scholarly journals Mapping and Use of a Sequence that Targets DNA Ligase I to Sites of DNA Replication In Vivo

1997 ◽  
Vol 139 (3) ◽  
pp. 579-587 ◽  
Author(s):  
M. Cristina Cardoso ◽  
Cuthbert Joseph ◽  
Hans-Peter Rahn ◽  
Regina Reusch ◽  
Bernardo Nadal-Ginard ◽  
...  
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Fluorescent Protein ◽  
Functional Organization ◽  
S Phase ◽  
Dna Ligase ◽  
Chimeric Proteins ◽  
Dna Ligase I ◽  
Replication Foci

The mammalian nucleus is highly organized, and nuclear processes such as DNA replication occur in discrete nuclear foci, a phenomenon often termed “functional organization” of the nucleus. We describe the identification and characterization of a bipartite targeting sequence (amino acids 1–28 and 111–179) that is necessary and sufficient to direct DNA ligase I to nuclear replication foci during S phase. This targeting sequence is located within the regulatory, NH2-terminal domain of the protein and is dispensable for enzyme activity in vitro but is required in vivo. The targeting domain functions position independently at either the NH2 or the COOH termini of heterologous proteins. We used the targeting sequence of DNA ligase I to visualize replication foci in vivo. Chimeric proteins with DNA ligase I and the green fluorescent protein localized at replication foci in living mammalian cells and thus show that these subnuclear functional domains, previously observed in fixed cells, exist in vivo. The characteristic redistribution of these chimeric proteins makes them unique markers for cell cycle studies to directly monitor entry into S phase in living cells.

scholarly journals Nuclear Dynamics of PCNA in DNA Replication and Repair

2005 ◽  
Vol 25 (21) ◽  
pp. 9350-9359 ◽  
Author(s):  
Jeroen Essers ◽  
Arjan F. Theil ◽  
Céline Baldeyron ◽  
Wiggert A. van Cappellen ◽  
Adriaan B. Houtsmuller ◽  
...  
Keyword(s):  
Dna Replication ◽  
Residence Time ◽  
Fluorescent Protein ◽  
De Novo ◽  
Dynamic Equilibrium ◽  
Excision Repair ◽  
S Phase ◽  
Nuclear Antigen ◽  
Dna Replication And Repair ◽  
Replication Foci

ABSTRACT The DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) is central to both DNA replication and repair. The ring-shaped homotrimeric PCNA encircles and slides along double-stranded DNA, acting as a “sliding clamp” that localizes proteins to DNA. We determined the behavior of green fluorescent protein-tagged human PCNA (GFP-hPCNA) in living cells to analyze its different engagements in DNA replication and repair. Photobleaching and tracking of replication foci revealed a dynamic equilibrium between two kinetic pools of PCNA, i.e., bound to replication foci and as a free mobile fraction. To simultaneously monitor PCNA action in DNA replication and repair, we locally inflicted UV-induced DNA damage. A surprisingly longer residence time of PCNA at damaged areas than at replication foci was observed. Using DNA repair mutants, we showed that the initial recruitment of PCNA to damaged sites was dependent on nucleotide excision repair. Local accumulation of PCNA at damaged regions was observed during all cell cycle stages but temporarily disappeared during early S phase. The reappearance of PCNA accumulation in discrete foci at later stages of S phase likely reflects engagements of PCNA in distinct genome maintenance processes dealing with stalled replication forks, such as translesion synthesis (TLS). Using a ubiquitination mutant of GFP-hPCNA that is unable to participate in TLS, we noticed a significantly shorter residence time in damaged areas. Our results show that changes in the position of PCNA result from de novo assembly of freely mobile replication factors in the nucleoplasmic pool and indicate different binding affinities for PCNA in DNA replication and repair.

scholarly journals Etoposide Induces the Dispersal of DNA Ligase I from Replication Factories

