Abstract
Nucleosome dimers containing, on average, a single molecule of histone H5 have been isolated from chicken erythrocyte nuclei and the associated DNA fragments cloned and sequenced. The average sequence organization of at least one of the two nucleosomes in the dimers is highly asymmetric and suggests that the torsional, as well as the axial, flexibility of DNA is a determinant of nucleosome positioning. On average the nucleosome dimer is a polar structure containing linker DNA of variable lengths. The sequences associated with H5 containing nucleosomes and core particles are sufficiently different to indicate that removal of histone H5 (or H1) from chromatin may result in the migration of the histone octamer and a consequent exposure of sites for regulatory proteins.
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- Allan J., Hartman P. G., Crane-Robinson C., Aviles F. X. The structure of histone H1 and its location in chromatin. Nature. 1980 Dec 25;288(5792):675–679. doi: 10.1038/288675a0. [DOI] [PubMed] [Google Scholar]
- Almer A., Rudolph H., Hinnen A., Hörz W. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 1986 Oct;5(10):2689–2696. doi: 10.1002/j.1460-2075.1986.tb04552.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Belyavsky A. V., Bavykin S. G., Goguadze E. G., Mirzabekov A. D. Primary organization of nucleosomes containing all five histones and DNA 175 and 165 base-pairs long. J Mol Biol. 1980 May 25;139(3):519–536. doi: 10.1016/0022-2836(80)90144-8. [DOI] [PubMed] [Google Scholar]
- Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bordas J., Perez-Grau L., Koch M. H., Vega M. C., Nave C. The superstructure of chromatin and its condensation mechanism. II. Theoretical analysis of the X-ray scattering patterns and model calculations. Eur Biophys J. 1986;13(3):175–185. doi: 10.1007/BF00542561. [DOI] [PubMed] [Google Scholar]
- Butler P. J. The folding of chromatin. CRC Crit Rev Biochem. 1983;15(1):57–91. doi: 10.3109/10409238309102801. [DOI] [PubMed] [Google Scholar]
- Calladine C. R., Drew H. R. Principles of sequence-dependent flexure of DNA. J Mol Biol. 1986 Dec 20;192(4):907–918. doi: 10.1016/0022-2836(86)90036-7. [DOI] [PubMed] [Google Scholar]
- Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
- Clark D. J., Thomas J. O. Salt-dependent co-operative interaction of histone H1 with linear DNA. J Mol Biol. 1986 Feb 20;187(4):569–580. doi: 10.1016/0022-2836(86)90335-9. [DOI] [PubMed] [Google Scholar]
- Drew H. R., Calladine C. R. Sequence-specific positioning of core histones on an 860 base-pair DNA. Experiment and theory. J Mol Biol. 1987 May 5;195(1):143–173. doi: 10.1016/0022-2836(87)90333-0. [DOI] [PubMed] [Google Scholar]
- Drew H. R., Travers A. A. DNA bending and its relation to nucleosome positioning. J Mol Biol. 1985 Dec 20;186(4):773–790. doi: 10.1016/0022-2836(85)90396-1. [DOI] [PubMed] [Google Scholar]
- Drew H. R., Weeks J. R., Travers A. A. Negative supercoiling induces spontaneous unwinding of a bacterial promoter. EMBO J. 1985 Apr;4(4):1025–1032. doi: 10.1002/j.1460-2075.1985.tb03734.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Drinkwater R. D., Wilson P. J., Skinner J. D., Burgoyne L. A. Chromatin structures: dissecting their mixed patterns in nuclease digests. Nucleic Acids Res. 1987 Oct 12;15(19):8087–8103. doi: 10.1093/nar/15.19.8087. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Finch J. T., Klug A. Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci U S A. 1976 Jun;73(6):1897–1901. doi: 10.1073/pnas.73.6.1897. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hattori M., Sakaki Y. Dideoxy sequencing method using denatured plasmid templates. Anal Biochem. 1986 Feb 1;152(2):232–238. doi: 10.1016/0003-2697(86)90403-3. [DOI] [PubMed] [Google Scholar]
- Hogan M. E., Rooney T. F., Austin R. H. Evidence for kinks in DNA folding in the nucleosome. Nature. 1987 Aug 6;328(6130):554–557. doi: 10.1038/328554a0. [DOI] [PubMed] [Google Scholar]
- Keene M. A., Elgin S. C. Micrococcal nuclease as a probe of DNA sequence organization and chromatin structure. Cell. 1981 Nov;27(1 Pt 2):57–64. doi: 10.1016/0092-8674(81)90360-3. [DOI] [PubMed] [Google Scholar]
