Search tips
Search criteria 


Logo of narLink to Publisher's site
Nucleic Acids Res. 1983 April 11; 11(7): 2093–2109.
PMCID: PMC325864

Different nucleosome spacing in transcribed and non-transcribed regions of the ribosomal RNA gene in Tetrahymena thermophila.


The chromatin structure of the palindromic macronuclear ribosomal RNA genes of Tetrahymena thermophila was probed with micrococcal nuclease. Independent of the state of transcriptional activity, the transcribed region had a shorter nucleosome repeat (184 +/- 3 base pairs) than the non-transcribed central spacer or bulk chromatin (both 200 base pairs). The transcribed region displayed an increased sensitivity to micrococcal nuclease in rapidly growing cells, which suggested an altered chromatin structure during transcription. At early stages of nuclease digestion, the central spacer appeared to be in a highly structured nucleosomal array. Based on the differences in nucleosome repeat distance and sensitivity to nuclease, we conclude that quite different chromatin structures are maintained in two adjacent regions of the Tetrahymena ribosomal RNA gene. The DNA of the non-transcribed terminal spacer was found to contain sequences which are highly susceptible to micrococcal nuclease, precluding any conclusions about nucleosome structure in this region.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.5M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Felsenfeld G. Chromatin. Nature. 1978 Jan 12;271(5641):115–122. [PubMed]
  • Camerini-Otero RD, Zasloff MA. Nucleosomal packaging of the thymidine kinase gene of herpes simplex virus transferred into mouse cells: an actively expressed single-copy gene. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5079–5083. [PubMed]
  • Wu C, Bingham PM, Livak KJ, Holmgren R, Elgin SC. The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. Cell. 1979 Apr;16(4):797–806. [PubMed]
  • Stalder J, Seebeck T, Braun R. Accessibility of the ribosomal genes to micrococcal nuclease in Physarum polycephalum. Biochim Biophys Acta. 1979 Feb 27;561(2):452–463. [PubMed]
  • Karrer KM, Gall JG. The macronuclear ribosomal DNA of Tetrahymena pyriformis is a palindrome. J Mol Biol. 1976 Jun 25;104(2):421–453. [PubMed]
  • 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. [PubMed]
  • Cech TR, Rio DC. Localization of transcribed regions on extrachromosomal ribosomal RNA genes of Tetrahymena thermophila by R-loop mapping. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5051–5055. [PubMed]
  • Engberg J, Nasir-ud-Din, Eckert WA, Kaffenberger W, Pearlman RE. Detailed transcription map of the extrachromosomal ribosomal RNA genes in Tetrahymena thermophila. J Mol Biol. 1980 Sep 25;142(3):289–313. [PubMed]
  • Leick V, Andersen SB. Polols and turnover rates of nuclear ribosomal RNA in Tetrahymena pyriformis. Eur J Biochem. 1970 Jul;14(3):460–464. [PubMed]
  • Sutton CA, Sylvan P, Hallberg RL. Ribosome biosynthesis in Tetrahymena thermophila. IV. Regulation of ribosomal RNA synthesis in growing and growth arrested cells. J Cell Physiol. 1979 Dec;101(3):503–513. [PubMed]
  • Eckert WA, Kaffenberger W. Regulation of rRNA metabolism in Tetrahymena pyriformis. I. Nutritional shift-down. Eur J Cell Biol. 1980 Apr;21(1):53–62. [PubMed]
  • Mathis DJ, Gorovsky MA. Subunit structure of rDNA-containing chromatin. Biochemistry. 1976 Feb 24;15(4):750–755. [PubMed]
  • Piper PW, Celis J, Kaltoft K, Leer JC, Nielsen OF, Westergaard O. Tetrahymena ribosomal RNA gene chromatin is digested by micrococcal nuclease at sites which have the same regular spacing on the DNA as corresponding sites in the bulk nuclear chromatin. Nucleic Acids Res. 1976 Feb;3(2):493–505. [PMC free article] [PubMed]
  • Cech TR, Karrer KM. Chromatin structure of the ribosomal RNA genes of Tetrahymena thermophila as analyzed by trimethylpsoralen crosslinking in vivo. J Mol Biol. 1980 Feb 5;136(4):395–416. [PubMed]
  • Blackburn EH, Chiou SS. Non-nucleosomal packaging of a tandemly repeated DNA sequence at termini of extrachromosomal DNA coding for rRNA in Tetrahymena. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2263–2267. [PubMed]
