Enrichment and Depletion of Hela Topoisomerase I Recognition Sites Among Specific Types of DNA Elements

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1988 Aug 25

PMID 2843808

Citations 12

Authors

C Perez-Stable

C C Shen

C K Shen

Affiliations

Soon will be listed here.

Abstract

The SDS-induced nicking of DNA helix by Hela topoisomerase I in vitro has been studied by using 2.9 kb of cloned human DNA as the substrate. The frequency of nicking is increased from 1/23 (nick/nt) to 1/19 (nick/nt) when camptothecin is present in the nicking reaction. The cytotoxic drug also induces DNA nicks without the addition of SDS. Although the consensus built from DNA sequences from -20 to +20 of more than one hundred of the nicking sites only shows a preference for T at position -1, the distributions of the topoisomerae I-cleavable sites among different categories of specific DNA sequences are apparently non- random. Long stretches of tandem (CA), A, or T residues, and the GC-rich promoter region of alpha 1 globin gene are all refractory to the nicking reaction. However, the nicking frequencies of short direct repeats flanking different Alu type sequences are as high as 1/6 (nick/nt). Finally, several tandemly arranged minirepeats of the form (TxAy)z, that are usually found at the 3' ends of the primate Alu family or Kpnl family repeats, can be cleaved efficiently in a regular pattern by the enzyme. These data are discussed in terms of the mode of recognition of DNA sequences/structures by topoisomerase I, and its possible roles in the nonhomologous insertion of repetitive DNA sequences.

Citing Articles

Topoisomerase I inhibitors and drug resistance.

Parchment R, Pessina A Cytotechnology. 2008; 27(1-3):149-64.

PMID: 19002789 PMC: 3449562. DOI: 10.1023/A:1008008719699.

Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.

Wang Y, Yang W, Li C, Doudeva L, Yuan H Nucleic Acids Res. 2006; 35(2):584-94.

PMID: 17175542 PMC: 1802626. DOI: 10.1093/nar/gkl621.

Sequential insertion of Alu family repeats into specific genomic sites of higher primates.

Bailey A, Shen C Proc Natl Acad Sci U S A. 1993; 90(15):7205-9.

PMID: 8394013 PMC: 47105. DOI: 10.1073/pnas.90.15.7205.

Induction of cleavage in topoisomerase I c-DNA by topoisomerase I enzymes from calf thymus and wheat germ in the presence and absence of camptothecin.

Tanizawa A, Kohn K, Pommier Y Nucleic Acids Res. 1993; 21(22):5157-66.

PMID: 8255771 PMC: 310631. DOI: 10.1093/nar/21.22.5157.

Topoisomerase I action on the heterochromatic DNA from the brine shrimp Artemia franciscana: studies in vivo and in vitro.

Carettoni D, Landsberger N, Zagni E, Benfante R, Badaracco G Biochem J. 1994; 299 ( Pt 3):623-9.

PMID: 8192650 PMC: 1138066. DOI: 10.1042/bj2990623.

References

Cozzarelli N . DNA topoisomerases. Cell. 1980; 22(2 Pt 2):327-8. DOI: 10.1016/0092-8674(80)90341-4. View

Weiner A, Deininger P, Efstratiadis A . Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986; 55:631-61. DOI: 10.1146/annurev.bi.55.070186.003215. View

Sternglanz R, DiNardo S, Voelkel K, Nishimura Y, Hirota Y, Becherer K . Mutations in the gene coding for Escherichia coli DNA topoisomerase I affect transcription and transposition. Proc Natl Acad Sci U S A. 1981; 78(5):2747-51. PMC: 319434. DOI: 10.1073/pnas.78.5.2747. View

Been M, Champoux J . DNA breakage and closure by rat liver type 1 topoisomerase: separation of the half-reactions by using a single-stranded DNA substrate. Proc Natl Acad Sci U S A. 1981; 78(5):2883-7. PMC: 319463. DOI: 10.1073/pnas.78.5.2883. View

Liu L, Miller K . Eukaryotic DNA topoisomerases: two forms of type I DNA topoisomerases from HeLa cell nuclei. Proc Natl Acad Sci U S A. 1981; 78(6):3487-91. PMC: 319594. DOI: 10.1073/pnas.78.6.3487. View

