Recombination Regulation by Transcription-Induced Cohesin Dissociation in rDNA Repeats

@article{Kobayashi2005RecombinationRB,
  title={Recombination Regulation by Transcription-Induced Cohesin Dissociation in rDNA Repeats},
  author={Takehiko Kobayashi and Austen R. D. Ganley},
  journal={Science},
  year={2005},
  volume={309},
  pages={1581 - 1584}
}
Organisms maintain ribosomal RNA gene repeats (rDNA) at stable copy numbers by recombination; the loss of repeats results in gene amplification. Here we report a mechanism of amplification regulation. We show that amplification is dependent on transcription from a noncoding bidirectional promoter (E-pro) within the rDNA spacer. E-pro transcription stimulates the dissociation of cohesin, a DNA binding protein complex that suppresses sister-chromatid-based changes in rDNA copy number. This… 

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References

SHOWING 1-10 OF 24 REFERENCES
SIR2 Regulates Recombination between Different rDNA Repeats, but Not Recombination within Individual rRNA Genes in Yeast
TLDR
It is concluded that SIR2 prevents unequal sister-chromatid recombination, probably by forming special cohesin structures, without significant effects on recombinational events within individual rRNA genes.
Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA
TLDR
Deletion and overexpression studies demonstrate that SIR2, but not SIR1, SIR3 or SIR4, is required for this rDNA position effect, and significantly, rDNA transcriptional silencing and rDNA chromatin accessibility respond to Sir2 dosage, indicating that S IR2 is a limiting component required for chromatin modeling in rDNA.
An unusual form of transcriptional silencing in yeast ribosomal DNA.
TLDR
A novel form of transcriptional silencing in S. cerevisiae in the ribosomal DNA (rDNA) tandem array is identified, suggesting that a specific chromatin structure in rDNA down-regulates polymerase II promoters.
Identification of DNA cis Elements Essential for Expansion of Ribosomal DNA Repeats inSaccharomyces cerevisiae
TLDR
Mutational analysis showed that not only the RFB site but also the adjacent ∼400-bp region in NTS1 are required for the FOB1-dependent repeat expansion, which defines a function unique to rDNA repeat expansion (and presumably contraction) separate from HOT1 and RFB activities.
The connection between transcription and genomic instability
TLDR
An integrative view is provided on how transcription can control different aspects of genomic integrity, by exploring different mechanisms that might be responsible for transcription‐associated mutation (TAM) and transcription‐ associated recombination (TAR).
Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I.
TLDR
It was found that the absence of an essential subunit of RNA polymerase I (Pol I) in rpa135 deletion mutants triggers a gradual decrease in rDNA repeat number, and Gene FOB1 was shown to be essential for both the decrease and increase of rDNA repeats.
Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast.
TLDR
It is proposed that a specialized chromatin structure exists in RDN1 that silences transcription of the Ty1 retrotransposon and deletion of the gene for the ubiquitin conjugating enzyme Ubc2p, which ubiquitinates histones in vitro, derepresses not only Ty1 transcription but also mitotic recombination in RDNs.
Holliday Junctions Accumulate in Replication Mutants via a RecA Homolog-Independent Mechanism
TLDR
The Holliday junction recombination intermediate, an X-shaped DNA molecule (xDNA), was analyzed at rDNA in mitotically growing yeast, revealing that defects in polymerase alpha and delta but not the epsilon complex stimulate the level of xDNA.
Chromosomal Addresses of the Cohesin Component Mcd1p
TLDR
The mapping of new Mcd1p-binding sites (cohesin-associated regions [CARs]) in single-copy sequences of several chromosomes establish their spacing, their sequestration to intergenic regions, and their association with AT-rich sequences as general genomic properties of CARs.
Recombinational Controls of rDNA Redundancy in Drosophila
TLDR
This review explores whether the systems controlling rDNA copy number in flies represent mechanisms unique to rDNA.
...
1
2
3
...