- Kefalas P., Gray F. C., Allan J. Precise nucleosome positioning in the promoter of the chicken beta A globin gene. Nucleic Acids Res. 1988 Jan 25;16(2):501–517. doi: 10.1093/nar/16.2.501. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Khachatrian A. T., Pospelov V. A., Svetlikova S. B., Vorob'ev V. I. Nucleodisome - a new repeat unit of chromatin revealed in nuclei of pigeon erythrocytes by DNase I digestion. FEBS Lett. 1981 Jun 1;128(1):90–92. doi: 10.1016/0014-5793(81)81087-3. [DOI] [PubMed] [Google Scholar]
- Klug A., Lutter L. C. The helical periodicity of DNA on the nucleosome. Nucleic Acids Res. 1981 Sep 11;9(17):4267–4283. doi: 10.1093/nar/9.17.4267. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kunkel G. R., Martinson H. G. Nucleosomes will not form on double-stranded RNa or over poly(dA).poly(dT) tracts in recombinant DNA. Nucleic Acids Res. 1981 Dec 21;9(24):6869–6888. doi: 10.1093/nar/9.24.6869. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lennard A. C., Thomas J. O. The arrangement of H5 molecules in extended and condensed chicken erythrocyte chromatin. EMBO J. 1985 Dec 16;4(13A):3455–3462. doi: 10.1002/j.1460-2075.1985.tb04104.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Linxweller W., Hörz W. Reconstitution experiments show that sequence-specific histone-DNA interactions are the basis for nucleosome phasing on mouse satellite DNA. Cell. 1985 Aug;42(1):281–290. doi: 10.1016/s0092-8674(85)80123-9. [DOI] [PubMed] [Google Scholar]
- 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]
- Lutter L. C. Kinetic analysis of deoxyribonuclease I cleavages in the nucleosome core: evidence for a DNA superhelix. J Mol Biol. 1978 Sep 15;124(2):391–420. doi: 10.1016/0022-2836(78)90306-6. [DOI] [PubMed] [Google Scholar]
- McGhee J. D., Felsenfeld G. Reaction of nucleosome DNA with dimethyl sulfate. Proc Natl Acad Sci U S A. 1979 May;76(5):2133–2137. doi: 10.1073/pnas.76.5.2133. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McGhee J. D., Wood W. I., Dolan M., Engel J. D., Felsenfeld G. A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion. Cell. 1981 Nov;27(1 Pt 2):45–55. doi: 10.1016/0092-8674(81)90359-7. [DOI] [PubMed] [Google Scholar]
- Morris N. R. A comparison of the structure of chicken erythrocyte and chicken liver chromatin. Cell. 1976 Dec;9(4 Pt 1):627–632. doi: 10.1016/0092-8674(76)90045-3. [DOI] [PubMed] [Google Scholar]
- Nelson H. C., Finch J. T., Luisi B. F., Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 1987 Nov 19;330(6145):221–226. doi: 10.1038/330221a0. [DOI] [PubMed] [Google Scholar]
- 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]
- Park K., Fasman G. D. The histone octamer, a conformationally flexible structure. Biochemistry. 1987 Dec 15;26(25):8042–8045. doi: 10.1021/bi00399a003. [DOI] [PubMed] [Google Scholar]
- Parsons C. A., West S. C. Resolution of model Holliday junctions by yeast endonuclease is dependent upon homologous DNA sequences. Cell. 1988 Feb 26;52(4):621–629. doi: 10.1016/0092-8674(88)90474-6. [DOI] [PubMed] [Google Scholar]
- Prunell A., Kornberg R. D. Variable center to center distance of nucleosomes in chromatin. J Mol Biol. 1982 Jan 25;154(3):515–523. doi: 10.1016/s0022-2836(82)80010-7. [DOI] [PubMed] [Google Scholar]
- Prunell A. Nucleosome reconstitution on plasmid-inserted poly(dA) . poly(dT). EMBO J. 1982;1(2):173–179. doi: 10.1002/j.1460-2075.1982.tb01143.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ramsay N. Deletion analysis of a DNA sequence that positions itself precisely on the nucleosome core. J Mol Biol. 1986 May 5;189(1):179–188. doi: 10.1016/0022-2836(86)90389-x. [DOI] [PubMed] [Google Scholar]
- Rhodes D. Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. Nucleic Acids Res. 1979;6(5):1805–1816. doi: 10.1093/nar/6.5.1805. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhodes D. Structural analysis of a triple complex between the histone octamer, a Xenopus gene for 5S RNA and transcription factor IIIA. EMBO J. 1985 Dec 16;4(13A):3473–3482. doi: 10.1002/j.1460-2075.1985.tb04106.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Richard-Foy H., Hager G. L. Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO J. 1987 Aug;6(8):2321–2328. doi: 10.1002/j.1460-2075.1987.tb02507.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Richmond T. J., Finch J. T., Rushton B., Rhodes D., Klug A. Structure of the nucleosome core particle at 7 A resolution. Nature. 1984 Oct 11;311(5986):532–537. doi: 10.1038/311532a0. [DOI] [PubMed] [Google Scholar]
