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Items: 16

1.

Rapid high-resolution measurement of DNA replication timing by droplet digital PCR

(Submitter supplied) Time of DNA replication is inversely proportional to the relative DNA copy number. Sort-seq is a technique that uses deep short read sequencing to determine relative copy number across genome from sorted S phase cells. We have applied sort-seq to HeLa cells and report their relative copy number profile. The high (close to 2) value means the region replicates early in S phase; the low (close to 1) value means the region is replicated late in S phase.
Organism:
Homo sapiens
Type:
Other
Platform:
GPL18573
2 Samples
Download data: BED
2.

Deep functional analysis of synII, a 770 kb synthetic yeast chromosome

(Submitter supplied) Herein we report the successful design, construction and characterization of a 770 kb synthetic yeast chromosome II (synII). Our study incorporates characterization at multiple levels, including phenomics, transcriptomics, proteomics, chromosome segregation and replication analysis to provide the most thorough and comprehensive analysis of a synthetic chromosome. Our “Trans-Omics” analyses reveal a modest but potentially significant pervasive up-regulation of translational machinery observed in synII is mainly caused by the deletion of 13 tRNAs. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
2 Samples
Download data: FA, WIG
3.

Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii by homologous recombination

(Submitter supplied) Eukaryotic genomes typically consist of multiple (linear) chromosomes that are replicated from multiple origins. Several hypothetical scenarios have been proposed to account for the evolution of multi-origin/multi-chromosome genomes, which are encountered in modern eukaryotes and archaea. Here we report an example of the generation of a new chromosome in the halophilic archaeon Haloferax volcanii through one of these scenarios: acquisition of new replication origins and splitting of an ancestral chromosome into two replication-competent chromosomes. more...
Organism:
Haloferax volcanii
Type:
Other
Platform:
GPL23691
4 Samples
Download data: BED
4.

Rif1 acts through Protein Phosphatase 1 and independent of replication timing to suppresses telomere extension in budding yeast

(Submitter supplied) The Rif1 protein negatively regulates telomeric TG repeat length in the budding yeast S. cerevisiae, but how it prevents telomere over-extension is unknown. Rif1 was recently shown to control DNA replication by acting as a Protein Phosphatase 1 (PP1)-targeting subunit. Therefore we investigated whether Rif1 controls telomere length by targeting PP1 activity. We find that a Rif1 mutant that cannot interact with PP1 causes a long-telomere phenotype, similar to that of rif1∆ cells. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL19756
6 Samples
Download data: WIG
5.

Regulation of DNA replication time is crucial for appropriate gene expression

(Submitter supplied) Eukaryotic genomes are replicated in a reproducible temporal order, however, the physiological significance is poorly understood. We compared replication dynamics in divergent yeast species and identified genomic features with conserved replication times. Histone genes were amongst the earliest replicating loci in all species. We delayed the replication of HTA1-HTB1 and discovered that this halved the histone gene expression. more...
Organism:
Saccharomyces cerevisiae; Naumovozyma castellii; Kluyveromyces lactis; Zygosaccharomyces rouxii; [Candida] glabrata; Lachancea kluyveri; Tetrapisispora blattae
Type:
Other
7 related Platforms
14 Samples
Download data: FASTA, WIG
6.

A global profile of replication polymerase usage

(Submitter supplied) We have established a novel sequencing approach to characterise usage of replicative DNA polymerases in S. pombe. This approach allows us to determine the roles of DNA polymerase delta and epsilon in lagging strand and leading strand DNA synthesis, respectively in genome-wide scale. Utilising the dataset of usage of these polymerases, we also successfully identified DNA replication initiation sites at high resolution. more...
Organism:
Schizosaccharomyces pombe
Type:
Other
Platform:
GPL13988
11 Samples
Download data: BEDGRAPH, WIG
7.

High-resolution genome replication profiles, modeling and single-cell imaging define the stochastic nature of replication initiation and termination

(Submitter supplied) Eukaryotic genome replication is stochastic with each cell using a different cohort of replication origins. Interpreting high-resolution genome replication profiles with a mathematical model allowed us to quantify the stochastic nature of genome replication. This approach included estimation of the activity of every replication origin and the genome-wide location of replication termination events. Single-cell measurements verified the inferred values for stochastic origin replication time. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL16234
16 Samples
Download data: WIG
8.

Accelerated growth in the absence of DNA replication origins

(Submitter supplied) DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery. Origins differ in number and structure across the three domains of life1 and their properties determine the dynamics of chromosome replication. Bacteria and some archaea replicate from single origins, whilst most archaea and all eukaryotes replicate using multiple origins. more...
Organism:
Haloferax volcanii
Type:
Other
Platform:
GPL16229
14 Samples
Download data: WIG
9.

