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 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 Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sajjad Asaf ◽  
Abdul Latif Khan ◽  
Muhammad Numan ◽  
Ahmed Al-Harrasi
Keyword(s):  
Chloroplast Genome ◽  
Related Species ◽  
Evolutionary Genetics ◽  
Single Copy ◽  
Avicennia Marina ◽  
Pairwise Distance ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mangrove Tree ◽  
High Degree

AbstractAvicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members’ specifically A. marina and related species.

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 Pipeline for the Rapid Development of Cytogenetic Markers Using Genomic Data of Related Species

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 113 ◽  
Author(s):  
Pavel Kroupin ◽  
Victoria Kuznetsova ◽  
Dmitry Romanov ◽  
Alina Kocheshkova ◽  
Gennady Karlov ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Related Species ◽  
Evolutionary Divergence ◽  
Whole Genome ◽  
Target Genome ◽  
Target Species ◽  
Closely Related Species ◽  
Chromosome Markers

Repetitive DNA including tandem repeats (TRs) is a significant part of most eukaryotic genomes. TRs include rapidly evolving satellite DNA (satDNA) that can be shared by closely related species, their abundance may be associated with evolutionary divergence, and they have been widely used for chromosome karyotyping using fluorescence in situ hybridization (FISH). The recent progress in the development of whole-genome sequencing and bioinformatics tools enables rapid and cost-effective searches for TRs including satDNA that can be converted into molecular cytogenetic markers. In the case of closely related taxa, the genome sequence of one species (donor) can be used as a base for the development of chromosome markers for related species or genomes (target). Here, we present a pipeline for rapid and high-throughput screening for new satDNA TRs in whole-genome sequencing of the donor genome and the development of chromosome markers based on them that can be applied in the target genome. One of the main peculiarities of the developed pipeline is that preliminary estimation of TR abundance using qPCR and ranking found TRs according to their copy number in the target genome; it facilitates the selection of the most prospective (most abundant) TRs that can be converted into cytogenetic markers. Another feature of our pipeline is the probe preparation for FISH using PCR with primers designed on the aligned TR unit sequences and the genomic DNA of a target species as a template that enables amplification of a whole pool of monomers inherent in the chromosomes of the target species. We demonstrate the efficiency of the developed pipeline by the example of FISH probes developed for A, B, and R subgenome chromosomes of hexaploid triticale (BBAARR) based on a bioinformatics analysis of the D genome of Aegilops tauschii (DD) whole-genome sequence. Our pipeline can be used to develop chromosome markers in closely related species for comparative cytogenetics in evolutionary and breeding studies.

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.

scholarly journals Activation of Silent Replication Origins at Autonomously Replicating Sequence Elements near the HML Locus in Budding Yeast

1999 ◽  
Vol 19 (9) ◽  
pp. 6098-6109 ◽  
Author(s):  
Marija Vujcic ◽  
Charles A. Miller ◽  
David Kowalski
Keyword(s):  
Replication Origin ◽  
Budding Yeast ◽  
Transcriptional Silencing ◽  
Growth Conditions ◽  
Replication Origins ◽  
Additional Time ◽  
Autonomously Replicating Sequence ◽  
Ars Elements ◽  
Active Replication ◽  
Chromosome Iii

ABSTRACT In the budding yeast, Saccharomyces cerevisiae, replicators can function outside the chromosome as autonomously replicating sequence (ARS) elements; however, within chromosome III, certain ARSs near the transcriptionally silent HML locus show no replication origin activity. Two of these ARSs comprise the transcriptional silencers E (ARS301) and I (ARS302). Another, ARS303, resides betweenHML and the CHA1 gene, and its function is not known. Here we further localized and characterized ARS303and in the process discovered a new ARS, ARS320. BothARS303 and ARS320 are competent as chromosomal replication origins since origin activity was seen when they were inserted at a different position in chromosome III. However, at their native locations, where the two ARSs are in a cluster withARS302, the I silencer, no replication origin activity was detected regardless of yeast mating type, special growth conditions that induce the transcriptionally repressed CHA1 gene,trans-acting mutations that abrogate transcriptional silencing at HML (sir3, orc5), orcis-acting mutations that delete the E and I silencers containing ARS elements. These results suggest that, for theHML ARS cluster (ARS303, ARS320, and ARS302), inactivity of origins is independent of local transcriptional silencing, even though origins and silencers share keycis- and trans-acting components. Surprisingly, deletion of active replication origins located 25 kb (ORI305) and 59 kb (ORI306) away led to detection of replication origin function at theHML ARS cluster, as well as at ARS301, the E silencer. Thus, replication origin silencing at HML ARSs is mediated by active replication origins residing at long distances fromHML in the chromosome. The distal active origins are known to fire early in S phase, and we propose that their inactivation delays replication fork arrival at HML, providing additional time for HML ARSs to fire as origins.

scholarly journals Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

2012 ◽  
Vol 23 (1) ◽  
pp. 1-11 ◽  
Author(s):  
G. I. Dellino ◽  
D. Cittaro ◽  
R. Piccioni ◽  
L. Luzi ◽  
S. Banfi ◽  
...  
Keyword(s):  
Dna Replication ◽  
Replication Timing ◽  
Replication Origins ◽  
Human Dna ◽  
Genome Wide ◽  
Dna Replication Origins

scholarly journals New, easy, quick and efficient DNA replication timing analysis by high-throughput approaches

2019 ◽  
Author(s):  
Djihad Hadjadj ◽  
Thomas Denecker ◽  
Eva Guérin ◽  
Su-Jung Kim ◽  
Fabien Fauchereau ◽  
...  
Keyword(s):  
Dna Replication ◽  
Cell Fate ◽  
Web Application ◽  
Global Analysis ◽  
Timing Analysis ◽  
Replication Timing ◽  
Experimental Conditions ◽  
Spatio Temporal ◽  
Dna Replication Timing ◽  
Temporal Program

AbstractDNA replication must be faithful and follow a well-defined spatio-temporal program closely linked to transcriptional activity, epigenomic marks, intra-nuclear structures, mutation rate and cell fate determination. Among the readouts of the DNA replication spatio-temporal program, replication timing (RT) analyses require complex, precise and time-consuming experimental procedures, and the study of large-size computer files. We improved the RT protocol to speed it up and increase its quality and reproducibility. Also, we partly automated the RT protocol and developed a user-friendly software: the START-R suite (Simple Tool for the Analysis of the Replication Timing based on R). START-R suite is an open source web application using an R script and an HTML interface to analyze DNA replication timing in a given cell line with microarray or deep-sequencing results. This novel approach can be used by every biologist without requiring specific knowledge in bioinformatics. It also reduces the time required for generating and analyzing simultaneously data from several samples. START-R suite detects constant timing regions (CTR) but also, and this is a novelty, it identifies temporal transition regions (TTR) and detects significant differences between two experimental conditions. The informatic global analysis requires less than 10 minutes.

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