scholarly journals An evolutionary model identifies the main selective pressures for the evolution of genome-replication profiles

2020 ◽  
Author(s):  
Rossana Droghetti ◽  
Nicolas Agier ◽  
Gilles Fischer ◽  
Marco Gherardi ◽  
Marco Cosentino Lagomarsino
Keyword(s):  
Yeast Species ◽  
Evolutionary Model ◽  
Replication Timing ◽  
Death Process ◽  
Genome Replication ◽  
Replication Forks ◽  
Evolutionary Models ◽  
Replication Origins ◽  
Selective Pressures ◽  
Evolutionary Studies

AbstractRecent results comparing the temporal program of genome replication of yeast species belonging to the Lachancea clade support the scenario that the evolution of replication timing program could be mainly driven by correlated acquisition and loss events of active replication origins. Using these results as a benchmark, we develop an evolutionary model defined as birth-death process for replication origins, and use it to identify the selective pressures that shape the replication timing profiles. Comparing different evolutionary models with data, we find that replication origin birth and death events are mainly driven by two evolutionary pressures, the first imposes that events leading to higher double-stall probability of replication forks are penalized, while the second makes less efficient origins more prone to evolutionary loss. This analysis provides an empirically grounded predictive framework for quantitative evolutionary studies of the replication timing program.

scholarly journals An evolutionary model identifies the main evolutionary biases for the evolution of genome-replication profiles

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Rossana Droghetti ◽  
Nicolas Agier ◽  
Gilles Fischer ◽  
Marco Gherardi ◽  
Marco Cosentino Lagomarsino
Keyword(s):  
Replication Origin ◽  
Yeast Species ◽  
Evolutionary Model ◽  
Replication Timing ◽  
Death Process ◽  
Genome Replication ◽  
Replication Forks ◽  
Evolutionary Models ◽  
Replication Origins ◽  
Evolutionary Studies

Recent results comparing the temporal program of genome replication of yeast species belonging to the Lachancea clade support the scenario that the evolution of replication timing program could be mainly driven by correlated acquisition and loss events of active replication origins. Using these results as a benchmark, we develop an evolutionary model defined as birth-death process for replication origins, and use it to identify the evolutionary biases that shape the replication timing profiles. Comparing different evolutionary models with data, we find that replication origin birth and death events are mainly driven by two evolutionary pressures, the first imposes that events leading to higher double-stall probability of replication forks are penalized, while the second makes less efficient origins more prone to evolutionary loss. This analysis provides an empirically grounded predictive framework for quantitative evolutionary studies of the replication timing program.

scholarly journals Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells

2016 ◽  
Vol 113 (39) ◽  
pp. E5757-E5764 ◽  
Author(s):  
Alberto Moreno ◽  
Jamie T. Carrington ◽  
Luca Albergante ◽  
Mohammed Al Mamun ◽  
Emma J. Haagensen ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Eukaryotic Cell ◽  
Nuclear Bodies ◽  
Genome Replication ◽  
Replication Forks ◽  
Replication Origins ◽  
Theoretical Predictions ◽  
Fork Stalling ◽  
Theoretical Evidence ◽  
Pass Through

To prevent rereplication of genomic segments, the eukaryotic cell cycle is divided into two nonoverlapping phases. During late mitosis and G1 replication origins are “licensed” by loading MCM2-7 double hexamers and during S phase licensed replication origins activate to initiate bidirectional replication forks. Replication forks can stall irreversibly, and if two converging forks stall with no intervening licensed origin—a “double fork stall” (DFS)—replication cannot be completed by conventional means. We previously showed how the distribution of replication origins in yeasts promotes complete genome replication even in the presence of irreversible fork stalling. This analysis predicts that DFSs are rare in yeasts but highly likely in large mammalian genomes. Here we show that complementary strand synthesis in early mitosis, ultrafine anaphase bridges, and G1-specific p53-binding protein 1 (53BP1) nuclear bodies provide a mechanism for resolving unreplicated DNA at DFSs in human cells. When origin number was experimentally altered, the number of these structures closely agreed with theoretical predictions of DFSs. The 53BP1 is preferentially bound to larger replicons, where the probability of DFSs is higher. Loss of 53BP1 caused hypersensitivity to licensing inhibition when replication origins were removed. These results provide a striking convergence of experimental and theoretical evidence that unreplicated DNA can pass through mitosis for resolution in the following cell cycle.