2001 ◽  
Vol 12 (7) ◽  
pp. 2109-2118 ◽  
Author(s):  
Alessandra Montecucco ◽  
Rossella Rossi ◽  
Giovanni Ferrari ◽  
A. Ivana Scovassi ◽  
Ennio Prosperi ◽  
...  
Keyword(s):  
Dna Replication ◽  
Ataxia Telangiectasia ◽  
Topoisomerase Ii ◽  
Molecular Mechanisms ◽  
Kinase Inhibitor ◽  
Protein A ◽  
S Phase ◽  
Nuclear Antigen ◽  
Dna Ligase ◽  
Dna Ligase I

In eukaryotic cells DNA replication occurs in specific nuclear compartments, called replication factories, that undergo complex rearrangements during S-phase. The molecular mechanisms underlying the dynamics of replication factories are still poorly defined. Here we show that etoposide, an anticancer drug that induces double-strand breaks, triggers the redistribution of DNA ligase I and proliferating cell nuclear antigen from replicative patterns and the ensuing dephosphorylation of DNA ligase I. Moreover, etoposide triggers the formation of RPA foci, distinct from replication factories. The effect of etoposide on DNA ligase I localization is prevented by aphidicolin, an inhibitor of DNA replication, and by staurosporine, a protein kinase inhibitor and checkpoints' abrogator. We suggest that dispersal of DNA ligase I is triggered by an intra-S-phase checkpoint activated when replicative forks meet topoisomerase II-DNA–cleavable complexes. However, etoposide treatment of ataxia telangiectasia cells demonstrated that ataxia-telangiectasia-mutated activity is not required for the disassembly of replication factories and the formation of replication protein A foci.

scholarly journals Nuclear Reorganization of Mammalian DNA Synthesis Prior to Cell Cycle Exit

2004 ◽  
Vol 24 (2) ◽  
pp. 595-607 ◽  
Author(s):  
David A. Barbie ◽  
Brian A. Kudlow ◽  
Richard Frock ◽  
Jiyong Zhao ◽  
Brett R. Johnson ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Dna Synthesis ◽  
Mammalian Cells ◽  
Large Scale ◽  
Replicative Senescence ◽  
S Phase ◽  
Serum Starvation ◽  
Cell Cycle Exit ◽  
Replication Foci

ABSTRACT In primary mammalian cells, DNA replication initiates in a small number of perinucleolar, lamin A/C-associated foci. During S-phase progression in proliferating cells, replication foci distribute to hundreds of sites throughout the nucleus. In contrast, we find that the limited perinucleolar replication sites persist throughout S phase as cells prepare to exit the cell cycle in response to contact inhibition, serum starvation, or replicative senescence. Proteins known to be involved in DNA synthesis, such as PCNA and DNA polymerase δ, are concentrated in perinucleolar foci throughout S phase under these conditions. Moreover, chromosomal loci are redirected toward the nucleolus and overlap with the perinucleolar replication foci in cells poised to undergo cell cycle exit. These same loci remain in the periphery of the nucleus during replication under highly proliferative conditions. These results suggest that mammalian cells undergo a large-scale reorganization of chromatin during the rounds of DNA replication that precede cell cycle exit.

scholarly journals DNA ligase I mediates essential functions in mammalian cells.

1995 ◽  
Vol 15 (8) ◽  
pp. 4303-4308 ◽  
Author(s):  
J H Petrini ◽  
Y Xiao ◽  
D T Weaver
Keyword(s):  
Mammalian Cells ◽  
Catalytic Domain ◽  
Embryonic Stem ◽  
Dna Ligase ◽  
Null Mutation ◽  
Dna Ligases ◽  
Dna Ligase I ◽  
The Creation ◽  
Stem Cell Lines

