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Identification of human satellite DNA sequences associated with chemically resistant nonhistone polypeptide adducts

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Abstract

A fraction of DNA fragments of highly purified and completely unfolded eukaryotic DNA inevitably remains associated with chemically resistant nonhistone DNA-polypeptide complexes. This fraction can be isolated by nitrocellulose filtration because the polypeptide-associated DNA fragments are retained on nitrocellulose filters while bulk DNA passes through the filters. The fraction of AluI-fragmented DNA from human placenta retained on filters as a result of the binding factors (R-DNA, ∼12%) represents a subset of genomic sequences with a sequence complexity different from unfractionated DNA and DNA recovered in the filtrate (F-DNA). DNA sequences prevalent in the retained fraction were detected by differential plaque hybridization of a recombinant λgt10 library with radiolabeled F- and R-DNA fractions. Several recombinant phages showing much stronger hybridization signals with the R-DNA probe than with the F-DNA probe were selected, plaque-purified and analyzed. Analysis of the inserts of such clones showed that repetitive DNA sequences of the alphoid dimeric and tetrameric family, satellite III and satellite III-like sequences are highly enriched in the retained fraction, which indicates that these sequences specifically attract the polypeptides involved in the tightly bound and resistant complexes. This property of repetitive sequences is of interest since tandemly repetitive sequences have been suggested to code for locus-specific fixation and stabilization of the chromatin fiber in the cell nucleus.

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References

  • Baldini A, Smith DI, Rocchi M, Miller OJ, Miller DA (1989) A human alphoid DNA clone from the EcoRI dimeric family: Genomic and internal organization and chromosomal assignment. Genomics 5:822–828

    Google Scholar 

  • Basler J, Hastie ND, Pietras D, Matsui SI, Sandberg AA, Berezney R (1981) Hybridization of nuclear matrix attached deoxyribonucleic acid fragments. Biochemistry 20:6921–6929

    Google Scholar 

  • Berezney R (1984) Organizations and functions of the nuclear matrix. In: Hnilica LS (ed) Chromosomal nonhistone proteins, vol 4. CRC Press, Boca Raton, pp 119–180

    Google Scholar 

  • Berezney R, Coffey DS (1976) The nuclear protein matrix: isolation, structure and function. Adv Enzyme Regul 14: 63–100

    Google Scholar 

  • Beridze T (1982) Satellite DNA. Springer, Berlin Heidelberg New York

    Google Scholar 

  • Blin N, Stafford DW (1976) Isolation of high molecular weight DNA. Nucleic Acids Res 3: 2303–2308

    Google Scholar 

  • Church GM, Gilbert W (1984) Genomic sequencing. Proc Natl Acad Sci USA 81: 1991–1995

    Google Scholar 

  • Ciejek EM, Tsai MJ, O'Malley BW (1983) Actively transcribed genes are associated with the nuclear matrix. Nature 306: 607–609

    Google Scholar 

  • Cook PR, Brazell IA (1975) Supercoils in human DNA. J Cell Sci 19: 261–279

    Google Scholar 

  • Feinberg AP, Vogelstein B (1984) A technique for radiolabeling DNA restriction nuclease fragments to high specific activity. Anal Biochem 132: 6–13

    Google Scholar 

  • Frommer M, Prosser J, Tkachuk D, Reisner AH, Vincent PC (1982) Simple repeated sequences in human satellite DNA. Nucleic Acids Res 10: 547–563

    Google Scholar 

  • Gasser SM (1988) Nuclear scaffold and the higher-order folding of eukaryotic DNA. In: Kahl G (ed) Architecture of eukaryotic genes. VCH, Weinheim, pp 461–471

    Google Scholar 

  • Goldberg GI, Collier I, Cassel A (1983) Specific DNA sequences associated with the nuclear matrix in synchronized mouse 3T3 cells. Proc Natl Acad Sci USA 80: 6887–6891

    Google Scholar 

  • Gross-Bellard M, Oudet P, Chambon P (1973) Isolation of high molecular weight DNA from mammalian cells. Eur J Biochem 36: 32–38

    Google Scholar 

  • Henninghausen L, Lubon H (1987) Interaction of protein with DNA in vitro. Methods Enzymol 152: 721–735

    Google Scholar 

  • Jackson DA, Cook PR, Patel SB (1984) Attachment of repeated sequences to the nuclear cage. Nucleic Acids Res 12: 6709–6726

    Google Scholar 

  • Juodka B, Pfütz M, Werner D (1991) Chemical and enzymatic analysis of covalent bonds between peptides and chromosomal DNA. Nucleic Acids Res 19: 6391–6398

    Google Scholar 

  • Käs E, Chasin LA (1987) Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs at intragenic regions. J Mol Biol 198: 677–692

    Google Scholar 

  • Lu X, Werner D (1988) Construction and quality of cDNA libraries from cytoplasmic RNA not enriched in poly(A+). Gene 71: 157–164

    Google Scholar 

  • Maio JJ (1971) DNA strand reassociation and polyribonucleotide binding in the African green monkley. J Mol Biol 56: 579–595

    Google Scholar 

  • Manuelidis L (1978) Chromosomal localization of complex and simple repeated human DNAs. Chromosoma 66: 23–32