scholarly journals The evolution of the temporal program of genome replication

2017 ◽  
Author(s):  
Nicolas Agier ◽  
Stéphane Delmas ◽  
Qing Zhang ◽  
Aubin Fleiss ◽  
Yan Jaszczyszyn ◽  
...  
Keyword(s):  
Related Species ◽  
Replication Timing ◽  
Evolutionary Divergence ◽  
Genome Replication ◽  
Last Common Ancestor ◽  
Replication Origins ◽  
Active Replication ◽  
Firing Efficiency ◽  
Gains And Losses ◽  
Temporal Program

AbstractComparative analyses of temporal programs of genome replication revealed either a nearly complete conservation between closely related species or a comprehensive reprogramming between distantly related species. Therefore, many important questions on the evolutionary remodeling of replication timing programs remain unanswered. To address this issue, we generated genome-wide replication timing profiles for ten yeast species from the genus Lachancea, covering a continuous evolutionary range from closely related to more divergent species. The comparative analysis of these profiles revealed that the replication program linearly evolves with increasing evolutionary divergence between these species. We found that the evolution of the timing program mainly results from a high evolutionary turnover rate of the cohort of active replication origins. We detected about one thousand evolutionary events of losses of active replication origins and gains of newborn origins since the species diverged from their last common ancestor about 80 million years ago. We show that the relocation of active replication origins is independent from synteny breakpoints, suggesting that chromosome rearrangements did not drive the evolution of the replication programs. Rather, origin gains and losses are linked both in space, along chromosomes, and in time, along the same branches of the phylogenetic tree. New origins continuously arise with on average low to medium firing efficiencies and increase in efficiency and earliness as they evolutionarily age. Yet, a subset of newborn origins emerges with high firing efficiency and origin losses occur concomitantly to their emergence and preferentially in their direct chromosomal vicinity. These key findings on the evolutionary birth, death and conservation of active replication origins provide the first description of how the temporal program of genome replication has evolved in eukaryotes.

scholarly journals The Remarkable Evolution of the Post-Agb Star FG SGE

1998 ◽  
Vol 11 (1) ◽  
pp. 363-363
Author(s):  
Johanna Jurcsik ◽  
Benjamin Montesinos
Keyword(s):  
Time Scales ◽  
Effective Temperature ◽  
Planetary Nebula ◽  
Planetary Nebulae ◽  
Central Star ◽  
Evolutionary Models ◽  
Single Star ◽  
Line Intensities ◽  
Evolutionary Changes ◽  
Evolutionary Studies

FG Sagittae is one of the most important key objects of post-AGB stellar evolutionary studies. As a consequence of a final helium shell flash, this unique variable has shown real evolutionary changes on human time scales during this century. The observational history was reviewed in comparison with predictions from evolutionary models. The central star of the old planetary nebula (Hel-5) evolved from left to right in the HR diagram, going in just hundred years from the hot region of exciting sources of planetary nebulae to the cool red supergiant domain just before our eyes becoming a newly-born post-AGB star. The effective temperature of the star was around 50,000 K at the beginning of this century, and the last estimates in the late 1980s give 5,000-6,500 K. Recent spectroscopic observations obtained by Ingemar Lundström show definite changes in the nebular line intensities. This fact undoubtedly rules out the possibility that, instead of FG Sge, a hidden hot object would be the true central star of the nebula. Consequently, the observed evolutionary changes are connected with the evolution of a single star.

scholarly journals Studying 3D genome evolution using genomic sequence

2019 ◽  
Author(s):  
Raphaël Mourad
Keyword(s):  
Genome Evolution ◽  
Genomic Sequence ◽  
Regulation Of Gene Expression ◽  
Replication Timing ◽  
Evolutionary Constraints ◽  
3D Genome ◽  
Chromatin Looping ◽  
Novel Approach ◽  
Evolutionary Studies ◽  
Ancestral Character Reconstruction

AbstractThe 3D genome is essential to numerous key processes such as the regulation of gene expression and the replication-timing program. In vertebrates, chromatin looping is often mediated by CTCF, and marked by CTCF motif pairs in convergent orientation. Comparative Hi-C recently revealed that chromatin looping evolves across species. However, Hi-C experiments are complex and costly, which currently limits their use for evolutionary studies over a large number of species. Here, we propose a novel approach to study the 3D genome evolution in vertebrates using the genomic sequence only, e.g. without the need for Hi-C data. The approach is simple and relies on comparing the distances between convergent and divergent CTCF motifs (ratio R). We show that R is a powerful statistic to detect CTCF looping encoded in the human genome sequence, thus reflecting strong evolutionary constraints encoded in DNA and associated with the 3D genome. When comparing vertebrate genomes, our results reveal that R which underlies CTCF looping and TAD organization evolves over time and suggest that ancestral character reconstruction can be used to infer R in ancestral genomes.