DNA replication, repair, and recombination are essential processes in mammalian cells. Hence, the application of gene targeting to the study of these DNA metabolic pathways requires the creation of nonnull mutations. We have developed a method for introducing partially defective mutants in murine embryonic stem cells that circumvents the problem of cellular lethality of targeted mutations at essential loci. Using this approach, we have determined that mammalian DNA ligase I is essential for cell viability. Thus, DNA ligases II and III are not redundant with DNA ligase I for the function(s) associated with cell proliferation. Partial complementation of the lethal DNA ligase I null mutation allowed the creation of deficient embryonic stem cell lines. We found that a wild-type DNA ligase I cDNA, as well as a variant DNA ligase I cDNA, was able to rescue the lethality of the homozygous null mutation, whereas an N-terminal deletion mutant consisting of the minimal DNA ligase I catalytic domain was not. This observation demonstrates that sequences outside the DNA ligase I catalytic domain are essential for DNA ligase I function in vivo.

scholarly journals Genetic Analyses of Schizosaccharomyces pombe dna2+ Reveal That Dna2 Plays an Essential Role in Okazaki Fragment Metabolism

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1055-1067
Author(s):  
Ho-Young Kang ◽  
Eunjoo Choi ◽  
Sung-Ho Bae ◽  
Kyoung-Hwa Lee ◽  
Byung-Soo Gim ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
S Phase ◽  
Dna Ligase ◽  
Temperature Sensitive ◽  
Restrictive Temperature ◽  
Direct Role ◽  
Okazaki Fragment ◽  
Dna Ligase I ◽  
Genes Encoding

Abstract In this report, we investigated the phenotypes caused by temperature-sensitive (ts) mutant alleles of dna2+ of Schizosaccharomyces pombe, a homologue of DNA2 of budding yeast, in an attempt to further define its function in vivo with respect to lagging-strand synthesis during the S-phase of the cell cycle. At the restrictive temperature, dna2 (ts) cells arrested at late S-phase but were unaffected in bulk DNA synthesis. Moreover, they exhibited aberrant mitosis when combined with checkpoint mutations, in keeping with a role for Dna2 in Okazaki fragment maturation. Similarly, spores in which dna2+ was disrupted duplicated their DNA content during germination and also arrested at late S-phase. Inactivation of dna2+ led to chromosome fragmentation strikingly similar to that seen when cdc17+, the DNA ligase I gene, is inactivated. The temperature-dependent lethality of dna2 (ts) mutants was suppressed by overexpression of genes encoding subunits of polymerase δ (cdc1+ and cdc27+), DNA ligase I (cdc17+), and Fen-1 (rad2+). Each of these gene products plays a role in the elongation or maturation of Okazaki fragments. Moreover, they all interacted with S. pombe Dna2 in a yeast two-hybrid assay, albeit to different extents. On the basis of these results, we conclude that dna2+ plays a direct role in the Okazaki fragment elongation and maturation. We propose that dna2+ acts as a central protein to form a complex with other proteins required to coordinate the multienzyme process for Okazaki fragment elongation and maturation.

DNA ligase I null mouse cells show normal DNA repair activity but altered DNA replication and reduced genome stability

2002 ◽  
Vol 115 (7) ◽  
pp. 1551-1561 ◽  
Author(s):  
Darren J. Bentley ◽  
Caroline Harrison ◽  
Ann-Marie Ketchen ◽  
Nicola J. Redhead ◽  
Kay Samuel ◽  
...  
Keyword(s):  
Dna Repair ◽  
Dna Replication ◽  
Mammalian Cells ◽  
Genome Stability ◽  
Genome Instability ◽  
Null Alleles ◽  
Dna Ligase ◽  
Null Mouse ◽  
Dna Ligase I ◽  
Mouse Cells

