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. 1983 Jun 11;11(11):3833–3851. doi: 10.1093/nar/11.11.3833

Nucleotide sequence-directed mapping of the nucleosomes.

G Mengeritsky, E N Trifonov
PMCID: PMC326006  PMID: 6856466

Abstract

The concept of sequence-dependent deformational anisotropy of DNA proposed earlier is further elaborated and a computational procedure is developed for the sequence-directed mapping of the nucleosomes along chromatin DNA nucleotide sequences. The deformational anisotropy is found to be nonuniform along the molecule of the nucleosomal DNA, suggesting that the DNA superhelix in the nucleosome is slightly oval rather than circular in projection. The number of superhelical turns in the nucleosome core particle is estimated to be 2.0 +/- 0.2. Preliminary mapping of the nucleosomes in various chromatin DNA sequences yields the distribution of linker lengths which shows several minima separated by about 10 base-pairs. This is explained by sterical exclusion effects due to overlapping of the nucleosomes in space when some specific linker lengths are chosen. The mapping procedure described is tested by comparing its results with all the most accurate experimental mapping data reported so far. The comparison demonstrates that the exact positions of all the nucleosomes appear to be determined exclusively by the nucleotide sequences.

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Selected References

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

  1. Baralle F. E., Shoulders C. C., Proudfoot N. J. The primary structure of the human epsilon-globin gene. Cell. 1980 Oct;21(3):621–626. doi: 10.1016/0092-8674(80)90425-0. [DOI] [PubMed] [Google Scholar]
  2. Bell G. I., Pictet R. L., Rutter W. J., Cordell B., Tischer E., Goodman H. M. Sequence of the human insulin gene. Nature. 1980 Mar 6;284(5751):26–32. doi: 10.1038/284026a0. [DOI] [PubMed] [Google Scholar]
  3. Bentley G. A., Finch J. T., Lewit-Bentley A. Neutron diffraction studies on crystals of nucleosome cores using contrast variation. J Mol Biol. 1981 Feb 5;145(4):771–784. doi: 10.1016/0022-2836(81)90314-4. [DOI] [PubMed] [Google Scholar]
  4. Chao M. V., Gralla J., Martinson H. G. DNA sequence directs placement of histone cores on restriction fragments during nucleosome formation. Biochemistry. 1979 Mar 20;18(6):1068–1074. doi: 10.1021/bi00573a021. [DOI] [PubMed] [Google Scholar]
  5. Deininger P., Esty A., LaPorte P., Friedmann T. Nucleotide sequence and genetic organization of the polyoma late region: features common to the polyoma early region and SV40. Cell. 1979 Nov;18(3):771–779. doi: 10.1016/0092-8674(79)90130-2. [DOI] [PubMed] [Google Scholar]
  6. Dickson R. C., Abelson J., Barnes W. M., Reznikoff W. S. Genetic regulation: the Lac control region. Science. 1975 Jan 10;187(4171):27–35. doi: 10.1126/science.1088926. [DOI] [PubMed] [Google Scholar]
  7. Farabaugh P. J. Sequence of the lacI gene. Nature. 1978 Aug 24;274(5673):765–769. doi: 10.1038/274765a0. [DOI] [PubMed] [Google Scholar]
  8. Fiers W., Contreras R., Haegemann G., Rogiers R., Van de Voorde A., Van Heuverswyn H., Van Herreweghe J., Volckaert G., Ysebaert M. Complete nucleotide sequence of SV40 DNA. Nature. 1978 May 11;273(5658):113–120. doi: 10.1038/273113a0. [DOI] [PubMed] [Google Scholar]
  9. Friedmann T., Esty A., LaPorte P., Deininger P. The nucleotide sequence and genome organization of the polyoma early region: extensive nucleotide and amino acid homology with SV40. Cell. 1979 Jul;17(3):715–724. doi: 10.1016/0092-8674(79)90278-2. [DOI] [PubMed] [Google Scholar]
  10. Hartley J. L., Donelson J. E. Nucleotide sequence of the yeast plasmid. Nature. 1980 Aug 28;286(5776):860–865. doi: 10.1038/286860a0. [DOI] [PubMed] [Google Scholar]
  11. Honjo T., Obata M., Yamawaki-Katoaka Y., Kataoka T., Kawakami T., Takahashi N., Mano Y. Cloning and complete nucleotide sequence of mouse immunoglobulin gamma 1 chain gene. Cell. 1979 Oct;18(2):559–568. doi: 10.1016/0092-8674(79)90072-2. [DOI] [PubMed] [Google Scholar]