    Google Scholar 

  • Matsumoto LH (1981) Enrichment of satellite DNA on the nuclear matrix of bovine cells. Nature 294: 481–482

    Google Scholar 

  • Mirkovitch J, Mirault ME, Laemmli UK (1984) Organization of the higher order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39: 223–232

    Google Scholar 

  • Musich PR, Brown FL, Maio JJ (1980) Highly repetitive component α and related alphoid DNAs in man and monkey. Chromosoma 80: 331–348

    Google Scholar 

  • Neuer B, Werner D (1985) Screening of isolated DNA for sequences released from anchorage sites in nuclear matrix. J Mol Biol 181: 15–25

    Google Scholar 

  • Neuer B, Plagens U, Werner D (1983) Phosphodiester bonds between polypeptides and chromosomal DNA. J Mol Biol 164: 213–235

    Google Scholar 

  • Neuer-Nitsche B, Werner D (1987) Sub-set characteristics of DNA sequences involved in tight DNA/polypeptide complexes and their homology to nuclear matrix DNA. Biochem Biophys Res Commun 147: 335–339

    Google Scholar 

  • Neuer-Nitsche B, Lu X, Werner D (1988) Functional role of a highly repetitive DNA sequence in anchorage of the mouse genome. Nucleic Acids Res 16: 8351–8360

    Google Scholar 

  • Paulson JR, Laemmli UK (1977) The structure of histone-depleted metaphase chromosomes. Cell 12: 817–828

    Google Scholar 

  • Robinson SJ, Nmall D, Idzerda R, McKnight GS, Vogelstein B (1983) The association of transcriptionally active genes with the nuclear matrix of the chicken oviduct. Nucleic Acids Res 11: 5113–5130

    Google Scholar 

  • Robinson SJ, Nelkin BD, Vogelstein B (1984) The ovalbumin gene is associated with the nuclear matrix of chiken oviduct cells. Cell 28: 99–106

    Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463–5467

    Google Scholar 

  • Strauss F, Varshavsky A (1984) A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome. Cell 37: 889–901

    Google Scholar 

  • Vissel B, Choo KH (1987) Human alpha satellite DNA-consensus sequence and conserved regions. Nucleic Acids Res 15: 6751

    Google Scholar 

  • Vogelstein B, Pardoll DM, Coffey DS (1980) Supercoiled loops and DNA replication. Cell 22: 79–85

    Google Scholar 

  • Vogt P (1990) Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved ‘chromatin folding code’. Hum Genet 84: 301–336

    Google Scholar 

  • Werner D, Neuer-Nitsche B (1989a) Discontinuities of peptide nature in DNA. In: Bekhor I, Liew CC (eds) Progress in nonhistone protein research, vol 3, CRC Press, Boca, Raton, pp 99–118

    Google Scholar 

  • Werner D, Neuer-Nitsche B (1989b) Site-specific location of covalent DNA-polypeptide complexes in the chicken genome. Nucleic Acids Res 17: 6005–6015

    Google Scholar 

  • Werner D, Rest R (1987) Radiolabelling of DNA/polypeptide complexes in isolated bulk DNA and in nuclear matrix DNA. Biochem Biophys Res Commun 147: 340–345

    Google Scholar 

  • Werner D, Chanpu S, Müller M, Spiess E, Plagens U (1984) Antibodies to the most tightly bound proteins in DNA. Formation of immuno-complexes with nuclear matrix components. Exp Cell Res 51: 384–395

    Google Scholar 

  • Werner D, Rest R, Neuer-Nitsche B (1988) Nuclear matrix. In: Kahl G (ed) Architecture of eukaryotic genes. VCH, Weinheim, pp 449–459

    Google Scholar 

  • Willard HF (1985) Chromosome-specific organization of human alpha satellite DNA. Am J Hum Genet 37: 524–532

    Google Scholar 

  • Willard HF, Waye JS (1987) Hierarchical order in chromosome-specific human alpha satellite DNA. Trends Genet 3: 192–198

    Google Scholar 

  • Wu JC, Manuelidis L (1980) Sequence definition and organization of a human repeated DNA. J Mol Biol 142: 363–386

    Google Scholar 

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Author notes

  1. Opher Gileadi

    Present address: Department of Cell Biosogy, Stanford School of Medicine, 94305, Stanford, CA, USA

Authors and Affiliations

  1. Institute of Cell and Tumor Biology, German Cancer Research Center, Im Neuenheimer Feld 280, W-6900, Heidelberg, Federal Republic of Germany

    Marita Pfütz, Opher Gileadi & Dieter Werner

Authors
  1. Marita Pfütz
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  2. Opher Gileadi
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  3. Dieter Werner
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by L. Manuelidis

This work contains parts of the Ph.D. thesis of M.P. (University of Giessen).

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Pfütz, M., Gileadi, O. & Werner, D. Identification of human satellite DNA sequences associated with chemically resistant nonhistone polypeptide adducts. Chromosoma 101, 609–617 (1992). https://doi.org/10.1007/BF00360538

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  • DOI: https://doi.org/10.1007/BF00360538

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