Mitochondrial tRNAs as light strand replication origins: Similarity between anticodon loops and the loop of the light strand replication origin predicts initiation of DNA replication

Biosystems ◽  
2010 ◽  
Vol 99 (2) ◽  
pp. 85-93 ◽  
Author(s):  
Hervé Seligmann
Keyword(s):  
Dna Replication ◽  
Replication Origin ◽  
Replication Origins ◽  
Initiation Of Dna Replication ◽  
Light Strand

scholarly journals Changes in association of the Xenopus origin recognition complex with chromatin on licensing of replication origins

1999 ◽  
Vol 112 (12) ◽  
pp. 2011-2018 ◽  
Author(s):  
A. Rowles ◽  
S. Tada ◽  
J.J. Blow
Keyword(s):  
Dna Replication ◽  
Single Molecule ◽  
Replication Origin ◽  
Origin Recognition Complex ◽  
S Phase ◽  
Replication Origins ◽  
Free System ◽  
Essential Function ◽  
Initiation Of Dna Replication ◽  
Origin Recognition

During late mitosis and early G1, a series of proteins are assembled onto replication origins that results in them becoming ‘licensed’ for replication in the subsequent S phase. In Xenopus this first involves the assembly onto chromatin of the Xenopus origin recognition complex XORC, and then XCdc6, and finally the RLF-M component of the replication licensing system. In this paper we examine changes in the way that XORC associates with chromatin in the Xenopus cell-free system as origins become licensed. Restricting the quantity of XORC on chromatin reduced the extent of replication as expected if a single molecule of XORC is sufficient to specify a single replication origin. During metaphase, XOrc1 associated only weakly with chromatin. In early interphase, XOrc1 formed a strong complex with chromatin, as evidenced by its resistance to elution by 200 mM salt, and this state persisted when XCdc6 was assembled onto the chromatin. As a consequence of origins becoming licensed the association of XOrc1 and XCdc6 with chromatin was destabilised, and XOrc1 became susceptible to removal from chromatin by exposure to either high salt or high Cdk levels. At this stage the essential function for XORC and XCdc6 in DNA replication had already been fulfilled. Since high Cdk levels are required for the initiation of DNA replication, this ‘licensing-dependent origin inactivation’ may contribute to mechanisms that prevent re-licensing of replication origins once S phase has started.

scholarly journals Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yongzheng Li ◽  
Boxin Xue ◽  
Mengling Zhang ◽  
Liwei Zhang ◽  
Yingping Hou ◽  
...  
Keyword(s):  
Dna Replication ◽  
Structural Dynamics ◽  
Replication Origin ◽  
High Efficiency ◽  
S Phase ◽  
Chromatin Domain ◽  
Replication Origins ◽  
Replication Efficiency ◽  
Topologically Associating Domains ◽  
Epigenetic Signatures

Abstract Background Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. Results We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired. Conclusion Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.

scholarly journals The B-Subunit of DNA Polymerase α-Primase Associates with the Origin Recognition Complex for Initiation of DNA Replication

2004 ◽  
Vol 24 (17) ◽  
pp. 7419-7434 ◽  
Author(s):  
Masashi Uchiyama ◽  
Teresa S.-F. Wang
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Dna Polymerase ◽  
Origin Recognition Complex ◽  
Replication Origins ◽  
Dna Polymerase Α ◽  
B Subunit ◽  
Initiation Of Dna Replication ◽  
Primase Complex ◽  
Origin Recognition

ABSTRACT The B-subunit (p70/Pol12p) of the DNA polymerase α-primase (Polα-primase) complex is thought to have a regulatory role in an early stage of S phase. We generated a panel of fission yeast thermosensitive mutants of the B-subunit (termed Spb70) to investigate its role in initiation of DNA replication by genetic and biochemical approaches. Here, we show that the fission yeast Spb70 genetically interacts and coprecipitates with origin recognition complex proteins Orp1/Orc1 and Orp2/Orc2 and primase coupling subunit Spp2/p58. A fraction of Spb70 associates with Orp2 on chromatin throughout the cell cycle independent of the other subunits of Polα-primase. Furthermore, primase Spp2/p58 subunit preferentially associates with the unphosphorylated Orp2, and the association requires Spb70. Mutations in orp2+ that abolish or mimic the Cdc2 phosphorylation of Orp2 suppress or exacerbate the thermosensitivity of the spb70 mutants, respectively, indicating that an unphosphorylated Orp2 promotes an Spb70-dependent replication event. Together, these results indicate that the chromatin-bound B-subunit in association with origin recognition complex mediates recruiting Polα-primase complex onto replication origins in G1 pre-Start through an interaction with primase Spp2/p58 subunit. Our results thus suggest a role for the recruited Polα-primase in the initiation of both leading and lagging strands at the replication origins.

