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Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes.

Joshi RS, Piña B, Roca J - EMBO J. (2010)

Bottom Line: The results revealed that, whereas the overwinding of DNA produced a general impairment of transcription initiation, genes situated at <100 kb from the chromosomal ends gradually escaped from the transcription stall.This novel positional effect seemed to be a simple function of the gene distance to the telomere: It occurred evenly in all 32 chromosome extremities and was independent of the atypical structure and transcription activity of subtelomeric chromatin.These results suggest that DNA helical tension dissipates at chromosomal ends and, therefore, provides a functional indication that yeast chromosome extremities are topologically open.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Diagnóstico Ambiental y Estudios del Agua (IDAEA), Instituto de Biologia Molecular de Barcelona-CSIC, Baldiri Reixac, Barcelona, Spain.

ABSTRACT
How DNA helical tension is constrained along the linear chromosomes of eukaryotic cells is poorly understood. In this study, we induced the accumulation of DNA (+) helical tension in Saccharomyces cerevisiae cells and examined how DNA transcription was affected along yeast chromosomes. The results revealed that, whereas the overwinding of DNA produced a general impairment of transcription initiation, genes situated at <100 kb from the chromosomal ends gradually escaped from the transcription stall. This novel positional effect seemed to be a simple function of the gene distance to the telomere: It occurred evenly in all 32 chromosome extremities and was independent of the atypical structure and transcription activity of subtelomeric chromatin. These results suggest that DNA helical tension dissipates at chromosomal ends and, therefore, provides a functional indication that yeast chromosome extremities are topologically open. The gradual escape from the transcription stall along the chromosomal flanks also indicates that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, might suffice to confine DNA helical tension along eukaryotic chromatin.

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Related in: MedlinePlus

Summary model. (A) Generation and diffusion of DNA helical stress. In the absence of cellular topoisomerase I and II activities and the presence of E. coli topoisomerase I, (+) helical tension is generated all along the yeast chromosomes because of unbalanced relaxation of the DNA supercoils produced during DNA transcription. In internal regions of the chromosome (core), DNA (+) helical tension cannot diffuse and accumulates until over-twisting of the duplex precludes transcription re-initiation. However, (+) helical tension can dissipate at the chromosomal ends, so allowing transcription to re-initiate at nearby regions of the chromosome (flanks). (B) DNA topological constrains along yeast chromosomes. (a) If DNA (+) helical stress could not dissipate at chromosome ends, a general stall of transcription would be expected throughout the entire chromosome. Our results discard this model. (b) If DNA (+) helical stress could dissipate at chromosome ends, but chromosomal DNA were organized as a succession of tight topological domains, a sharp transcription stall would be observed between the relaxed terminal domains and the rest of the chromosome. Our results do not support this model, unless distal topological boundaries were located beyond 100 kb from the telomere in all chromosomal arms. (c) If DNA (+) helical stress can dissipate at chromosome ends, but DNA twist diffusion is mainly restricted by the large rotational drag of chromatin, a gradual escape from the transcription stall would be expected in all chromosomal flanks, alike the observed in our results. As less DNA torque is needed in the chromosomal flanks to overcome the rotational drag of chromatin, the probability of transcription initiation is gradually restored towards the chromosomal ends.
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f6: Summary model. (A) Generation and diffusion of DNA helical stress. In the absence of cellular topoisomerase I and II activities and the presence of E. coli topoisomerase I, (+) helical tension is generated all along the yeast chromosomes because of unbalanced relaxation of the DNA supercoils produced during DNA transcription. In internal regions of the chromosome (core), DNA (+) helical tension cannot diffuse and accumulates until over-twisting of the duplex precludes transcription re-initiation. However, (+) helical tension can dissipate at the chromosomal ends, so allowing transcription to re-initiate at nearby regions of the chromosome (flanks). (B) DNA topological constrains along yeast chromosomes. (a) If DNA (+) helical stress could not dissipate at chromosome ends, a general stall of transcription would be expected throughout the entire chromosome. Our results discard this model. (b) If DNA (+) helical stress could dissipate at chromosome ends, but chromosomal DNA were organized as a succession of tight topological domains, a sharp transcription stall would be observed between the relaxed terminal domains and the rest of the chromosome. Our results do not support this model, unless distal topological boundaries were located beyond 100 kb from the telomere in all chromosomal arms. (c) If DNA (+) helical stress can dissipate at chromosome ends, but DNA twist diffusion is mainly restricted by the large rotational drag of chromatin, a gradual escape from the transcription stall would be expected in all chromosomal flanks, alike the observed in our results. As less DNA torque is needed in the chromosomal flanks to overcome the rotational drag of chromatin, the probability of transcription initiation is gradually restored towards the chromosomal ends.

