Science Research Ideas
Biology
2001:
“At this point we do not fully understand how the actual replication initiation machinery (e.g. DNA polymerase a-primase and replication protein A) is recruited to the origin.”(Bielinsky & Gerbi, 2001)
“How components of the initiation complex, such as Mcm proteins or Cdc45p, rearrange to become part of elongating replication forks also remains unclear.” (Bielinsky & Gerbi, 2001)
“The question of whether the protein-DNA interactions detected at the lamin B2 origin are due to pre-RC (during G1 phase) and post-RC (during S phase) formation remains unanswered. However, recent RIP-mapping analyses (modified by LM-PCR) at this locus place the replication start points close to the site of protein-DNA interaction.” (Bielinsky & Gerbi, 2001)
“It remains to be seen whether Cdc6p and/or possibly other, unidentified factors modulate ORC binding in higher eukaryotes and whether this modulation affects origin choice at the ‘origin decision point’ in mammalian cells.” (Bielinsky & Gerbi, 2001)
“It is currently unclear whether ORCs of more highly evolved organisms recognize specific sequences or structural features similar to the AT-rich regions in the replicators of S. pombe.” (Bielinsky & Gerbi, 2001)
“The mechanism by which the iron rule of initiating DNA replication ‘once and only once per cell cycle’ is overridden remains obscure. However, recent in vitro studies demonstrate that ORC binds to the amplification control element 3 and to ori b, both of which lie in the general region of initiation , as detected previously by two dimensional gels.” (Bielinsky & Gerbi, 2001)
“The initiation pattern of the chorion origin has not yet been determined at the nucleotide level. Therefore, the relationship between the replication start sites and the ORC-binding sites remains to be illuminated.” (Bielinsky & Gerbi, 2001)
“A candidate for a human ORC-binding site is the 74-bp region protected by the origin-binding protein (OBP) at the human lamin B2 origin (Fig. 3B). Although HoxC10p and HoxC13p can bind to the 74-bp region, it is unclear whether ORC occupies this site as well.” (Bielinsky & Gerbi, 2001)
“As for the lagging strand (Okazaki fragment) start sites, they do not share any consensus sequence, even within a given locus, and the mechanism underlying their regular spacing remains to be clarified.” (Bielinsky & Gerbi, 2001)
“Whether Fission Yeast Cdt1 (SpCdt1) is regulated post-translationally by phosphorylation and/or proteolysis remains unknown. The timely expression of SpCdt1 appears important for once per cell cycle replication, because its ectopic expression potentiates the Cdc18-induced re-replication.” (Nishitani, Taraviras, Lygerou, & Nishimoto, 2001)
“Alternatively, hCdt1 and hCdc6/18, in addition to their common involvement in licensing, may have other roles in the cell, which remain to be identified.” (Nishitani, Taraviras, Lygerou, & Nishimoto, 2001)
Function of the gene 2BE2121 is unknown. (Gilbert, 2001)
Rapid replication in early Xenopus development is accomplished by initiating replication at sites that appear random with respect to sequence but are regularly spaced every 9 to 12 kb. The mechanism that establishes this regular origin spacing is unknown but, under conditions where chromatin is saturated with pre-RCs, any mechanism that prevents more than one pre-RC from assembling or firing per 10 kb would produce the observed spacing. (Gilbert, 2001)
The mechanism that determines the frequency with which a given pre-RC (pre replication complex)will be activated is not known, however, chromosomal context and epigenetic elements clearly play a role. (Gilbert, 2001)
At present, it is difficult to predict the significance of transcription to origin localization. Clearly, we need to determine the sites where pre-RCs assemble during telophase and whether the onset of transcription after mitosis does, indeed, displace pre-RCs from transcription units. (Gilbert, 2001)
The more pressing question becomes why origins are localized at all in most eukaryotic systems. The answer to this question may be different for different loci. Although this indeed complicates the analysis of eukaryotic origins, it should by no means discourage investigators from entertaining creative hypotheses and pursuing directions that will likely reveal new insights into the organization of complex genomes. (Gilbert, 2001)