  12. Igo-Kemenes T., Omori A., Zachau H. G. Non-random arrangement of nucleosomes in satellite I containing chromatin of rat liver. Nucleic Acids Res. 1980 Nov 25;8(22):5377–5390. doi: 10.1093/nar/8.22.5377. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Ingolia T. D., Craig E. A., McCarthy B. J. Sequence of three copies of the gene for the major Drosophila heat shock induced protein and their flanking regions. Cell. 1980 Oct;21(3):669–679. doi: 10.1016/0092-8674(80)90430-4. [DOI] [PubMed] [Google Scholar]
  14. Karpov V. L., Bavykin S. G., Preobrazhenskaya O. V., Belyavsky A. V., Mirzabekov A. D. Alignment of nucleosomes along DNA and organization of spacer DNA in Drosophila chromatin. Nucleic Acids Res. 1982 Jul 24;10(14):4321–4337. doi: 10.1093/nar/10.14.4321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Kawakami T., Takahashi N., Honjo T. Complete nucleotide sequence of mouse immunoglobulin mu gene and comparison with other immunoglobulin heavy chain genes. Nucleic Acids Res. 1980 Sep 11;8(17):3933–3945. doi: 10.1093/nar/8.17.3933. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Konkel D. A., Maizel J. V., Jr, Leder P. The evolution and sequence comparison of two recently diverged mouse chromosomal beta--globin genes. Cell. 1979 Nov;18(3):865–873. doi: 10.1016/0092-8674(79)90138-7. [DOI] [PubMed] [Google Scholar]
  17. Kornberg R. The location of nucleosomes in chromatin: specific or statistical. Nature. 1981 Aug 13;292(5824):579–580. doi: 10.1038/292579a0. [DOI] [PubMed] [Google Scholar]
  18. Lawn R. M., Efstratiadis A., O'Connell C., Maniatis T. The nucleotide sequence of the human beta-globin gene. Cell. 1980 Oct;21(3):647–651. doi: 10.1016/0092-8674(80)90428-6. [DOI] [PubMed] [Google Scholar]
  19. Lee C. H., Charney E. Solution conformation of DNA. J Mol Biol. 1982 Oct 25;161(2):289–303. doi: 10.1016/0022-2836(82)90154-1. [DOI] [PubMed] [Google Scholar]
  20. Lohr D., Van Holde K. E. Organization of spacer DNA in chromatin. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6326–6330. doi: 10.1073/pnas.76.12.6326. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. doi: 10.1146/annurev.bi.49.070180.005343. [DOI] [PubMed] [Google Scholar]
  23. Miller J. R., Cartwright E. M., Brownlee G. G., Fedoroff N. V., Brown D. D. The nucleotide sequence of oocyte 5S DNA in Xenopus laevis. II. The GC-rich region. Cell. 1978 Apr;13(4):717–725. doi: 10.1016/0092-8674(78)90221-0. [DOI] [PubMed] [Google Scholar]
  24. Mirzabekov A. D. Nucleosomes structure and its dynamic transitions. Q Rev Biophys. 1980 May;13(2):255–295. doi: 10.1017/s0033583500001670. [DOI] [PubMed] [Google Scholar]
  25. Moss T., Boseley P. G., Birnstiel M. L. More ribosomal spacer sequences from Xenopus laevis. Nucleic Acids Res. 1980 Feb 11;8(3):467–485. doi: 10.1093/nar/8.3.467. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Musich P. R., Brown F. L., Maio J. J. Nucleosome phasing and micrococcal nuclease cleavage of African green monkey component alpha DNA. Proc Natl Acad Sci U S A. 1982 Jan;79(1):118–122. doi: 10.1073/pnas.79.1.118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Ng R., Abelson J. Isolation and sequence of the gene for actin in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3912–3916. doi: 10.1073/pnas.77.7.3912. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Pech M., Igo-Kemenes T., Zachau H. G. Nucleotide sequence of a highly repetitive component of rat DNA. Nucleic Acids Res. 1979 Sep 25;7(2):417–432. doi: 10.1093/nar/7.2.417. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Ponder B. A., Crawford L. V. The arrangement of nucleosomes in nucleoprotein complexes from polyoma virus and SV40. Cell. 1977 May;11(1):35–49. doi: 10.1016/0092-8674(77)90315-4. [DOI] [PubMed] [Google Scholar]
  30. Reddy V. B., Thimmappaya B., Dhar R., Subramanian K. N., Zain B. S., Pan J., Ghosh P. K., Celma M. L., Weissman S. M. The genome of simian virus 40. Science. 1978 May 5;200(4341):494–502. doi: 10.1126/science.205947. [DOI] [PubMed] [Google Scholar]