Mentions: The intriguing question here is why all chromosomal flanks escape from the global transcription stall. The simplest explanation for this neat positional effect is that DNA helical stress cannot build up in the chromosome flanking regions because DNA is torsionally unconstrained at the chromosomal ends. Still, our results could have alternative explanations related to other structural and functional traits that are known to characterize subtelomeric regions. These traits vary substantially from telomere to telomere and are responsible for transcriptional silencing of genes located at <10–20 kb from chromosomal ends (Gottschling et al, 1990; Renauld et al, 1993; Pryde and Louis, 1999). We found, however, that the positional response discovered here is independent of the reduced transcription activity of subtelomeric genes or to the distinctive structure of subtelomeric chromatin. The observed effect seems to be a simple physical function of the gene distance to the telomere. In contrast to telomere silencing effects, this functionality occurs just after accumulation of DNA (+) helical tension, applies evenly to all 32 chromosomal extremities, and spreads up to 100 kb inwards. We conclude, therefore, that the dissipation of DNA helical stress at the chromosomal ends is the most likely cause for the differential response of chromosomal flanking genes reported here (Figure 6A).


Positional dependence of transcriptional inhibition by DNA torsional stress in yeast chromosomes.

Joshi RS, Piña B, Roca J - EMBO J. (2010)

Summary model. (A) Generation and diffusion of DNA helical stress. In the absence of cellular topoisomerase I and II activities and the presence of E. coli topoisomerase I, (+) helical tension is generated all along the yeast chromosomes because of unbalanced relaxation of the DNA supercoils produced during DNA transcription. In internal regions of the chromosome (core), DNA (+) helical tension cannot diffuse and accumulates until over-twisting of the duplex precludes transcription re-initiation. However, (+) helical tension can dissipate at the chromosomal ends, so allowing transcription to re-initiate at nearby regions of the chromosome (flanks). (B) DNA topological constrains along yeast chromosomes. (a) If DNA (+) helical stress could not dissipate at chromosome ends, a general stall of transcription would be expected throughout the entire chromosome. Our results discard this model. (b) If DNA (+) helical stress could dissipate at chromosome ends, but chromosomal DNA were organized as a succession of tight topological domains, a sharp transcription stall would be observed between the relaxed terminal domains and the rest of the chromosome. Our results do not support this model, unless distal topological boundaries were located beyond 100 kb from the telomere in all chromosomal arms. (c) If DNA (+) helical stress can dissipate at chromosome ends, but DNA twist diffusion is mainly restricted by the large rotational drag of chromatin, a gradual escape from the transcription stall would be expected in all chromosomal flanks, alike the observed in our results. As less DNA torque is needed in the chromosomal flanks to overcome the rotational drag of chromatin, the probability of transcription initiation is gradually restored towards the chromosomal ends.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2805846&req=5