“At this point we do not fully understand how the actual replication initiation machinery (e.g. DNA polymerase a-primase and replication protein A) is recruited to the origin.”(Bielinsky & Gerbi, 2001)
“How components of the initiation complex, such as Mcm proteins or Cdc45p, rearrange to become part of elongating replication forks also remains unclear.” (Bielinsky & Gerbi, 2001)
“The question of whether the protein-DNA interactions detected at the lamin B2 origin are due to pre-RC (during G1 phase) and post-RC (during S phase) formation remains unanswered. However, recent RIP-mapping analyses (modified by LM-PCR) at this locus place the replication start points close to the site of protein-DNA interaction.” (Bielinsky & Gerbi, 2001)
“It remains to be seen whether Cdc6p and/or possibly other, unidentified factors modulate ORC binding in higher eukaryotes and whether this modulation affects origin choice at the ‘origin decision point’ in mammalian cells.” (Bielinsky & Gerbi, 2001)
“It is currently unclear whether ORCs of more highly evolved organisms recognize specific sequences or structural features similar to the AT-rich regions in the replicators of S. pombe.” (Bielinsky & Gerbi, 2001)
“The mechanism by which the iron rule of initiating DNA replication ‘once and only once per cell cycle’ is overridden remains obscure. However, recent in vitro studies demonstrate that ORC binds to the amplification control element 3 and to ori b, both of which lie in the general region of initiation , as detected previously by two dimensional gels.” (Bielinsky & Gerbi, 2001)
“The initiation pattern of the chorion origin has not yet been determined at the nucleotide level. Therefore, the relationship between the replication start sites and the ORC-binding sites remains to be illuminated.” (Bielinsky & Gerbi, 2001)
“A candidate for a human ORC-binding site is the 74-bp region protected by the origin-binding protein (OBP) at the human lamin B2 origin (Fig. 3B). Although HoxC10p and HoxC13p can bind to the 74-bp region, it is unclear whether ORC occupies this site as well.” (Bielinsky & Gerbi, 2001)
“As for the lagging strand (Okazaki fragment) start sites, they do not share any consensus sequence, even within a given locus, and the mechanism underlying their regular spacing remains to be clarified.” (Bielinsky & Gerbi, 2001)
“Whether Fission Yeast Cdt1 (SpCdt1) is regulated post-translationally by phosphorylation and/or proteolysis remains unknown. The timely expression of SpCdt1 appears important for once per cell cycle replication, because its ectopic expression potentiates the Cdc18-induced re-replication.” (Nishitani, Taraviras, Lygerou, & Nishimoto, 2001)
“Alternatively, hCdt1 and hCdc6/18, in addition to their common involvement in licensing, may have other roles in the cell, which remain to be identified.” (Nishitani, Taraviras, Lygerou, & Nishimoto, 2001)
Function of the gene 2BE2121 is unknown. (Gilbert, 2001)
Rapid replication in early Xenopus development is accomplished by initiating replication at sites that appear random with respect to sequence but are regularly spaced every 9 to 12 kb. The mechanism that establishes this regular origin spacing is unknown but, under conditions where chromatin is saturated with pre-RCs, any mechanism that prevents more than one pre-RC from assembling or firing per 10 kb would produce the observed spacing. (Gilbert, 2001)
The mechanism that determines the frequency with which a given pre-RC (pre replication complex)will be activated is not known, however, chromosomal context and epigenetic elements clearly play a role. (Gilbert, 2001)
At present, it is difficult to predict the significance of transcription to origin localization. Clearly, we need to determine the sites where pre-RCs assemble during telophase and whether the onset of transcription after mitosis does, indeed, displace pre-RCs from transcription units. (Gilbert, 2001)
The more pressing question becomes why origins are localized at all in most eukaryotic systems. The answer to this question may be different for different loci. Although this indeed complicates the analysis of eukaryotic origins, it should by no means discourage investigators from entertaining creative hypotheses and pursuing directions that will likely reveal new insights into the organization of complex genomes. (Gilbert, 2001)
