Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of DNA replication time is crucial for appropriate gene expression

ABSTRACT: 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. Finally, we show that histone and cell cycle genes in general are exempt from dosage compensation mechanisms. Thus we have uncovered one of the first physiological requirements for regulated replication time and demonstrate a direct link between replication time and gene expression.

ORGANISM(S): Nakaseomyces glabratus Naumovozyma castellii Lachancea kluyveri Saccharomyces cerevisiae Henningerozyma blattae Zygosaccharomyces rouxii Kluyveromyces lactis

PROVIDER: GSE89337 | GEO | 2017/06/28

SECONDARY ACCESSION(S): PRJNA351839

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Project description: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. paradoxus, S. arboricolus and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae / S. bayanus hybrid strain and find that there are both local and global regulators of origin function. Measurement of genome replication time from 4 budding yeast species (Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus) and a hybrid (between Saccharomyces cerevisiae and S. bayanus). For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase) The reference genome sequences for each yeast species are available as Series supplementary file [sac*.fa]

2012-06-19 | E-GEOD-36045 | biostudies-arrayexpress

Regulation of DNA replication time is crucial for appropriate gene expression

Project description:Regulation of DNA replication time is crucial for appropriate gene expression

| PRJNA351839 | ENA

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

Project description: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. To pinpoint replication origins we have synchronously released a checkpoint mutant (rad53-delta) into S phase under conditions of depleted dNTPs (200 mM hydroxyurea; HU) and measured the increase in DNA copy number after 60 minutes. Finally 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. We have compared and contrasted these approaches and developed the tools required for interpreting the deep sequencing data. Measurement of genome replication time for various S. cerevisiae strains. For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase).

2013-10-02 | E-GEOD-48212 | biostudies-arrayexpress

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

2013-10-02 | GSE48212 | GEO

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

2012-06-19 | GSE36045 | GEO

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

Project description: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. Measurement of genome replication time for various S. cerevisiae strains. For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase).

2013-06-20 | E-GEOD-42243 | biostudies-arrayexpress

Replication origin mapping in nda3-km311 and nda3-km311 rad3∆ in S. pombe

Project description:Identification of sites of replication initiation by copy number analysis, replicated DNA (time 80) vs unreplicated DNA (time 0).

2018-05-31 | GSE98445 | GEO

RNA sequencing discerns sub-populations of pancreatic β-cells and dynamics of gene expression in partial pancreatectomy model

Project description:We employed single-cell RNA sequencing of islets in young mice subjected to partial pancreatectomy (PPTx). Four clusters of pancreatic beta cells including a subpopulation of replicating beta cells. Pseudo-time course analysis clarified the gradual changes in gene expression from non-replicating beta cells to replicating ones. Upstream analysis visualized the transcriptional networks associated with beta cell replication by PPTx.

2020-11-04 | GSE152731 | GEO

Single-cell Transcriptome Analysis Dissects the Replicating Process of Pancreatic Beta Cells in Partial Pancreatectomy Model.

2020-11-04 | GSE152730 | GEO

Yeast replication in the presence of MMS: WT and isw2 nhp10 strains

Project description:The eukaryotic DNA replication machinery must traverse every nucleosome present in the eukaryotic genome during S phase. Since nucleosomes are generally inhibitory to DNA-dependent processes, it is thought that chromatin structure must undergo extensive reorganization to facilitate DNA synthesis. However, the identity of chromatin-remodeling factors involved in replication and how they affect DNA synthesis is largely unknown. Here we show that two ATP-dependent chromatin-remodeling complexes in Saccharomyces cerevisiae, Isw2 and Ino80, function in parallel to promote DNA replication, especially during periods of replication stress. The rate of replication-fork progression is slowed when both chromatin-remodeling pathways are compromised. Both Isw2 and Ino80 complexes are recruited to actively replicating chromatin suggesting that these chromatin-remodeling complexes act directly to promote replication-fork progression. These findings support an important role for ATP-dependent chromatin-remodeling complexes in promoting DNA replication, and define specific stages of replication that require remodeling activity for normal function. A critical part of this study was the use of microarrays to measure DNA replication progression throughout the genome during MMS treatment. These samples are from experiments where we competed newly replicated DNA against unreplicated DNA on the same microarrays. Keywords: Time course

2007-11-30 | GSE9122 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data