DNA ligase I is the key ligase for DNA replication in mammalian cells and has also been reported to be involved in a number of recombination and repair processes. Our previous finding that Lig1 knockout mouse embryos developed normally to mid-term before succumbing to a specific haematopoietic defect was difficult to reconcile with a report that DNA ligase I is essential for the viability of cultured mammalian cells. To address this issue, we generated a second Lig1 targeted allele and found that the phenotypes of our two Lig1 mutant mouse lines are identical. Widely different levels of Lig1 fusion transcripts were detected from the two targeted alleles, but we could not detect any DNA ligase I protein, and we believe both are effective Lig1 null alleles. Using foetal liver cells to repopulate the haematopoietic system of lethally irradiated adult mice, we demonstrate that the haematopoietic defect in DNA-ligase-I-deficient embryos is a quantitative deficiency relating to reduced proliferation rather than a qualitative block in any haematopoietic lineage. DNA ligase I null fibroblasts from Lig1 mutant embryos showed an accumulation of DNA replication intermediates and increased genome instability. In the absence of a demonstrable deficiency in DNA repair we postulate that, unusually, genome instability may result directly from the DNA replication defect. Lig1null mouse cells performed better in the survival and replication assays than a human LIG1 point mutant, and we suggest that the complete absence of DNA ligase I may make it easier for another ligase to compensate for DNA ligase I deficiency.

scholarly journals Chromatin decondensation in S-phase involves recruitment of Cdk2 by Cdc45 and histone H1 phosphorylation

2005 ◽  
Vol 168 (6) ◽  
pp. 875-886 ◽  
Author(s):  
Mark G. Alexandrow ◽  
Joyce L. Hamlin
Keyword(s):  
Mammalian Cells ◽  
Large Scale ◽  
Histone H1 ◽  
S Phase ◽  
Wild Type ◽  
Chromatin Decondensation ◽  
Replication Foci ◽  
Phase Progression ◽  
Initiation Of Dna Replication

Cdc45 is required for initiation of DNA replication and fork progression, but its function in these processes remains unknown. We show that targeting Cdc45 to specific chromosomal sites in mammalian cells results in large-scale chromatin decondensation that strongly correlates with histone H1 phosphorylation. Cdk2 is recruited to sites of Cdc45 decondensation, and Cdk2 inhibitors reduce the level of decondensation. Targeting wild-type Cdk2, but not kinase-defective Cdk2, to chromatin is also effective at inducing decondensation involving phospho-H1. Cdc45, Cdk2, Cyclin A, and phospho-H1 associate with chromatin during S-phase, and Cdc45, Cdk2, and an active H1 kinase physically interact. Replicating DNA and phospho-H1 foci colocalize in vivo, and S-phase progression and H1 phosphorylation are directly related and Cdk2 dependent. Because Cdk2 colocalizes with replication foci and H1 regulates higher-order chromatin, we suggest a model in which Cdc45 recruits Cdk2 to replication foci, resulting in H1 phosphorylation, chromatin decondensation, and facilitation of fork progression.

Overexpression of kin17 protein disrupts nuclear morphology and inhibits the growth of mammalian cells

1999 ◽  
Vol 112 (19) ◽  
pp. 3215-3224 ◽  
Author(s):  
P. Kannouche ◽  
J.F. Angulo
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Cell Cycle Progression ◽  
Reca Protein ◽  
S Phase ◽  
Expression Vectors ◽  
Nuclear Morphology ◽  
Functional Domain ◽  
Genetic Response ◽  
Cycle Progression

UVC or ionizing radiation of mammalian cells elicits a complex genetic response that allows recovery and cell survival. Kin17 gene, which is highly conserved among mammals, is upregulated during this response. Kin17 gene encodes a 45 kDa protein which binds to DNA and presents a limited similarity with a functional domain of the bacterial RecA protein. Kin17 protein is accumulated in the nucleus of proliferating fibroblasts and forms intranuclear foci. Using expression vectors, we show that overexpression of kin17 protein inhibits cell-cycle progression into S phase. Our results indicate that growth inhibition correlates with disruption of the nuclear morphology which seems to modify the intranuclear network required during the early steps of DNA replication. We report that a mutant encoding a protein deleted from the central domain of kin17 protein enhanced these effects whereas the deletion of the C-terminal domain considerably reduced them. These mutants will be used to elucidate the molecular mechanism by which kin17 protein alters cell growth and DNA replication.

