• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of narLink to Publisher's site
Nucleic Acids Res. Dec 21, 1981; 9(24): 6869–6888.
PMCID: PMC327648

Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA.

Abstract

We have been unable to "force" double-stranded RNA to fold into nucleosome-like structures using several different histone-RNA "reconstitution" procedures. Even if the histones are first stabilized in octameric form by dimethylsuberimidate cross-linking they are still unable to form specific complexes with the RNA. Moreover double-stranded RNA is unable to induce histones to assemble into octamers although we confirm that the non-nucleic acid homopolymer, polyglutamic acid, has this ability. We have also determined, using pyrimidine tract analysis, that nucleosomes will not form over a sufficiently long segment of poly(dA).poly(dT) in a recombinant DNA molecule. Thus nucleosomes cannot fold DNA containing an 80 base pair poly(dA).poly(dT) segment but a 20 base pair segment can be accommodated in nucleosomes fairly well. Segments of intermediate length can be accommodated but are clearly selected against. Poly(dA).poly(dT) differs only slightly from natural DNA in helix structure. Therefore either this homopolymer resists folding, or nucleosomes are very exacting in the nucleic acid steroid parameters they will tolerate. Such constraints may be relevant to nucleosome positioning in chromatin.

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 (2.4M), 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

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Wells RD, Goodman TC, Hillen W, Horn GT, Klein RD, Larson JE, Müller UR, Neuendorf SK, Panayotatos N, Stirdivant SM. DNA structure and gene regulation. Prog Nucleic Acid Res Mol Biol. 1980;24:167–267. [PubMed]
  • Leslie AG, Arnott S, Chandrasekaran R, Ratliff RL. Polymorphism of DNA double helices. J Mol Biol. 1980 Oct 15;143(1):49–72. [PubMed]
  • Dickerson RE, Drew HR. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J Mol Biol. 1981 Jul 15;149(4):761–786. [PubMed]
  • Strauss F, Gaillard C, Prunell A. Helical periodicity of DNA, Poly(dA) . poly(dT) and poly(dA-dT). poly(dA-dT) in solution. Eur J Biochem. 1981 Aug;118(2):215–222. [PubMed]
  • Peck LJ, Wang JC. Sequence dependence of the helical repeat of DNA in solution. Nature. 1981 Jul 23;292(5821):375–378. [PubMed]
  • Shindo H, Wooten JB, Pheiffer BH, Zimmerman SB. Nonuniform backbone conformation of deoxyribonucleic acid indicated by phosphorus-31 nuclear magnetic resonance chemical shift anisotropy. Biochemistry. 1980 Feb 5;19(3):518–526. [PubMed]
  • Zimmerman SB, Pheiffer BH. A RNA.DNA hybrid that can adopt two conformations: an x-ray diffraction study of poly(rA).poly(dT) in concentrated solution or in fibers. Proc Natl Acad Sci U S A. 1981 Jan;78(1):78–82. [PMC free article] [PubMed]
  • Kłysik J, Stirdivant SM, Larson JE, Hart PA, Wells RD. Left-handed DNA in restriction fragments and a recombinant plasmid. Nature. 1981 Apr 23;290(5808):672–677. [PubMed]
  • Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE. Crystal structure analysis of a complete turn of B-DNA. Nature. 1980 Oct 23;287(5784):755–758. [PubMed]
  • Rhodes D, Klug A. Sequence-dependent helical periodicity of DNA. Nature. 1981 Jul 23;292(5821):378–380. [PubMed]
  • Trifonov EN. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res. 1980 Sep 11;8(17):4041–4053. [PMC free article] [PubMed]
  • Behe M, Felsenfeld G. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619–1623. [PMC free article] [PubMed]
  • Kunkel GR, Martinson HG. Histone-DNA interactions within chromatin. Isolation of histones from DNA-histone adducts induced in nuclei by UV light. Nucleic Acids Res. 1978 Nov;5(11):4263–4272. [PMC free article] [PubMed]
  • Chao MV, Gralla J, Martinson HG. DNA sequence directs placement of histone cores on restriction fragments during nucleosome formation. Biochemistry. 1979 Mar 20;18(6):1068–1074. [PubMed]
  • McGhee JD, Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. [PubMed]