  31. Robertson M. A., Staden R., Tanaka Y., Catterall J. F., O'Malley B. W., Brownlee G. G. Sequence of three introns in the chick ovalbumin gene. Nature. 1979 Mar 22;278(5702):370–372. doi: 10.1038/278370a0. [DOI] [PubMed] [Google Scholar]
  32. Rosenberg H., Singer M., Rosenberg M. Highly reiterated sequences of SIMIANSIMIANSIMIANSIMIANSIMIAN. Science. 1978 Apr 28;200(4340):394–402. doi: 10.1126/science.205944. [DOI] [PubMed] [Google Scholar]
  33. Rubtsov P. M., Musakhanov M. M., Zakharyev V. M., Krayev A. S., Skryabin K. G., Bayev A. A. The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae. Nucleic Acids Res. 1980 Dec 11;8(23):5779–5794. doi: 10.1093/nar/8.23.5779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sakano H., Hüppi K., Heinrich G., Tonegawa S. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature. 1979 Jul 26;280(5720):288–294. doi: 10.1038/280288a0. [DOI] [PubMed] [Google Scholar]
  35. Sakano H., Maki R., Kurosawa Y., Roeder W., Tonegawa S. Two types of somatic recombination are necessary for the generation of complete immunoglobulin heavy-chain genes. Nature. 1980 Aug 14;286(5774):676–683. doi: 10.1038/286676a0. [DOI] [PubMed] [Google Scholar]
  36. Seif I., Khoury G., Dhar R. The genome of human papovavirus BKV. Cell. 1979 Dec;18(4):963–977. doi: 10.1016/0092-8674(79)90209-5. [DOI] [PubMed] [Google Scholar]
  37. Simpson R. T. Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry. 1978 Dec 12;17(25):5524–5531. doi: 10.1021/bi00618a030. [DOI] [PubMed] [Google Scholar]
  38. Slightom J. L., Blechl A. E., Smithies O. Human fetal G gamma- and A gamma-globin genes: complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes. Cell. 1980 Oct;21(3):627–638. doi: 10.1016/0092-8674(80)90426-2. [DOI] [PubMed] [Google Scholar]
  39. Spritz R. A., DeRiel J. K., Forget B. G., Weissman S. M. Complete nucleotide sequence of the human delta-globin gene. Cell. 1980 Oct;21(3):639–646. doi: 10.1016/0092-8674(80)90427-4. [DOI] [PubMed] [Google Scholar]
  40. Strauss F., Prunell A. Organization of internucleosomal DNA in rat liver chromatin. EMBO J. 1983;2(1):51–56. doi: 10.1002/j.1460-2075.1983.tb01379.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sures I., Lowry J., Kedes L. H. The DNA sequence of sea urchin (S. purpuratus) H2A, H2B and H3 histone coding and spacer regions. Cell. 1978 Nov;15(3):1033–1044. doi: 10.1016/0092-8674(78)90287-8. [DOI] [PubMed] [Google Scholar]
  42. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  43. Trifonov E. N. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res. 1980 Sep 11;8(17):4041–4053. doi: 10.1093/nar/8.17.4041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Trifonov E. N., Sussman J. L. The pitch of chromatin DNA is reflected in its nucleotide sequence. Proc Natl Acad Sci U S A. 1980 Jul;77(7):3816–3820. doi: 10.1073/pnas.77.7.3816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Tsujimoto Y., Suzuki Y. The DNA sequence of Bombyx mori fibroin gene including the 5' flanking, mRNA coding, entire intervening and fibroin protein coding regions. Cell. 1979 Oct;18(2):591–600. doi: 10.1016/0092-8674(79)90075-8. [DOI] [PubMed] [Google Scholar]
  46. Tucker P. W., Marcu K. B., Newell N., Richards J., Blattner F. R. Sequence of the cloned gene for the constant region of murine gamma 2b immunoglobulin heavy chain. Science. 1979 Dec 14;206(4424):1303–1306. doi: 10.1126/science.117549. [DOI] [PubMed] [Google Scholar]
  47. Zachau H. G., Igo-Kemenes T. Face to phase with nucleosomes. Cell. 1981 Jun;24(3):597–598. doi: 10.1016/0092-8674(81)90084-2. [DOI] [PubMed] [Google Scholar]
  48. van Ooyen A., van den Berg J., Mantei N., Weissmann C. Comparison of total sequence of a cloned rabbit beta-globin gene and its flanking regions with a homologous mouse sequence. Science. 1979 Oct 19;206(4416):337–344. doi: 10.1126/science.482942. [DOI] [PubMed] [Google Scholar]

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