  • Borchsenius S, Bonven B, Leer JC, Westergaard O. Nuclease-sensitive regions on the extrachromosomal r-chromatin from Tetrahymena pyriformis. Eur J Biochem. 1981 Jul;117(2):245–250. [PubMed]
  • Zaug AJ, Cech TR. In vitro splicing of the ribosomal RNA precursor in nuclei of Tetrahymena. Cell. 1980 Feb;19(2):331–338. [PubMed]
  • Cech TR, Brehm SL. Replication of the extrachromosomal ribosomal RNA genes of Tetrahymena thermophilia. Nucleic Acids Res. 1981 Jul 24;9(14):3531–3543. [PMC free article] [PubMed]
  • Higashinakagawa T, Tashiro F, Mita T. DNA-dependent RNA polymerase from a protozoan, Tetrahymena pyriformis. Extraction and partial characterization. J Biochem. 1975 Apr;77(4):783–793. [PubMed]
  • Birnboim HC, Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. [PMC free article] [PubMed]
  • Dretzen G, Bellard M, Sassone-Corsi P, Chambon P. A reliable method for the recovery of DNA fragments from agarose and acrylamide gels. Anal Biochem. 1981 Apr;112(2):295–298. [PubMed]
  • Maniatis T, Jeffrey A, Kleid DG. Nucleotide sequence of the rightward operator of phage lambda. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1184–1188. [PubMed]
  • Denhardt DT. A membrane-filter technique for the detection of complementary DNA. Biochem Biophys Res Commun. 1966 Jun 13;23(5):641–646. [PubMed]
  • Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. [PubMed]
  • Blackburn EH, Gall JG. 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. [PubMed]
  • Hörz W, Altenburger W. Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res. 1981 Jun 25;9(12):2643–2658. [PMC free article] [PubMed]
  • Dingwall C, Lomonossoff GP, Laskey RA. High sequence specificity of micrococcal nuclease. Nucleic Acids Res. 1981 Jun 25;9(12):2659–2673. [PMC free article] [PubMed]
  • LaFond RE, Goguen J, Einck L, Woodcock CL. Micrococcal nuclease cleavage of chromatin displays nonrandom properties. Biochemistry. 1981 Apr 14;20(8):2127–2132. [PubMed]
  • Kiss GB, Amin AA, Pearlman RE. 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. [PMC free article] [PubMed]
  • Reeves R. Structure of Xenopus ribosomal gene chromatin during changes in genomic transcription rates. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):709–722. [PubMed]
  • Johnson EM, Matthews HR, Littau VC, Lothstein L, Bradbury EM, Allfrey VG. The structure of chromatin containing DNA complementary to 19 S and 26 S ribosomal RNA in active and inactive stages of Physarum polycephalum. Arch Biochem Biophys. 1978 Dec;191(2):537–560. [PubMed]
  • Johnson EM, Campbell GR, Allfrey VG. Different nucleosome structures on transcribing and nontranscribing ribosomal gene sequences. Science. 1979 Dec 7;206(4423):1192–1194. [PubMed]
  • Pruitt SC, Grainger RM. A mosaicism in the higher order structure of Xenopus oocyte nucleolar chromatin prior to and during ribosomal gene transcription. Cell. 1981 Mar;23(3):711–720. [PubMed]
  • Reeder RH, Wahn HL, Botchan P, Hipskind R, Sollner-Webb B. Ribosomal genes and their proteins from Xenopus. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1167–1177. [PubMed]
  • Allis CD, Glover CV, Bowen JK, Gorovsky MA. Histone variants specific to the transcriptionally active, amitotically dividing macronucleus of the unicellular eucaryote, Tetrahymena thermophila. Cell. 1980 Jul;20(3):609–617. [PubMed]
  • Allis CD, Gorovsky MA. Histone phosphorylation in macro- and micronuclei of Tetrahymena thermophila. Biochemistry. 1981 Jun 23;20(13):3828–3833. [PubMed]
  • Vavra KJ, Allis CD, Gorovsky MA. Regulation of histone acetylation in Tetrahymena macro- and micronuclei. J Biol Chem. 1982 Mar 10;257(5):2591–2598. [PubMed]
  • Foe VE. Modulation of ribosomal RNA synthesis in Oncopeltus fasciatus: an electron microscopic study of the relationship between changes in chromatin structure and transcriptional activity. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):723–740. [PubMed]

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