scholarly journals A Coordinated Temporal Interplay of Nucleosome Reorganization Factor, Sister Chromatin Cohesion Factor, and DNA Polymerase α Facilitates DNA Replication

2004 ◽  
Vol 24 (21) ◽  
pp. 9568-9579 ◽  
Author(s):  
Yanjiao Zhou ◽  
Teresa S.-F. Wang
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
S Phase ◽  
Terminal Region ◽  
Replication Complex ◽  
Dna Polymerase Α ◽  
Chromatid Cohesion ◽  
Phase Progression

ABSTRACT DNA replication depends critically upon chromatin structure. Little is known about how the replication complex overcomes the nucleosome packages in chromatin during DNA replication. To address this question, we investigate factors that interact in vivo with the principal initiation DNA polymerase, DNA polymerase α (Polα). The catalytic subunit of budding yeast Polα (Pol1p) has been shown to associate in vitro with the Spt16p-Pob3p complex, a component of the nucleosome reorganization system required for both replication and transcription, and with a sister chromatid cohesion factor, Ctf4p. Here, we show that an N-terminal region of Polα (Pol1p) that is evolutionarily conserved among different species interacts with Spt16p-Pob3p and Ctf4p in vivo. A mutation in a glycine residue in this N-terminal region of POL1 compromises the ability of Pol1p to associate with Spt16p and alters the temporal ordered association of Ctf4p with Pol1p. The compromised association between the chromatin-reorganizing factor Spt16p and the initiating DNA polymerase Pol1p delays the Pol1p assembling onto and disassembling from the late-replicating origins and causes a slowdown of S-phase progression. Our results thus suggest that a coordinated temporal and spatial interplay between the conserved N-terminal region of the Polα protein and factors that are involved in reorganization of nucleosomes and promoting establishment of sister chromatin cohesion is required to facilitate S-phase progression.

Temporal order of DNA replication in the H-2 major histocompatibility complex of the mouse

1992 ◽  
Vol 12 (11) ◽  
pp. 5174-5188
Author(s):  
E G Spack ◽  
E D Lewis ◽  
B Paradowski ◽  
R T Schimke ◽  
P P Jones
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Temporal Order ◽  
Chromosomal Region ◽  
S Phase ◽  
Major Histocompatibility ◽  
Histocompatibility Complex ◽  
T Lymphoma Cells ◽  
Initiation Of Dna Replication ◽  
T Lymphoma

As an approach to mapping replicons in an extended chromosomal region, the temporal order of DNA replication was analyzed in the murine major histocompatibility gene complex (MHC). Replicating DNA from T-lymphoma and myelomonocyte cell lines was density labeled with bromodeoxyuridine and extracted from cells which had been fractionated into different stages of S phase by centrifugal elutriation. The replicating DNA from each fraction of S phase was separated from nonreplicating DNA on density gradients, blotted, and hybridized with 34 specific MHC probes. The earliest replication occurred in the vicinity of transcribed genes K, HAM1 and HAM2, RD, B144, D, L, T18, and T3. The temporal order of replication of groups of DNA segments suggests the location of five or six replicons within the H-2 complex, some of which appear to be either unidirectional or markedly asymmetric. The rates of replication through each of these apparent replicons appear to be similar. The TL region of the S49.1 T-lymphoma cells, which contains at least three transcribed genes, replicates earlier than the inactive TL region of WEHI-3 myelomonocytic cells. These results provide further evidence of a relationship between transcription and the initiation of DNA replication in mammalian cells. The mouse MHC examined in this study is the largest chromosomal region (> 2,000 kb) measured for timing of replication to date.

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