Long-range Organization and Sequence-directed Curvature of Xenopus Laevis Satellite 1 DNA

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1993 Oct 11

PMID 7901836

Citations 15

Authors

P Pasero

N Sjakste

C Blettry

C Got

M Marilley

Affiliations

Soon will be listed here.

Abstract

We have investigated the long-range organization and the intrinsic curvature of satellite 1 DNA, an unusual tandemly-repeated DNA family of Xenopus laevis presenting sequence homologies to SINEs. PFGE was used in combination with frequent-cutter restriction enzymes not likely to cut within satellite 1 DNA and revealed that almost all the repeating units are tandemly organized to form large arrays (200 kb to 2 Mb) that are marked by restriction length polymorphism and contain intra-array domains of sequence variation. Besides that, we have analysed the secondary structure of satellite 1 DNA by computer modelling. Theoretical maps of curvature obtained from three independent models of DNA bending (the dinucleotide wedge model of Trifonov, the junction model of Crothers and the model of de Santis) showed that satellite 1 DNA is intrinsically curved and these results were confirmed experimentally by polyacrylamide gel electrophoresis. Moreover, we observed that this bending element is highly conserved among all the members of the satellite 1 DNA family that are accessible to analysis. A potential genetic role for satellite 1 DNA based on this unusual structural feature is discussed.

Citing Articles

Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome.

Zattera M, Bruschi D Cells. 2022; 11(21).

PMID: 36359770 PMC: 9659126. DOI: 10.3390/cells11213373.

Conversion of DNA Sequences: From a Transposable Element to a Tandem Repeat or to a Gene.

Paco A, Freitas R, Vieira-da-Silva A Genes (Basel). 2019; 10(12).

PMID: 31817529 PMC: 6947457. DOI: 10.3390/genes10121014.

Structural and functional liaisons between transposable elements and satellite DNAs.

Mestrovic N, Mravinac B, Pavlek M, Vojvoda-Zeljko T, Satovic E, Plohl M Chromosome Res. 2015; 23(3):583-96.

PMID: 26293606 DOI: 10.1007/s10577-015-9483-7.

Tandem repeats derived from centromeric retrotransposons.

Sharma A, Wolfgruber T, Presting G BMC Genomics. 2013; 14:142.

PMID: 23452340 PMC: 3648361. DOI: 10.1186/1471-2164-14-142.

Intrinsically bent DNA sites in the Drosophila melanogaster third chromosome amplified domain.

Gimenes F, Assis M, Fiorini A, Mareze V, Monesi N, Fernandez M Mol Genet Genomics. 2009; 281(5):539-49.

PMID: 19219620 DOI: 10.1007/s00438-009-0430-1.

References

Brutlag D . Molecular arrangement and evolution of heterochromatic DNA. Annu Rev Genet. 1980; 14:121-44. DOI: 10.1146/annurev.ge.14.120180.001005. View

Turmel C, Brassard E, Slater G, Noolandi J . Molecular detrapping and band narrowing with high frequency modulation of pulsed field electrophoresis. Nucleic Acids Res. 1990; 18(3):569-75. PMC: 333463. DOI: 10.1093/nar/18.3.569. View

Hagerman P . Straightening out the bends in curved DNA. Biochim Biophys Acta. 1992; 1131(2):125-32. DOI: 10.1016/0167-4781(92)90066-9. View

Warburton P, Willard H . Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogeneous sequence domains within arrays of alpha-satellite DNA. J Mol Biol. 1990; 216(1):3-16. DOI: 10.1016/s0022-2836(05)80056-7. View

Vogt P . Code domains in tandem repetitive DNA sequence structures. Chromosoma. 1992; 101(10):585-9. DOI: 10.1007/BF00360534. View

Vogt P . Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code". Hum Genet. 1990; 84(4):301-36. DOI: 10.1007/BF00196228. View

Koo H, Crothers D . Calibration of DNA curvature and a unified description of sequence-directed bending. Proc Natl Acad Sci U S A. 1988; 85(6):1763-7. PMC: 279859. DOI: 10.1073/pnas.85.6.1763. View

Chu G, Vollrath D, Davis R . Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science. 1986; 234(4783):1582-5. DOI: 10.1126/science.3538420. View

Bolshoy A, McNamara P, Harrington R, Trifonov E . Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A. 1991; 88(6):2312-6. PMC: 51221. DOI: 10.1073/pnas.88.6.2312. View

10.

Pasero P, Marilley M . Size variation of rDNA clusters in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Mol Gen Genet. 1993; 236(2-3):448-52. DOI: 10.1007/BF00277147. View

11.

De Santis P, Palleschi A, Savino M, Scipioni A . A theoretical model of DNA curvature. Biophys Chem. 1988; 32(2-3):305-17. DOI: 10.1016/0301-4622(88)87016-9. View

12.

Carrera P, Martinez-Balbas M, Portugal J, Azorin F . Identification of sequence elements contributing to the intrinsic curvature of the mouse satellite DNA repeat. Nucleic Acids Res. 1991; 19(20):5639-44. PMC: 328969. DOI: 10.1093/nar/19.20.5639. View

13.

Hibino Y, Nakamura K, Asano S, Sugano N . Affinity of a highly repetitive bent DNA for nuclear scaffold proteins from rat liver. Biochem Biophys Res Commun. 1992; 184(2):853-8. DOI: 10.1016/0006-291x(92)90668-b. View

14.

Strauss F, Varshavsky A . 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. 1984; 37(3):889-901. DOI: 10.1016/0092-8674(84)90424-0. View

15.

Vollrath D, Davis R . Resolution of DNA molecules greater than 5 megabases by contour-clamped homogeneous electric fields. Nucleic Acids Res. 1987; 15(19):7865-76. PMC: 306313. DOI: 10.1093/nar/15.19.7865. View

16.

Marini J, Levene S, Crothers D, Englund P . Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982; 79(24):7664-8. PMC: 347408. DOI: 10.1073/pnas.79.24.7664. View

17.

Radic M, Lundgren K, Hamkalo B . Curvature of mouse satellite DNA and condensation of heterochromatin. Cell. 1987; 50(7):1101-8. DOI: 10.1016/0092-8674(87)90176-0. View

18.

Boffelli D, De Santis P, Palleschi A, Risuleo G, Savino M . A theoretical method to predict DNA permutation gel electrophoresis from the sequence. FEBS Lett. 1992; 300(2):175-8. DOI: 10.1016/0014-5793(92)80190-r. View

19.

Okada N . SINEs. Curr Opin Genet Dev. 1991; 1(4):498-504. DOI: 10.1016/s0959-437x(05)80198-4. View

20.

Muzard G, Theveny B, Revet B . Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models. EMBO J. 1990; 9(4):1289-98. PMC: 551807. DOI: 10.1002/j.1460-2075.1990.tb08238.x. View