  • Finch JT, Brown RS, Richmond T, Rushton B, Lutter LC, Klug A. X-ray diffraction study of a new crystal form of the nucleosome core showing higher resolution. J Mol Biol. 1981 Feb 5;145(4):757–769. [PubMed]
  • Weischet WO, Allen JR, Riedel G, Van Holde KE. The effects of salt concentration and H-1 depletion on the digestion of calf thymus chromatin by micrococcal nuclease. Nucleic Acids Res. 1979;6(5):1843–1862. [PMC free article] [PubMed]
  • Klug A, Rhodes D, Smith J, Finch JT, Thomas JO. A low resolution structure for the histone core of the nucleosome. Nature. 1980 Oct 9;287(5782):509–516. [PubMed]
  • Bryan PN, Wright EB, Hsie MH, Olins AL, Olins DE. Physical properties of inner histone-DNA complexes. Nucleic Acids Res. 1978 Oct;5(10):3603–3617. [PMC free article] [PubMed]
  • Dunn K, Griffith JD. The presence of RNA in a double helix inhibits its interaction with histone protein. Nucleic Acids Res. 1980 Feb 11;8(3):555–566. [PMC free article] [PubMed]
  • Simpson RT, Künzler P. Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. Nucleic Acids Res. 1979 Apr;6(4):1387–1415. [PMC free article] [PubMed]
  • Rhodes D. Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. Nucleic Acids Res. 1979;6(5):1805–1816. [PMC free article] [PubMed]
  • Hovemann B, Galler R, Walldorf U, Küpper H, Bautz EK. Vitellogenin in Drosophila melanogaster: sequence of the yolk protein I gene and its flanking regions. Nucleic Acids Res. 1981 Sep 25;9(18):4721–4734. [PMC free article] [PubMed]
  • D'Andrea R, Harvey R, Wells JR. Vertebrate histone genes: nucleotide sequence of a chicken H2A gene and regulatory flanking sequences. Nucleic Acids Res. 1981 Jul 10;9(13):3119–3128. [PMC free article] [PubMed]
  • Day LE, Hirst AJ, Lai EC, Mace M, Jr, Woo SL. 5' Domain and nucleotide sequence of an adult chicken chromosomal beta-globin gene. Biochemistry. 1981 Apr 14;20(8):2091–2098. [PubMed]
  • Grosschedl R, Birnstiel ML. Spacer DNA sequences upstream of the T-A-T-A-A-A-T-A sequence are essential for promotion of H2A histone gene transcription in vivo. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7102–7106. [PMC free article] [PubMed]
  • Valenzuela P, Bell GI, Masiarz FR, DeGennaro LJ, Rutter WJ. Nucleotide sequence of the yeast 5S ribosomal RNA gene and adjacent putative control regions. Nature. 1977 Jun 16;267(5612):641–643. [PubMed]
  • Maxam AM, Tizard R, Skryabin KG, Gilbert W. Promotor region for yeast 5S ribosomal RNA. Nature. 1977 Jun 16;267(5612):643–645. [PubMed]
  • Vogeli G, Ohkubo H, Sobel ME, Yamada Y, Pastan I, de Crombrugghe B. Structure of the promoter for chicken alpha 2 type I collagen gene. Proc Natl Acad Sci U S A. 1981 Sep;78(9):5334–5338. [PMC free article] [PubMed]
  • Firtel RA, Timm R, Kimmel AR, McKeown M. Unusual nucleotide sequences at the 5' end of actin genes in Dictyostelium discoideum. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6206–6210. [PMC free article] [PubMed]
  • Pan J, Elder JT, Duncan CH, Weissman SM. Structural analysis of interspersed repetitive polymerase III transcription units in human DNA. Nucleic Acids Res. 1981 Mar 11;9(5):1151–1170. [PMC free article] [PubMed]
  • Holm CA, Oliver SG, Newman AM, Holland LE, McLaughlin CS, Wagner EK, Warner RC. The molecular weight of yeast P1 double-stranded RNA. J Biol Chem. 1978 Nov 25;253(22):8332–8336. [PubMed]
  • Fried HM, Fink GR. Electron microscopic heteroduplex analysis of "killer" double-stranded RNA species from yeast. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4224–4228. [PMC free article] [PubMed]
  • Katz L, Kingsbury DT, Helinski DR. Stimulation by cyclic adenosine monophosphate of plasmid deoxyribonucleic acid replication and catabolite repression of the plasmid deoxyribonucleic acid-protein relaxation complex. J Bacteriol. 1973 May;114(2):577–591. [PMC free article] [PubMed]
  • Martinson HG, True R, Burch JB, Kunkel G. Semihistone protein A24 replaces H2A as an integral component of the nucleosome histone core. Proc Natl Acad Sci U S A. 1979 Mar;76(3):1030–1034. [PMC free article] [PubMed]
  • Simon RH, Felsenfeld G. A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res. 1979 Feb;6(2):689–696. [PMC free article] [PubMed]