scholarly journals Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation

2021 ◽  
Author(s):  
Guillaume Guilbaud ◽  
Pierre Murat ◽  
Helen S Wilkes ◽  
Leticia Koch Lerner ◽  
Julian Sale ◽  
...  
Keyword(s):  
Dna Replication ◽  
Replication Origin ◽  
Gradient Centrifugation ◽  
Initiation Site ◽  
Efficiency Score ◽  
Replication Initiation ◽  
Equilibrium Density ◽  
Replication Origins ◽  
Origin Firing ◽  
Dna Replication Origin

Replication of the human genome initiates within broad zones of ~ 150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq) based on density substitution. Newly-replicated DNA is rendered heavy-light (HL) by incorporation of BrdUTP, unreplicated DNA remaining light-light (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.

scholarly journals HOXD13 Binds DNA Replication Origins To Promote Origin Licensing and Is Inhibited by Geminin

2009 ◽  
Vol 29 (21) ◽  
pp. 5775-5788 ◽  
Author(s):  
Valentina Salsi ◽  
Silvia Ferrari ◽  
Roberta Ferraresi ◽  
Andrea Cossarizza ◽  
Alexis Grande ◽  
...  
Keyword(s):  
Dna Replication ◽  
Dna Synthesis ◽  
Replication Origin ◽  
Cultured Cells ◽  
Cell Aggregation ◽  
Replication Origins ◽  
Protein Activity ◽  
Hox Proteins ◽  
Origin Licensing

ABSTRACT HOX DNA-binding proteins control patterning during development by regulating processes such as cell aggregation and proliferation. Recently, a possible involvement of HOX proteins in replication origin activity was suggested by results showing that a number of HOX proteins interact with the DNA replication licensing regulator geminin and bind a characterized human origin of replication. The functional significance of these observations, however, remained unclear. We show that HOXD13, HOXD11, and HOXA13 bind in vivo all characterized human replication origins tested. We furthermore show that HOXD13 interacts with the CDC6 loading factor, promotes pre-replication complex (pre-RC) proteins assembly at origins, and stimulates DNA synthesis in an in vivo replication assay. HOXD13 expression in cultured cells accelerates DNA synthesis initiation in correlation with the earlier pre-RC recruitment onto origins during G1 phase. Geminin, which interacts with HOXD13 as well, blocks HOXD13-mediated assembly of pre-RC proteins and inhibits HOXD13-induced DNA replication. Our results uncover a function for Hox proteins in the regulation of replication origin activity and reveal an unforeseen role for the inhibition of HOX protein activity by geminin in the context of replication origin licensing.

scholarly journals CDK promotes interactions of Sld3 and Drc1 with Cut5 for initiation of DNA replication in fission yeast

2011 ◽  
Vol 22 (14) ◽  
pp. 2620-2633 ◽  
Author(s):  
Masayoshi Fukuura ◽  
Koji Nagao ◽  
Chikashi Obuse ◽  
Tatsuro S. Takahashi ◽  
Takuro Nakagawa ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Ternary Complex ◽  
Budding Yeast ◽  
S Phase ◽  
Replication Proteins ◽  
Cyclin Dependent Kinase ◽  
Replication Origins ◽  
Initiation Of Dna Replication

Cyclin-dependent kinase (CDK) plays essential roles in the initiation of DNA replication in eukaryotes. Although interactions of CDK-phosphorylated Sld2/Drc1 and Sld3 with Dpb11 have been shown to be essential in budding yeast, it is not known whether the mechanism is conserved. In this study, we investigated how CDK promotes the assembly of replication proteins onto replication origins in fission yeast. Phosphorylation of Sld3 was found to be dependent on CDK in S phase. Alanine substitutions at CDK sites decreased the interaction with Cut5/Dpb11 at the N-terminal BRCT motifs and decreased the loading of Cut5 onto replication origins. This defect was suppressed by overexpression of drc1+. Phosphorylation of a conserved CDK site, Thr-111, in Drc1 was critical for interaction with Cut5 at the C-terminal BRCT motifs and was required for loading of Cut5. In a yeast three-hybrid assay, Sld3, Cut5, and Drc1 were found to form a ternary complex dependent on the CDK sites of Sld3 and Drc1, and Drc1–Cut5 binding enhanced the Sld3–Cut5 interaction. These results show that the mechanism of CDK-dependent loading of Cut5 is conserved in fission yeast in a manner similar to that elucidated in budding yeast.

scholarly journals Germline DNA replication shapes the recombination landscape in mammals

2020 ◽  
Author(s):  
Florencia Pratto ◽  
Kevin Brick ◽  
Gang Cheng ◽  
Gabriel Lam ◽  
Jeffrey M. Cloutier ◽  
...  
Keyword(s):  
Dna Replication ◽  
Replication Origin ◽  
Genetic Recombination ◽  
Chromosome Size ◽  
Replication Pattern ◽  
Replication Origins ◽  
Origin Firing ◽  
Recombination Hotspots ◽  
Novel Approach ◽  
Germline Variation

Summary:Genetic recombination generates novel trait combinations and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots, however megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns, therefore we devised a novel approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis and a distinctive replication pattern in human males underlies the sub-telomeric increase in recombination. We detected a robust correlation between replication and both contemporary and ancestral recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have far-reaching implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.

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