f6: Summary model. (A) Generation and diffusion of DNA helical stress. In the absence of cellular topoisomerase I and II activities and the presence of E. coli topoisomerase I, (+) helical tension is generated all along the yeast chromosomes because of unbalanced relaxation of the DNA supercoils produced during DNA transcription. In internal regions of the chromosome (core), DNA (+) helical tension cannot diffuse and accumulates until over-twisting of the duplex precludes transcription re-initiation. However, (+) helical tension can dissipate at the chromosomal ends, so allowing transcription to re-initiate at nearby regions of the chromosome (flanks). (B) DNA topological constrains along yeast chromosomes. (a) If DNA (+) helical stress could not dissipate at chromosome ends, a general stall of transcription would be expected throughout the entire chromosome. Our results discard this model. (b) If DNA (+) helical stress could dissipate at chromosome ends, but chromosomal DNA were organized as a succession of tight topological domains, a sharp transcription stall would be observed between the relaxed terminal domains and the rest of the chromosome. Our results do not support this model, unless distal topological boundaries were located beyond 100 kb from the telomere in all chromosomal arms. (c) If DNA (+) helical stress can dissipate at chromosome ends, but DNA twist diffusion is mainly restricted by the large rotational drag of chromatin, a gradual escape from the transcription stall would be expected in all chromosomal flanks, alike the observed in our results. As less DNA torque is needed in the chromosomal flanks to overcome the rotational drag of chromatin, the probability of transcription initiation is gradually restored towards the chromosomal ends.
Mentions: The intriguing question here is why all chromosomal flanks escape from the global transcription stall. The simplest explanation for this neat positional effect is that DNA helical stress cannot build up in the chromosome flanking regions because DNA is torsionally unconstrained at the chromosomal ends. Still, our results could have alternative explanations related to other structural and functional traits that are known to characterize subtelomeric regions. These traits vary substantially from telomere to telomere and are responsible for transcriptional silencing of genes located at <10–20 kb from chromosomal ends (Gottschling et al, 1990; Renauld et al, 1993; Pryde and Louis, 1999). We found, however, that the positional response discovered here is independent of the reduced transcription activity of subtelomeric genes or to the distinctive structure of subtelomeric chromatin. The observed effect seems to be a simple physical function of the gene distance to the telomere. In contrast to telomere silencing effects, this functionality occurs just after accumulation of DNA (+) helical tension, applies evenly to all 32 chromosomal extremities, and spreads up to 100 kb inwards. We conclude, therefore, that the dissipation of DNA helical stress at the chromosomal ends is the most likely cause for the differential response of chromosomal flanking genes reported here (Figure 6A).

Bottom Line: The results revealed that, whereas the overwinding of DNA produced a general impairment of transcription initiation, genes situated at <100 kb from the chromosomal ends gradually escaped from the transcription stall.This novel positional effect seemed to be a simple function of the gene distance to the telomere: It occurred evenly in all 32 chromosome extremities and was independent of the atypical structure and transcription activity of subtelomeric chromatin.These results suggest that DNA helical tension dissipates at chromosomal ends and, therefore, provides a functional indication that yeast chromosome extremities are topologically open.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Diagnóstico Ambiental y Estudios del Agua (IDAEA), Instituto de Biologia Molecular de Barcelona-CSIC, Baldiri Reixac, Barcelona, Spain.

ABSTRACT
How DNA helical tension is constrained along the linear chromosomes of eukaryotic cells is poorly understood. In this study, we induced the accumulation of DNA (+) helical tension in Saccharomyces cerevisiae cells and examined how DNA transcription was affected along yeast chromosomes. The results revealed that, whereas the overwinding of DNA produced a general impairment of transcription initiation, genes situated at <100 kb from the chromosomal ends gradually escaped from the transcription stall. This novel positional effect seemed to be a simple function of the gene distance to the telomere: It occurred evenly in all 32 chromosome extremities and was independent of the atypical structure and transcription activity of subtelomeric chromatin. These results suggest that DNA helical tension dissipates at chromosomal ends and, therefore, provides a functional indication that yeast chromosome extremities are topologically open. The gradual escape from the transcription stall along the chromosomal flanks also indicates that friction restrictions to DNA twist diffusion, rather than tight topological boundaries, might suffice to confine DNA helical tension along eukaryotic chromatin.

Show MeSH
Related in: MedlinePlus