Gellert M . DNA topoisomerases. Annu Rev Biochem. 1981; 50:879-910. DOI: 10.1146/annurev.bi.50.070181.004311. View

Van Arsdell S, Denison R, BERNSTEIN L, Weiner A, Manser T, GESTELAND R . Direct repeats flank three small nuclear RNA pseudogenes in the human genome. Cell. 1981; 26(1 Pt 1):11-7. DOI: 10.1016/0092-8674(81)90028-3. View

Jagadeeswaran P, Forget B, Weissman S . Short interspersed repetitive DNA elements in eucaryotes: transposable DNA elements generated by reverse transcription of RNA pol III transcripts?. Cell. 1981; 26(2 Pt 2):141-2. DOI: 10.1016/0092-8674(81)90296-8. View

Halligan B, Davis J, Edwards K, Liu L . Intra- and intermolecular strand transfer by HeLa DNA topoisomerase I. J Biol Chem. 1982; 257(7):3995-4000. View

10.

Singer M . SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell. 1982; 28(3):433-4. DOI: 10.1016/0092-8674(82)90194-5. View

11.

Edwards K, Halligan B, Davis J, Nivera N, Liu L . Recognition sites of eukaryotic DNA topoisomerase I: DNA nucleotide sequencing analysis of topo I cleavage sites on SV40 DNA. Nucleic Acids Res. 1982; 10(8):2565-76. PMC: 320634. DOI: 10.1093/nar/10.8.2565. View

12.

Hess J, Schmid C, Shen C . A gradient of sequence divergence in the human adult alpha-globin duplication units. Science. 1984; 226(4670):67-70. DOI: 10.1126/science.6474190. View

13.

Fleischmann G, PFLUGFELDER G, Steiner E, Javaherian K, Howard G, Wang J . Drosophila DNA topoisomerase I is associated with transcriptionally active regions of the genome. Proc Natl Acad Sci U S A. 1984; 81(22):6958-62. PMC: 392055. DOI: 10.1073/pnas.81.22.6958. View

14.

Kirkegaard K, PFLUGFELDER G, Wang J . The cleavage of DNA by type-I DNA topoisomerases. Cold Spring Harb Symp Quant Biol. 1984; 49:411-9. DOI: 10.1101/sqb.1984.049.01.047. View

15.

Yang L, Wold M, Li J, Kelly T, Liu L . Roles of DNA topoisomerases in simian virus 40 DNA replication in vitro. Proc Natl Acad Sci U S A. 1987; 84(4):950-4. PMC: 304337. DOI: 10.1073/pnas.84.4.950. View

16.

Gilmour D, Elgin S . Localization of specific topoisomerase I interactions within the transcribed region of active heat shock genes by using the inhibitor camptothecin. Mol Cell Biol. 1987; 7(1):141-8. PMC: 365050. DOI: 10.1128/mcb.7.1.141-148.1987. View

17.

Brill S, DiNardo S, Sternglanz R . Need for DNA topoisomerase activity as a swivel for DNA replication for transcription of ribosomal RNA. Nature. 1987; 326(6111):414-6. DOI: 10.1038/326414a0. View

18.

Wobbe C, Weissbach L, Borowiec J, Dean F, Murakami Y, Bullock P . Replication of simian virus 40 origin-containing DNA in vitro with purified proteins. Proc Natl Acad Sci U S A. 1987; 84(7):1834-8. PMC: 304535. DOI: 10.1073/pnas.84.7.1834. View

19.

Garg L, Diangelo S, Jacob S . Role of DNA topoisomerase I in the transcription of supercoiled rRNA gene. Proc Natl Acad Sci U S A. 1987; 84(10):3185-8. PMC: 304833. DOI: 10.1073/pnas.84.10.3185. View

20.

Busk H, Thomsen B, Bonven B, Kjeldsen E, Nielsen O, Westergaard O . Preferential relaxation of supercoiled DNA containing a hexadecameric recognition sequence for topoisomerase I. Nature. 1987; 327(6123):638-40. DOI: 10.1038/327638a0. View