from the micronuclear DNA in hypotrichous ciliate, Stylonychia pustulata. Nucleic Acids Res. 1983 Jul 11;11(13):4325–4333. doi: 10.1093/nar/11.13.4325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Oka Y., Shiota S., Nakai S., Nishida Y., Okubo S. Inverted terminal repeat sequence in the macronuclear DNA of Stylonychia pustulata. Gene. 1980 Sep;10(4):301–306. doi: 10.1016/0378-1119(80)90150-x. [DOI] [PubMed] [Google Scholar]
  28. Palen T. E., Cech T. R. Chromatin structure at the replication origins and transcription-initiation regions of the ribosomal RNA genes of Tetrahymena. Cell. 1984 Apr;36(4):933–942. doi: 10.1016/0092-8674(84)90043-6. [DOI] [PubMed] [Google Scholar]
  29. Pickup D. J., Bastia D., Stone H. O., Joklik W. K. Sequence of terminal regions of cowpox virus DNA: arrangement of repeated and unique sequence elements. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7112–7116. doi: 10.1073/pnas.79.23.7112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Pluta A. F., Kaine B. P., Spear B. B. The terminal organization of macronuclear DNA in Oxytricha fallax. Nucleic Acids Res. 1982 Dec 20;10(24):8145–8154. doi: 10.1093/nar/10.24.8145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Proudfoot N. J., Brownlee G. G. 3' non-coding region sequences in eukaryotic messenger RNA. Nature. 1976 Sep 16;263(5574):211–214. doi: 10.1038/263211a0. [DOI] [PubMed] [Google Scholar]
  32. Rigby P. W., Dieckmann M., Rhodes C., Berg P. Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I. J Mol Biol. 1977 Jun 15;113(1):237–251. doi: 10.1016/0022-2836(77)90052-3. [DOI] [PubMed] [Google Scholar]
  33. Rimm D. L., Horness D., Kucera J., Blattner F. R. Construction of coliphage lambda Charon vectors with BamHI cloning sites. Gene. 1980 Dec;12(3-4):301–309. doi: 10.1016/0378-1119(80)90113-4. [DOI] [PubMed] [Google Scholar]
  34. Rubin G. M. Isolation of a telomeric DNA sequence from Drosophila melanogaster. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1041–1046. doi: 10.1101/sqb.1978.042.01.104. [DOI] [PubMed] [Google Scholar]
  35. 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]
  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. Swanton M. T., Heumann J. M., Prescott D. M. Gene-sized DNA molecules of the macronuclei in three species of hypotrichs: size distributions and absence of nicks. DNA of ciliated protozoa. VIII. Chromosoma. 1980;77(2):217–227. doi: 10.1007/BF00329546. [DOI] [PubMed] [Google Scholar]
  38. Van der Ploeg L. H., Liu A. Y., Borst P. Structure of the growing telomeres of Trypanosomes. Cell. 1984 Feb;36(2):459–468. doi: 10.1016/0092-8674(84)90239-3. [DOI] [PubMed] [Google Scholar]
  39. Yao M. C., Blackburn E., Gall J. G. Amplification of the rRNA genes in Tetrahymena. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 2):1293–1296. doi: 10.1101/sqb.1979.043.01.147. [DOI] [PubMed] [Google Scholar]
  40. Yao M. C. Elimination of specific DNA sequences from the somatic nucleus of the ciliate Tetrahymena. J Cell Biol. 1982 Mar;92(3):783–789. doi: 10.1083/jcb.92.3.783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Yao M. C., Gall J. G. A single integrated gene for ribosomal RNA in a eucaryote, Tetrahymena pyriformis. Cell. 1977 Sep;12(1):121–132. doi: 10.1016/0092-8674(77)90190-8. [DOI] [PubMed] [Google Scholar]
  42. Yao M. C., Gorovsky M. A. Comparison of the sequences of macro- and micronuclear DNA of Tetrahymena pyriformis. Chromosoma. 1974;48(1):1–18. doi: 10.1007/BF00284863. [DOI] [PubMed] [Google Scholar]
  43. Yao M. C., Kimmel A. R., Gorovsky M. A. A small number of cistrons for ribosomal RNA in the germinal nucleus of a eukaryote, Tetrahymena pyriformis. Proc Natl Acad Sci U S A. 1974 Aug;71(8):3082–3086. doi: 10.1073/pnas.71.8.3082. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Yao M. C., Yao C. H. Repeated hexanucleotide C-C-C-C-A-A is present near free ends of macronuclear DNA of Tetrahymena. Proc Natl Acad Sci U S A. 1981 Dec;78(12):7436–7439. doi: 10.1073/pnas.78.12.7436. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Yao M. C., Zhu S. G., Yao C. H. Gene amplification in Tetrahymena thermophila: formation of extrachromosomal palindromic genes coding for rRNA. Mol Cell Biol. 1985 Jun;5(6):1260–1267. doi: 10.1128/mcb.5.6.1260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Young B. S., Pession A., Traverse K. L., French C., Pardue M. L. Telomere regions in Drosophila share complex DNA sequences with pericentric heterochromatin. Cell. 1983 Aug;34(1):85–94. doi: 10.1016/0092-8674(83)90138-1. [DOI] [PubMed] [Google Scholar]

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

RESOURCES