Abstract
Photo-induced thymine dimer formation was used to probe nucleosome structure in nuclei. The distribution of thymine dimers in the nucleosome and recent studies of the structure of thymine dimer-containing DNA suggest that the rate of thymine dimer formation is affected by the direction and degree of DNA bending. This premise was used to construct a model of the path of DNA in the nucleosome, which has the following features. (i) There are four regions of sharp bending, two which have been seen previously by x-ray crystallography of the core particle. (ii) The DNA in H1-containing nucleosomes deviates from its superhelical path near the midpoint; this is not seen with H1-stripped chromatin. (iii) The internucleosomal (linker) DNA appears to be relatively straight.
Full text
PDF![9149](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5028/298451/c9dfb1563817/pnas00290-0107.png)
![9150](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5028/298451/b44653b90c06/pnas00290-0108.png)
![9151](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5028/298451/854fee50a836/pnas00290-0109.png)
![9152](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5028/298451/dd47c8d29e1b/pnas00290-0110.png)
![9153](https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5028/298451/10b4875eaf96/pnas00290-0111.png)
Images in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Crothers D. M., Dattagupta N., Hogan M., Klevan L., Lee K. S. Transient electric dichroism studies of nucleosomal particles. Biochemistry. 1978 Oct 17;17(21):4525–4533. doi: 10.1021/bi00614a026. [DOI] [PubMed] [Google Scholar]
- Doetsch P. W., Chan G. L., Haseltine W. A. T4 DNA polymerase (3'-5') exonuclease, an enzyme for the detection and quantitation of stable DNA lesions: the ultraviolet light example. Nucleic Acids Res. 1985 May 10;13(9):3285–3304. doi: 10.1093/nar/13.9.3285. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gale J. M., Nissen K. A., Smerdon M. J. UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6644–6648. doi: 10.1073/pnas.84.19.6644. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gale J. M., Smerdon M. J. Photofootprint of nucleosome core DNA in intact chromatin having different structural states. J Mol Biol. 1988 Dec 20;204(4):949–958. doi: 10.1016/0022-2836(88)90054-x. [DOI] [PubMed] [Google Scholar]
- Gale J. M., Smerdon M. J. UV-induced pyrimidine dimers and trimethylpsoralen cross-links do not alter chromatin folding in vitro. Biochemistry. 1988 Sep 20;27(19):7197–7205. doi: 10.1021/bi00419a006. [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]
- Husain I., Griffith J., Sancar A. Thymine dimers bend DNA. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2558–2562. doi: 10.1073/pnas.85.8.2558. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lutter L. C. Precise location of DNase I cutting sites in the nucleosome core determined by high resolution gel electrophoresis. Nucleic Acids Res. 1979 Jan;6(1):41–56. doi: 10.1093/nar/6.1.41. [DOI] [PMC free article] [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., Felsenfeld G. Reconstitution of nucleosome core particles containing glucosylated DNA. J Mol Biol. 1982 Jul 15;158(4):685–698. doi: 10.1016/0022-2836(82)90254-6. [DOI] [PubMed] [Google Scholar]
- Meistrich M. L., Lamola A. A., Gabbay E. Sensitized photoinactivation of bacteriophage T4. Photochem Photobiol. 1970 Mar;11(3):169–178. doi: 10.1111/j.1751-1097.1970.tb05985.x. [DOI] [PubMed] [Google Scholar]
- Meistrich M. L., Lamola A. A. Triplet-state sensitization of thymine photodimerization in bacteriophage T4. J Mol Biol. 1972 Apr 28;66(1):83–95. doi: 10.1016/s0022-2836(72)80007-x. [DOI] [PubMed] [Google Scholar]
- Mitra S., Sen D., Crothers D. M. Orientation of nucleosomes and linker DNA in calf thymus chromatin determined by photochemical dichroism. Nature. 1984 Mar 15;308(5956):247–250. doi: 10.1038/308247a0. [DOI] [PubMed] [Google Scholar]
- Noll M., Kornberg R. D. Action of micrococcal nuclease on chromatin and the location of histone H1. J Mol Biol. 1977 Jan 25;109(3):393–404. doi: 10.1016/s0022-2836(77)80019-3. [DOI] [PubMed] [Google Scholar]
- Pearlman D. A., Holbrook S. R., Pirkle D. H., Kim S. H. Molecular models for DNA damaged by photoreaction. Science. 1985 Mar 15;227(4692):1304–1308. doi: 10.1126/science.3975615. [DOI] [PubMed] [Google Scholar]
- Pehrson J. R., Cohen L. H. Embryonal histone H1 subtypes of the sea urchin Strongylocentrotus purpuratus: purification, characterization, and immunological comparison with H1 subtypes of the adult. Biochemistry. 1984 Dec 18;23(26):6761–6764. doi: 10.1021/bi00321a074. [DOI] [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]
- Richmond T. J., Searles M. A., Simpson R. T. Crystals of a nucleosome core particle containing defined sequence DNA. J Mol Biol. 1988 Jan 5;199(1):161–170. doi: 10.1016/0022-2836(88)90386-5. [DOI] [PubMed] [Google Scholar]
- Rose S. M., Garrard W. T. Differentiation-dependent chromatin alterations precede and accompany transcription of immunoglobulin light chain genes. J Biol Chem. 1984 Jul 10;259(13):8534–8544. [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]
- 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]
- Spadafora C., Oudet P., Chambon P. Rearrangement of chromatin structure induced by increasing ionic strength and temperature. Eur J Biochem. 1979 Oct;100(1):225–235. doi: 10.1111/j.1432-1033.1979.tb02053.x. [DOI] [PubMed] [Google Scholar]
- Strauss F., Prunell A. Nucleosome spacing in rat liver chromatin. A study with exonuclease III. Nucleic Acids Res. 1982 Apr 10;10(7):2275–2293. doi: 10.1093/nar/10.7.2275. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Watkins J. F., Smerdon M. J. Nucleosome rearrangement in vitro. 1. Two phases of salt-induced nucleosome migration in nuclei. Biochemistry. 1985 Dec 3;24(25):7279–7287. doi: 10.1021/bi00346a039. [DOI] [PubMed] [Google Scholar]