  • Philip M, Jamaluddin M, Sastry RV, Chandra HS. Nucleosome core histone complex isolated gently and rapidly in 2 M NaCl is octameric. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5178–5182. [PMC free article] [PubMed]
  • Burch JB, Martinson HG. The roles of H1, the histone core and DNA length in the unfolding of nucleosomes at low ionic strength. Nucleic Acids Res. 1980 Nov 11;8(21):4969–4987. [PMC free article] [PubMed]
  • Stein A, Bina-Stein M, Simpson RT. Crosslinked histone octamer as a model of the nucleosome core. Proc Natl Acad Sci U S A. 1977 Jul;74(7):2780–2784. [PMC free article] [PubMed]
  • Lau CK, Fujitaki JM. An improved method of microdialysis. Anal Biochem. 1981 Jan 1;110(1):144–145. [PubMed]
  • Tatchell K, Van Holde KE. Reconstitution of chromatin core particles. Biochemistry. 1977 Nov 29;16(24):5295–5303. [PubMed]
  • Camerini-Otero RD, Sollner-Webb B, Felsenfeld G. The organization of histones and DNA in chromatin: evidence for an arginine-rich histone kernel. Cell. 1976 Jul;8(3):333–347. [PubMed]
  • Birnboim HC, Mitchel RE, Straus NA. Analysis of long pyrimidine polynucleotides in HeLa cell nuclear DNA: absence of polydeoxythymidylate. Proc Natl Acad Sci U S A. 1973 Aug;70(8):2189–2192. [PMC free article] [PubMed]
  • Loening UE. The determination of the molecular weight of ribonucleic acid by polyacrylamide-gel electrophresis. The effects of changes in conformation. Biochem J. 1969 Jun;113(1):131–138. [PMC free article] [PubMed]
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. [PubMed]
  • Maniatis T, Jeffrey A, van deSande H. Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry. 1975 Aug 26;14(17):3787–3794. [PubMed]
  • Stein A, Whitlock JP, Jr, Bina M. Acidic polypeptides can assemble both histones and chromatin in vitro at physiological ionic strength. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5000–5004. [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]
  • Noll M, Zimmer S, Engel A, Dubochet J. Self-assembly of single and closely spaced nucleosome core particles. Nucleic Acids Res. 1980 Jan 11;8(1):21–42. [PMC free article] [PubMed]
  • Kallenbach NR, Berman HM. RNA structure. Q Rev Biophys. 1977 May;10(2):138–236. [PubMed]
  • Mirzabekov AD, Rich A. Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending. Proc Natl Acad Sci U S A. 1979 Mar;76(3):1118–1121. [PMC free article] [PubMed]
  • Palter KB, Alberts BM. The use of DNA-cellulose for analyzing histone-DNA interactions. Discovery of nucleosome-like histone binding to single-stranded DNA. J Biol Chem. 1979 Nov 10;254(21):11160–11169. [PubMed]
  • Nelson T, Wiegand R, Brutlag D. Ribonucleic acid and other polyanions facilitate chromatin assembly in vitro. Biochemistry. 1981 Apr 28;20(9):2594–2601. [PubMed]
  • Thomas JO, Kornberg RD. An octamer of histones in chromatin and free in solution. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2626–2630. [PMC free article] [PubMed]
  • Birnboim HC, Holford RM, Seligy VL. Random phasing of polypyrimidine/polypurine segments and nucleosome monomers in chromatin from mouse L cells. Cold Spring Harb Symp Quant Biol. 1978;42(Pt 2):1161–1165. [PubMed]
  • Chao MV, Martinson HG, Gralla JD. lac Operator nucleosomes. 2. lac Nucleosomes can change conformation to strengthen binding by lac repressor. Biochemistry. 1980 Jul 8;19(14):3260–3269. [PubMed]
  • Villeponteau B, Martinson H. Isolation and characterization of the complete chicken beta-globin gene region: frequent deletion of the adult beta-globin genes in lambda. Nucleic Acids Res. 1981 Aug 11;9(15):3731–3746. [PMC free article] [PubMed]
  • Gronenborn B, Messing J. Methylation of single-stranded DNA in vitro introduces new restriction endonuclease cleavage sites. Nature. 1978 Mar 23;272(5651):375–377. [PubMed]
  • Richards RI, Shine J, Ullrich A, Wells JR, Goodman HM. Molecular cloning and sequence analysis of adult chicken betal globin cDNA. Nucleic Acids Res. 1979 Nov 10;7(5):1137–1146. [PMC free article] [PubMed]

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

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • Compound
    Compound
    PubChem Compound links
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...