The Abundance of Fob1 Modulates the Efficiency of RRFBs to Stall Replication Forks

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2017 Oct 4

PMID 28973451

Citations 5

Authors

Alicia Castan

Pablo Hernandez

Dora B Krimer

Jorge B Schvartzman

Affiliations

Soon will be listed here.

Abstract

In eukaryotes, ribosomal genes (rDNA) are organized in tandem repeats localized in one or a few clusters. Each repeat encompasses a transcription unit and a non-transcribed spacer. Replication forks moving in the direction opposite to transcription are blocked at specific sites called replication fork barriers (rRFBs) in the non-transcribed spacer close to the 3' end of the transcription unit. Here, we investigated and quantified the efficiency of rRFBs in Saccharomyces cerevisiae and to this end transfected budding yeast cells that express dissimilar quantities of Fob1 with circular minichromosomes containing different copies of the minimal 20-bp DNA segment that bind Fob1. To identify fork stalling we used high-resolution 2D agarose gel electrophoresis. The results obtained indicated that neighbor DNA sequences and the relative abundance of Fob1 modulate the efficiency of rRFBs to stall replication forks.

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References

Calzada A, Hodgson B, Kanemaki M, Bueno A, Labib K . Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev. 2005; 19(16):1905-19. PMC: 1186190. DOI: 10.1101/gad.337205. View

Martin-Parras L, Hernandez P, Martinez-Robles M, Schvartzman J . Unidirectional replication as visualized by two-dimensional agarose gel electrophoresis. J Mol Biol. 1991; 220(4):843-53. DOI: 10.1016/0022-2836(91)90357-c. View

Benguria A, Hernandez P, Krimer D, Schvartzman J . Sir2p suppresses recombination of replication forks stalled at the replication fork barrier of ribosomal DNA in Saccharomyces cerevisiae. Nucleic Acids Res. 2003; 31(3):893-8. PMC: 149208. DOI: 10.1093/nar/gkg188. View

Rothstein R, Michel B, Gangloff S . Replication fork pausing and recombination or "gimme a break". Genes Dev. 2000; 14(1):1-10. View

Bairwa N, Zzaman S, Mohanty B, Bastia D . Replication fork arrest and rDNA silencing are two independent and separable functions of the replication terminator protein Fob1 of Saccharomyces cerevisiae. J Biol Chem. 2010; 285(17):12612-9. PMC: 2857089. DOI: 10.1074/jbc.M109.082388. View

Friedman K, Brewer B . Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. Methods Enzymol. 1995; 262:613-27. DOI: 10.1016/0076-6879(95)62048-6. View

LITTLE R, Platt T, SCHILDKRAUT C . Initiation and termination of DNA replication in human rRNA genes. Mol Cell Biol. 1993; 13(10):6600-13. PMC: 364718. DOI: 10.1128/mcb.13.10.6600-6613.1993. View

Petes T . Yeast ribosomal DNA genes are located on chromosome XII. Proc Natl Acad Sci U S A. 1979; 76(1):410-4. PMC: 382949. DOI: 10.1073/pnas.76.1.410. View

Brewer B, FANGMAN W . A replication fork barrier at the 3' end of yeast ribosomal RNA genes. Cell. 1988; 55(4):637-43. DOI: 10.1016/0092-8674(88)90222-x. View

10.

Cox M, Goodman M, Kreuzer K, Sherratt D, Sandler S, Marians K . The importance of repairing stalled replication forks. Nature. 2000; 404(6773):37-41. DOI: 10.1038/35003501. View

11.

Olavarrieta L, Hernandez P, Krimer D, Schvartzman J . DNA knotting caused by head-on collision of transcription and replication. J Mol Biol. 2002; 322(1):1-6. DOI: 10.1016/s0022-2836(02)00740-4. View

12.

Ivessa A, Zakian V . To fire or not to fire: origin activation in Saccharomyces cerevisiae ribosomal DNA. Genes Dev. 2002; 16(19):2459-64. DOI: 10.1101/gad.1033702. View

13.

Kobayashi T . Ribosomal RNA gene repeats, their stability and cellular senescence. Proc Jpn Acad Ser B Phys Biol Sci. 2014; 90(4):119-29. PMC: 4055705. DOI: 10.2183/pjab.90.119. View

14.

Olavarrieta L, Martinez-Robles M, Hernandez P, Krimer D, Schvartzman J . Knotting dynamics during DNA replication. Mol Microbiol. 2002; 46(3):699-707. DOI: 10.1046/j.1365-2958.2002.03217.x. View

15.

Brewer B, FANGMAN W . The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 1987; 51(3):463-71. DOI: 10.1016/0092-8674(87)90642-8. View

16.

Krings G, Bastia D . swi1- and swi3-dependent and independent replication fork arrest at the ribosomal DNA of Schizosaccharomyces pombe. Proc Natl Acad Sci U S A. 2004; 101(39):14085-90. PMC: 521093. DOI: 10.1073/pnas.0406037101. View

17.

Deshpande A, Newlon C . DNA replication fork pause sites dependent on transcription. Science. 1996; 272(5264):1030-3. DOI: 10.1126/science.272.5264.1030. View

18.

Grummt I, Rosenbauer H, Niedermeyer I, Maier U, Ohrlein A . A repeated 18 bp sequence motif in the mouse rDNA spacer mediates binding of a nuclear factor and transcription termination. Cell. 1986; 45(6):837-46. DOI: 10.1016/0092-8674(86)90558-1. View

19.

Schvartzman J, Krimer D, Hernandez P . Co-localization of polar replication fork barriers and rRNA transcription terminators in mouse rDNA. J Mol Biol. 1998; 277(2):249-56. DOI: 10.1006/jmbi.1997.1607. View

20.

Mirkin E, Mirkin S . Replication fork stalling at natural impediments. Microbiol Mol Biol Rev. 2007; 71(1):13-35. PMC: 1847372. DOI: 10.1128/MMBR.00030-06. View