Revisiting Hull's Evolutionary Model of Science

2021 ◽  
Vol 13 (2) ◽  
pp. 145-152
Author(s):  
Mohammad Mahdi Hatef ◽  
Keyword(s):  
Natural Selection ◽  
Selection Process ◽  
Biological Evolution ◽  
Evolutionary Model ◽  
Scientific Change ◽  
Evolutionary Models ◽  
Natural Evolution ◽  
The Difference

Evolutionary models for scientific change are generally based on an analogy between scientific changes and biological evolution. Some dissimilarity cases, however, challenge this analogy. An issue discussed in this essay is that despite natural evolution, which is currently considered to be non-globally progressive, science is a phenomenon that we understand as globally progressive. David Hull's solution to this disanalogy is to trace the difference back to their environments, in which processes of natural selection and conceptual selection occur. I will provide two arguments against this solution, showing that Hull's formulation of natural selection prohibits him from removing the environment from the selection process. Then I point to a related tension in his theory, between realism and externalism in science, and give some suggestions to solve these tensions.

Method of mapping DNA replication origins

1985 ◽  
Vol 5 (1) ◽  
pp. 85-92
Author(s):  
L D Spotila ◽  
J A Huberman
Keyword(s):  
Dna Replication ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Replication Forks ◽  
Replication Origins ◽  
Chromosomal Dna ◽  
Dna Restriction Fragments ◽  
Dna Restriction ◽  
Dna Replication Origins

We have developed a method which allows determination of the direction in which replication forks move through segments of chromosomal DNA for which cloned probes are available. The method is based on the facts that DNA restriction fragments containing replication forks migrate more slowly through agarose gels than do non-fork-containing fragments and that the extent of retardation of the fork-containing fragments is a function of the extent of replication. The procedure allows the identification of DNA replication origins as sites from which replication forks diverge. In this paper we demonstrate the feasibility of this procedure, with simian virus 40 DNA as a model, and we discuss its applicability to other systems.

scholarly journals Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase

2016 ◽  
Vol 26 (3) ◽  
pp. 365-375 ◽  
Author(s):  
Jared M. Peace ◽  
Sandra K. Villwock ◽  
John L. Zeytounian ◽  
Yan Gan ◽  
Oscar M. Aparicio
Keyword(s):  
Replication Timing ◽  
G1 Phase ◽  
Replication Origins ◽  
Rate Limiting

scholarly journals Excess Mcm2–7 license dormant origins of replication that can be used under conditions of replicative stress

2006 ◽  
Vol 173 (5) ◽  
pp. 673-683 ◽  
Author(s):  
Anna M. Woodward ◽  
Thomas Göhler ◽  
M. Gloria Luciani ◽  
Maren Oehlmann ◽  
Xinquan Ge ◽  
...  
Keyword(s):  
Complete Genome ◽  
S Phase ◽  
Genome Replication ◽  
Replication Origins ◽  
Observable Effect ◽  
Minichromosome Maintenance ◽  
Replicative Stress ◽  
Origins Of Replication ◽  
Checkpoint Pathway ◽  
Egg Extracts

In late mitosis and early G1, replication origins are licensed for subsequent use by loading complexes of the minichromosome maintenance proteins 2–7 (Mcm2–7). The number of Mcm2–7 complexes loaded onto DNA greatly exceeds the number of replication origins used during S phase, but the function of the excess Mcm2–7 is unknown. Using Xenopus laevis egg extracts, we show that these excess Mcm2–7 complexes license additional dormant origins that do not fire during unperturbed S phases because of suppression by a caffeine-sensitive checkpoint pathway. Use of these additional origins can allow complete genome replication in the presence of replication inhibitors. These results suggest that metazoan replication origins are actually comprised of several candidate origins, most of which normally remain dormant unless cells experience replicative stress. Consistent with this model, using Caenorhabditis elegans, we show that partial RNAi-based knockdown of MCMs that has no observable effect under normal conditions causes lethality upon treatment with low, otherwise nontoxic, levels of the replication inhibitor hydroxyurea.

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