- SWARTZ M. N., TRAUTNER T. A., KORNBERG A. Enzymatic synthesis of deoxyribonucleic acid. XI. Further studies on nearest neighbor base sequences in deoxyribonucleic acids. J Biol Chem. 1962 Jun;237:1961–1967. [PubMed] [Google Scholar]
- Satchwell S. C., Drew H. R., Travers A. A. Sequence periodicities in chicken nucleosome core DNA. J Mol Biol. 1986 Oct 20;191(4):659–675. doi: 10.1016/0022-2836(86)90452-3. [DOI] [PubMed] [Google Scholar]
- Schlissel M. S., Brown D. D. The transcriptional regulation of Xenopus 5s RNA genes in chromatin: the roles of active stable transcription complexes and histone H1. Cell. 1984 Jul;37(3):903–913. doi: 10.1016/0092-8674(84)90425-2. [DOI] [PubMed] [Google Scholar]
- Simpson R. T., 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. doi: 10.1093/nar/6.4.1387. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Snyder M., Buchman A. R., Davis R. W. Bent DNA at a yeast autonomously replicating sequence. Nature. 1986 Nov 6;324(6092):87–89. doi: 10.1038/324087a0. [DOI] [PubMed] [Google Scholar]
- Staden R. Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):521–538. doi: 10.1093/nar/12.1part2.521. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staden R. The current status and portability of our sequence handling software. Nucleic Acids Res. 1986 Jan 10;14(1):217–231. doi: 10.1093/nar/14.1.217. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Sullivan K. M., Lilley D. M. A dominant influence of flanking sequences on a local structural transition in DNA. Cell. 1986 Dec 5;47(5):817–827. doi: 10.1016/0092-8674(86)90524-6. [DOI] [PubMed] [Google Scholar]
- Thoma F., Koller T., Klug A. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol. 1979 Nov;83(2 Pt 1):403–427. doi: 10.1083/jcb.83.2.403. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thomas J. O., Rees C. Exchange of histones H1 and H5 between chromatin fragments. A preference of H5 for higher-order structures. Eur J Biochem. 1983 Jul 15;134(1):109–115. doi: 10.1111/j.1432-1033.1983.tb07538.x. [DOI] [PubMed] [Google Scholar]
- Thomas J. O. The higher order structure of chromatin and histone H1. J Cell Sci Suppl. 1984;1:1–20. doi: 10.1242/jcs.1984.supplement_1.1. [DOI] [PubMed] [Google Scholar]
- Travers A. A., Klug A. The bending of DNA in nucleosomes and its wider implications. Philos Trans R Soc Lond B Biol Sci. 1987 Dec 15;317(1187):537–561. doi: 10.1098/rstb.1987.0080. [DOI] [PubMed] [Google Scholar]
- Turnell W. G., Satchwell S. C., Travers A. A. A decapeptide motif for binding to the minor groove of DNA. A proposal. FEBS Lett. 1988 May 23;232(2):263–268. doi: 10.1016/0014-5793(88)80750-6. [DOI] [PubMed] [Google Scholar]
- Uberbacher E. C., Bunick G. J. X-ray structure of the nucleosome core particle. J Biomol Struct Dyn. 1985 Jun;2(6):1033–1055. doi: 10.1080/07391102.1985.10507623. [DOI] [PubMed] [Google Scholar]
- Varshavsky A. J., Bakayev V. V., Georgiev G. P. Heterogeneity of chromatin subunits in vitro and location of histone H1. Nucleic Acids Res. 1976 Feb;3(2):477–492. doi: 10.1093/nar/3.2.477. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Widmer R. M., Lezzi M., Koller T. Structural transition in inactive Balbiani ring chromatin of Chironomus during micrococcus nuclease digestion. EMBO J. 1987 Mar;6(3):743–748. doi: 10.1002/j.1460-2075.1987.tb04816.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Widom J., Finch J. T., Thomas J. O. Higher-order structure of long repeat chromatin. EMBO J. 1985 Dec 1;4(12):3189–3194. doi: 10.1002/j.1460-2075.1985.tb04064.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Widom J., Klug A. Structure of the 300A chromatin filament: X-ray diffraction from oriented samples. Cell. 1985 Nov;43(1):207–213. doi: 10.1016/0092-8674(85)90025-x. [DOI] [PubMed] [Google Scholar]
- Williams S. P., Athey B. D., Muglia L. J., Schappe R. S., Gough A. H., Langmore J. P. Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophys J. 1986 Jan;49(1):233–248. doi: 10.1016/S0006-3495(86)83637-2. [DOI] [PMC free article] [PubMed] [Google Scholar]