FOB1 affects DNA topoisomerase I in vivo cleavages in the enhancer region of the Saccharomyces cerevisiae ribosomal DNA locus

In Saccharomyces cerevisiae the FOB1 gene affects replication fork blocking activity at the replication fork block (RFB) sequences and promotes recombination events within the rDNA cluster. Using in vivo footprinting assays we mapped two in vivo Fob1p-binding sites, RFB1 and RFB3, located in the rDNA enhancer region and coincident with those previously reported to be in vitro binding sites. We previously provided evidences that DNA topoisomerase I is able to cleave two sites within this region. The results reported in this paper, indicate that the DNA topoisomerase I cleavage specific activity at the enhancer region is affected by the presence of Fob1p and independent of replication and transcription activities. We thus hypothesize that the binding to DNA of Fob1p itself may be the cause of the DNA topoisomerase I activity in the rDNA enhancer.

• Publication year

  2005

• Venue

  Nucleic Acids Research

• Publication date

  2005-11-03

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/nar/gki950PMID 16269824PMCID 1277812
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Budding Yeast Silencing Complexes and Regulation of Sir2 Activity by Protein-Protein Interactions

  2004cited by this paper
• Human topoisomerase I mediates illegitimate recombination leading to DNA insertion into the ribosomal DNA locus in Saccharomyces cerevisiae

  2004cited by this paper
• rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication.

  2004cited by this paper
• In vivo analysis of chromatin following nystatin-mediated import of active enzymes into Saccharomyces cerevisiae

  2004cited by this paper
• The Replication Fork Barrier Site Forms a Unique Structure with Fob1p and Inhibits the Replication Fork

  2003cited by this paper
• Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing.

  2003influential reference
• Silencing in yeast rDNA chromatin: reciprocal relationship in gene expression between RNA polymerase I and II.

  2003cited by this paper
• RNA polymerase I propagates unidirectional spreading of rDNA silent chromatin.

  2002cited by this paper
• Ribosomal RNA genes, RNA polymerases, nucleolar structures, and synthesis of rRNA in the yeast Saccharomyces cerevisiae.

  2001cited by this paper
• In vivo binding and hierarchy of assembly of the yeast RNA polymerase I transcription factors.

  2001cited by this paper
• Replication fork pausing and recombination or "gimme a break".

  2000cited by this paper
• Complete deletion of yeast chromosomal rDNA repeats and integration of a new rDNA repeat: use of rDNA deletion strains for functional analysis of rDNA promoter elements in vivo.

  2000cited by this paper
• Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex.

  1999cited by this paper
• Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity.

  1999cited by this paper
• Elimination of replication block protein Fob1 extends the life span of yeast mother cells.

  1999cited by this paper
• Site-specific in vivo cleavages by DNA topoisomerase I in the regulatory regions of the 35 S rRNA in Saccharomyces cerevisiae are transcription independent.

  1999cited by this paper
• DNA protein-interactions at the Saccharomyces cerevisiae 35 S rRNA promoter and in its surrounding region.

  1998cited by this paper
• Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I.

  1998cited by this paper
• Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast.

  1997cited by this paper
• DNA topoisomerases.

  1996cited by this paper
• Multiprotein transcription factor UAF interacts with the upstream element of the yeast RNA polymerase I promoter and forms a stable preinitiation complex.

  1996cited by this paper
• A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities

  1996influential reference
• Gene RPA43 in Saccharomyces cerevisiae Encodes an Essential Subunit of RNA Polymerase I (*)

  1995cited by this paper
• The yeast RNA polymerase I promoter: ribosomal DNA sequences involved in transcription initiation and complex formation in vitro.

  1991cited by this paper
• Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I.

  1991cited by this paper
• Termination of transcription by yeast RNA polymerase I.

  1989cited by this paper
• In vitro preferential topoisomerization of bent DNA.

  1989cited by this paper
• A replication fork barrier at the 3' end of yeast ribosomal RNA genes.

  1988cited by this paper
• A new method of sequencing DNA.

  1988cited by this paper
• Mitotic recombination in the rDNA of S. cerevisiae is suppressed by the combined action of DNA topoisomerases I and II.

  1988cited by this paper
• Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast.

  1986cited by this paper
• Camptothecin induces protein-linked DNA breaks via mammalian DNA topoisomerase I.

  1985cited by this paper
• The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I

  1980cited by this paper
• Methods in yeast genetics

  1979cited by this paper
• Yeast ribosomal DNA genes are located on chromosome XII.

  1979cited by this paper
• A new method for sequencing DNA.

  1977cited by this paper
• Sequential gene function in the initiation of Saccharomyces cerevisiae DNA synthesis.

  1974cited by this paper
• Identification and Characterization of the Genes for Two Topoisomerase I-Interacting Proteins from Saccharomyces cerevisiae

  year unknowncited by this paper

• Multiple mechanisms of termination modulate the dynamics of RNAPI transcription

  2025cites this paper
• rDNA transcription, replication and stability in Saccharomyces cerevisiae.

  2024cites this paper
• Approaching Protein Barriers: Emerging Mechanisms of Replication Pausing in Eukaryotes

  2021cites this paper
• Saccharomyces cerevisiae rDNA as super-hub: the region where replication, transcription and recombination meet

  2020cites this paper
• Fob1p recruits DNA topoisomerase I to ribosomal genes locus and contributes to its transcriptional silencing maintenance.

  2019cites this paper
• qDSB-Seq: quantitative DNA double-strand break sequencing

  2019cites this paper
• Fork pausing complex engages topoisomerases at the replisome

  2019cites this paper
• qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing

  2019cites this paper
• Quantitative DSB sequencing (qDSB-Seq): a method for genome-wide accurate estimation of absolute DNA double-strand break frequencies per cell

  2017cites this paper
• Mechanism of Regulation of Intrachromatid Recombination and Long-Range Chromosome Interactions in Saccharomyces cerevisiae

  2016cites this paper
• More than 10% of yeast genes are related to genome stability and influence cellular senescence via rDNA maintenance

  2016cites this paper
• Mechanism of regulation of ‘chromosome kissing’ induced by Fob1 and its physiological significance

  2015cites this paper
• Reversible Top1 cleavage complexes are stabilized strand-specifically at the ribosomal replication fork barrier and contribute to ribosomal DNA stability

  2014cites this paper
• Transcription-associated genome instability.

  2013cites this paper
• DNA Topoisomerases

  2013cites this paper
• Eukaryotic Replication Barriers: How, Why and Where Forks Stall

  2011cites this paper
• DNA ligase 4 stabilizes the ribosomal DNA array upon fork collapse at the replication fork barrier.

  2010cites this paper
• Replication fork arrest, recombination and the maintenance of ribosomal DNA stability.

  2008cites this paper
• Nucleosomes represent a physical barrier for cleavage activity of DNA topoisomerase I in vivo.

  2008cites this paper
• A redundancy of processes that cause replication fork stalling enhances recombination at two distinct sites in yeast rDNA

  2008cites this paper
• Replication fork barriers: pausing for a break or stalling for time?

  2007cites this paper
• Current awareness on yeast

  2006cites this paper
• Condensin Function in Mitotic Nucleolar Segregation is Regulated by rDNA Transcription

  2006cites this paper
• Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer.

  2006cites this paper