Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide distribution of histones modifications in mouse ESC Rif1+/+ and Rif1-/-

ABSTRACT: Analyzed histones modifications: H3K9 H3K4 H3K27 H4K20

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Rossana Foti

PROVIDER: E-MTAB-3743 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.

Foti Rossana R Gnan Stefano S Cornacchia Daniela D Dileep Vishnu V Bulut-Karslioglu Aydan A Diehl Sarah S Buness Andreas A Klein Felix A FA Huber Wolfgang W Johnstone Ewan E Loos Remco R Bertone Paul P Gilbert David M DM Manke Thomas T Jenuwein Thomas T Buonomo Sara C B SC

Molecular cell 20151224 2

DNA replication is temporally and spatially organized in all eukaryotes, yet the molecular control and biological function of the replication-timing program are unclear. Rif1 is required for normal genome-wide regulation of replication timing, but its molecular function is poorly understood. Here we show that in mouse embryonic stem cells, Rif1 coats late-replicating domains and, with Lamin B1, identifies most of the late-replicating genome. Rif1 is an essential determinant of replication timing ...[more]

PMID: 26725008

Similar Datasets

Genome-wide occupancy of Rif1FH in mouse ESC

Project description:Mammalian Rif1 defines the architecture of replication-timing domains interactions through the three-dimensional organization of the nuclear volume. