Limits...
Atomic force microscopy of DNA in solution and DNA modelling show that structural properties specify the eukaryotic replication initiation site.

Marilley M, Milani P, Thimonier J, Rocca-Serra J, Baldacci G - Nucleic Acids Res. (2007)

Bottom Line: On pORC unwinding, this site shifts towards the apex of the curvature, thus potentiating DNA melting there.Our model is entirely consistent with the sequence variability, large size and A+T-richness of ORIs, and also accounts for the multistep nature of the initiation process, the specificity of pORC-binding site(s), and the specific location of RIP.We show that the particular DNA features and dynamic properties identified in Spars1 are present in other eukaryotic origins.

View Article: PubMed Central - PubMed

Affiliation: Régulation génique et fonctionnelle & microscopie champ proche, EA 3290, IFR 125, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille cedex 5, France. monique.marilley@medecine.univ-mrs.fr

ABSTRACT
The replication origins (ORIs) of Schizosaccharomyces pombe, like those in most eukaryotes, are long chromosomal regions localized within A+T-rich domains. Although there is no consensus sequence, the interacting proteins are strongly conserved, suggesting that DNA structure is important for ORI function. We used atomic force microscopy in solution and DNA modelling to study the structural properties of the Spars1 origin. We show that this segment is the least stable of the surrounding DNA (9 kb), and contains regions of intrinsically bent elements (strongly curved and inherently supercoiled DNAs). The pORC-binding site co-maps with a superhelical DNA region, where the spatial arrangement of adenine/thymine stretches may provide the binding substrate. The replication initiation site (RIP) is located within a strongly curved DNA region. On pORC unwinding, this site shifts towards the apex of the curvature, thus potentiating DNA melting there. Our model is entirely consistent with the sequence variability, large size and A+T-richness of ORIs, and also accounts for the multistep nature of the initiation process, the specificity of pORC-binding site(s), and the specific location of RIP. We show that the particular DNA features and dynamic properties identified in Spars1 are present in other eukaryotic origins.

Show MeSH

Related in: MedlinePlus

Curved and supercoiled structures are unique. The Spars1 sequence is shown by black solid lines, and grey solid lines indicate sequences outside Spars1. Phasing is between 8 and 12 with steps of 0.25. The sliding window is 200 bp and each step 10 bp. For simplification, only the informative curves corresponding to the phases 10.5, 10.25 and 9.25 are shown. Exploration of 9000 nt around Spars1 shows that the main curvature and the positively supercoiled region are unique.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2175326&req=5

Figure 8: Curved and supercoiled structures are unique. The Spars1 sequence is shown by black solid lines, and grey solid lines indicate sequences outside Spars1. Phasing is between 8 and 12 with steps of 0.25. The sliding window is 200 bp and each step 10 bp. For simplification, only the informative curves corresponding to the phases 10.5, 10.25 and 9.25 are shown. Exploration of 9000 nt around Spars1 shows that the main curvature and the positively supercoiled region are unique.

Mentions: We extended our analysis to the 9000 nt surrounding Spars1 using the conditions described in Figure 5. The substantial curvature described earlier is the only major curvature in the region (Figure 8); the same applies to the positive superhelical region.Figure 8.


Atomic force microscopy of DNA in solution and DNA modelling show that structural properties specify the eukaryotic replication initiation site.

Marilley M, Milani P, Thimonier J, Rocca-Serra J, Baldacci G - Nucleic Acids Res. (2007)

Curved and supercoiled structures are unique. The Spars1 sequence is shown by black solid lines, and grey solid lines indicate sequences outside Spars1. Phasing is between 8 and 12 with steps of 0.25. The sliding window is 200 bp and each step 10 bp. For simplification, only the informative curves corresponding to the phases 10.5, 10.25 and 9.25 are shown. Exploration of 9000 nt around Spars1 shows that the main curvature and the positively supercoiled region are unique.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2175326&req=5

Figure 8: Curved and supercoiled structures are unique. The Spars1 sequence is shown by black solid lines, and grey solid lines indicate sequences outside Spars1. Phasing is between 8 and 12 with steps of 0.25. The sliding window is 200 bp and each step 10 bp. For simplification, only the informative curves corresponding to the phases 10.5, 10.25 and 9.25 are shown. Exploration of 9000 nt around Spars1 shows that the main curvature and the positively supercoiled region are unique.
Mentions: We extended our analysis to the 9000 nt surrounding Spars1 using the conditions described in Figure 5. The substantial curvature described earlier is the only major curvature in the region (Figure 8); the same applies to the positive superhelical region.Figure 8.

Bottom Line: On pORC unwinding, this site shifts towards the apex of the curvature, thus potentiating DNA melting there.Our model is entirely consistent with the sequence variability, large size and A+T-richness of ORIs, and also accounts for the multistep nature of the initiation process, the specificity of pORC-binding site(s), and the specific location of RIP.We show that the particular DNA features and dynamic properties identified in Spars1 are present in other eukaryotic origins.

View Article: PubMed Central - PubMed

Affiliation: Régulation génique et fonctionnelle & microscopie champ proche, EA 3290, IFR 125, Faculté de Médecine, Université de la Méditerranée, 27 Bd Jean Moulin, 13385 Marseille cedex 5, France. monique.marilley@medecine.univ-mrs.fr

ABSTRACT
The replication origins (ORIs) of Schizosaccharomyces pombe, like those in most eukaryotes, are long chromosomal regions localized within A+T-rich domains. Although there is no consensus sequence, the interacting proteins are strongly conserved, suggesting that DNA structure is important for ORI function. We used atomic force microscopy in solution and DNA modelling to study the structural properties of the Spars1 origin. We show that this segment is the least stable of the surrounding DNA (9 kb), and contains regions of intrinsically bent elements (strongly curved and inherently supercoiled DNAs). The pORC-binding site co-maps with a superhelical DNA region, where the spatial arrangement of adenine/thymine stretches may provide the binding substrate. The replication initiation site (RIP) is located within a strongly curved DNA region. On pORC unwinding, this site shifts towards the apex of the curvature, thus potentiating DNA melting there. Our model is entirely consistent with the sequence variability, large size and A+T-richness of ORIs, and also accounts for the multistep nature of the initiation process, the specificity of pORC-binding site(s), and the specific location of RIP. We show that the particular DNA features and dynamic properties identified in Spars1 are present in other eukaryotic origins.

Show MeSH
Related in: MedlinePlus