High throughput sequencing enables detailed analysis of S. cerevisiae DNA replication

(Submitter supplied) We have used three complementary deep sequencing approaches to characterise the temporal order of genome replication in S. cerevisiae. Each approach measures the increase in DNA copy number as a genomic region is replicated (in a large population of cells). We find that the use of deep sequencing provided high spatial resolution. For maximum temporal resolution we have measured replication dynamics at multiple time points during a synchronous S phase. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platforms:
GPL16234 GPL13821
14 Samples
Download data: WIG
10.

Genome-wide EMSA (gEMSA) of ORC and yeast genomic DNA

(Submitter supplied) Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal DNA, triggering a series of molecular events that culminate in the initiation of DNA replication (a.k.a. origin firing) during S-phase. Each chromosome requires multiple origins for its duplication, and each origin fires at a characteristic time during S-phase, creating a cell-type specific genome replication pattern with relevance to differentiation, genome stability and evolution. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL9529
3 Samples
Download data: PAIR
Series
Accession:
GSE48440
ID:
200048440
11.

Avoiding chromosome pathology when replication forks collide

(Submitter supplied) Chromosome duplication normally initiates via the assembly of replication fork complexes at defined origins. DNA synthesis by any one fork is thought to cease when it meets another travelling in the opposite direction, at which stage the replication machinery may simply dissociate before the nascent strands are finally ligated. But what actually happens is not clear. Here we present evidence consistent with the idea that every fork collision has the potential to trigger re-replication of the already replicated DNA, thus posing a threat to genomic integrity. more...
Organism:
Escherichia coli
Type:
Other
Platform:
GPL16232
33 Samples
Download data: TXT, WIG
12.

High throughput sequencing enables detailed analysis of S. cerevisiae DNA replication

(Submitter supplied) For rapid characterisation of replication dynamics in wild-type cells from an unperturbed cell cycle we have obtained replicating (S phase) and non-replicating (G2 phase) cells by fluorescence activated cell sorting (FACS) and subjected the DNA to copy number analysis.
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL16234
4 Samples
Download data: WIG
13.

Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment

(Submitter supplied) Centromeres play several important roles in ensuring proper chromosome segregation. Not only do they promote kinetochore assembly for microtubule attachment, but they also support robust sister chromatid cohesion at pericentromeres and facilitate replication of centromeric DNA early in S phase. However, it is still elusive how centromeres orchestrate all these functions at the same site. Here we show that the budding yeast Dbf4-dependent kinase (DDK) accumulates at kinetochores in telophase, facilitated by the Ctf19 kinetochore complex. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL16234
8 Samples
Download data: WIG
14.

Conservation of replication timing reveals global and local regulation of replication origin activity.

(Submitter supplied) DNA replication initiates from defined locations called replication origins; some origins are highly active whereas others are dormant and rarely used. Origins also differ in their activation time resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. more...
Organism:
Saccharomyces cerevisiae; Saccharomyces paradoxus; Saccharomyces bayanus x Saccharomyces cerevisiae; Saccharomyces bayanus; Saccharomyces arboricola
Type:
Genome variation profiling by high throughput sequencing
5 related Platforms
10 Samples
Download data: FA, TXT, WIG
Series
Accession:
GSE36045
ID:
200036045
15.

Small RNA sequences from Schizosaccharomyces japonicus

(Submitter supplied) Small interfering RNAs (siRNAs) are known to be involved in both transposon silencing and centromere function, leading us to investigate the interplay between these two roles in the Schizosaccharomyces lineage. In S. pombe, the centromeric repeats produce dicer-dependent siRNAs that are required for maintenance of centromeric structure, function and transcriptional silencing via Argonaute-dependent heterochromatin formation13. more...
Organism:
Schizosaccharomyces japonicus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13256
2 Samples
Download data: BED, FA
Series
Accession:
GSE27837
ID:
200027837
16.

The Origin Recognition Complex interacts with a subset of metabolic genes tightly linked to origins of replication.

(Submitter supplied) The origin recognition complex (ORC) marks chromosomal sites as replication origins and is essential for replication initiation. In yeast, ORC also binds to DNA elements called silencers, where its primary function is to recruit silent information regulator (SIR) proteins to establish transcriptional silencing. Indeed, silencers function poorly as chromosomal origins. Several genetic, molecular, and biochemical studies of HMR-E have led to a model proposing that when ORC becomes limiting in the cell, such as in the orc2-1 mutant, only sites that bind ORC tightly, such as HMR-E, remain fully occupied by ORC, while lower affinity sites, including most origins, lose ORC occupancy. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by genome tiling array
Platform:
GPL9529
2 Samples
Download data: TXT
Series
Accession:
GSE18895
ID:
200018895
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