Sequence-dependent Deformational Anisotropy of Chromatin DNA

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1980 Sep 11

PMID 7443521

Citations 57

Authors

E N Trifonov

Affiliations

Soon will be listed here.

Abstract

As found in previous work (E.N. Trifonov and J.L. Sussman, Proc. Natl. Acad. Sci. USA, in press) some dinucleotides of the chromatin DNA sequences have a clear tendency to be repeated along the sequences with a period of about 10.5 bases. A special iteration procedure is developed to find if there are phase relationships between different periodically repeating dinucleotides of chromatin DNA. A very specific symmetrical pattern of preferences of different dinucleotides to certain positions within a repeating 10.5 base frame is indeed found. This is interpreted as a manifestation of sequence-dependent deformational anisotropy of the chromatin DNA which facilitates its smooth folding in chromatin. The pattern found can be used for locating unidirectionally curved portions of the DNA molecules, possibly corresponding to nucleosomal DNA. This implies that the DNA is bound to the nucleosomes by one specific side which corresponds to the direction of the sequence-dependent curving of the DNA axis. The 10.5 base periodicity found can be considered as the second message present in chromatin DNA sequences together with 3 base frame coding message.

Citing Articles

Manipulating chromatin architecture in C. elegans.

Carter J, Kempton C, Hales E, Johnson S Epigenetics Chromatin. 2022; 15(1):38.

PMID: 36443798 PMC: 9706983. DOI: 10.1186/s13072-022-00472-5.

Coupling between Sequence-Mediated Nucleosome Organization and Genome Evolution.

Barbier J, Vaillant C, Volff J, Brunet F, Audit B Genes (Basel). 2021; 12(6).

PMID: 34205881 PMC: 8228248. DOI: 10.3390/genes12060851.

The "Genomic Code": DNA Pervasively Moulds Chromatin Structures Leaving no Room for "Junk".

Bernardi G Life (Basel). 2021; 11(4).

PMID: 33924668 PMC: 8070607. DOI: 10.3390/life11040342.

Effects of size, cooperativity, and competitive binding on protein positioning on DNA.

McCormack L, Efremov A, Yan J Biophys J. 2021; 120(10):2040-2053.

PMID: 33771470 PMC: 8204397. DOI: 10.1016/j.bpj.2021.03.016.

Distinctive regulatory architectures of germline-active and somatic genes in .

Serizay J, Dong Y, Janes J, Chesney M, Cerrato C, Ahringer J Genome Res. 2020; 30(12):1752-1765.

PMID: 33093068 PMC: 7706728. DOI: 10.1101/gr.265934.120.

References

Arnott S, Hukins D . Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. J Mol Biol. 1973; 81(2):93-105. DOI: 10.1016/0022-2836(73)90182-4. View

Crick F, Klug A . Kinky helix. Nature. 1975; 255(5509):530-3. DOI: 10.1038/255530a0. View

Germond J, Hirt B, Oudet P, Chambon P . Folding of the DNA double helix in chromatin-like structures from simian virus 40. Proc Natl Acad Sci U S A. 1975; 72(5):1843-7. PMC: 432643. DOI: 10.1073/pnas.72.5.1843. View

Corden J, Engelking H, Pearson G . Chromatin-like organization of the adenovirus chromosome. Proc Natl Acad Sci U S A. 1976; 73(2):401-4. PMC: 335916. DOI: 10.1073/pnas.73.2.401. View

Sobell H, Tsai C, Gilbert S, Jain S, Sakore T . Organization of DNA in chromatin. Proc Natl Acad Sci U S A. 1976; 73(9):3068-72. PMC: 430931. DOI: 10.1073/pnas.73.9.3068. View

Namoradze N, Goryunov A, Birshtein T . On conformations of the superhelix structure. Biophys Chem. 1977; 7(1):59-70. DOI: 10.1016/0301-4622(77)87015-4. View

Kallenbach N, Appleby D, Bradley C . 31P magnetic resonance of DNA in nucleosome core particles of chromatin. Nature. 1978; 272(5649):134-8. DOI: 10.1038/272134a0. View

Sussman J, Trifonov E . Possibility of nonkinked packing of DNA in chromatin. Proc Natl Acad Sci U S A. 1978; 75(1):103-7. PMC: 411192. DOI: 10.1073/pnas.75.1.103. View

Levitt M . How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations. Proc Natl Acad Sci U S A. 1978; 75(2):640-4. PMC: 411311. DOI: 10.1073/pnas.75.2.640. View

10.

Fiers W, Contreras R, Haegemann G, Rogiers R, Van de Voorde A, Van Heuverswyn H . Complete nucleotide sequence of SV40 DNA. Nature. 1978; 273(5658):113-20. DOI: 10.1038/273113a0. View

11.

Reddy V, Thimmappaya B, Dhar R, Subramanian K, Zain B, Pan J . The genome of simian virus 40. Science. 1978; 200(4341):494-502. DOI: 10.1126/science.205947. View

12.

Sures I, Lowry J, Kedes L . The DNA sequence of sea urchin (S. purpuratus) H2A, H2B and H3 histone coding and spacer regions. Cell. 1978; 15(3):1033-44. DOI: 10.1016/0092-8674(78)90287-8. View

13.

Trifonov E, Bettecken T . Noninteger pitch and nuclease sensitivity of chromatin DNA. Biochemistry. 1979; 18(3):454-6. DOI: 10.1021/bi00570a011. View

14.

Van Ormondt H, Maat J, de Waard A, Van Der Eb A . The nucleotide sequence of the transforming HpaI-E fragment of adenovirus type 5 DNA. Gene. 1978; 4(4):309-28. DOI: 10.1016/0378-1119(78)90048-3. View

15.

ROBERTSON M, Staden R, Tanaka Y, Catterall J, OMalley B, Brownlee G . Sequence of three introns in the chick ovalbumin gene. Nature. 1979; 278(5702):370-2. DOI: 10.1038/278370a0. View

16.

Zhurkin V, Lysov Y, Ivanov V . Anisotropic flexibility of DNA and the nucleosomal structure. Nucleic Acids Res. 1979; 6(3):1081-96. PMC: 327755. DOI: 10.1093/nar/6.3.1081. View

17.

Feigon J, Kearns D . 1H NMR investigation of the conformational states of DNA in nucleosome core particles. Nucleic Acids Res. 1979; 6(6):2327-37. PMC: 327853. DOI: 10.1093/nar/6.6.2327. View

18.

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; 17(3):715-24. DOI: 10.1016/0092-8674(79)90278-2. View

19.

Maat J, Van Ormondt H . The nucleotide sequence of the transforming HindIII-G fragment of adenovirus type 5 DNA. The region between map positions 4.5 (HpaI site) and 8.0 (HindIII site). Gene. 1979; 6(1):75-90. DOI: 10.1016/0378-1119(79)90086-6. View

20.

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; 18(2):591-600. DOI: 10.1016/0092-8674(79)90075-8. View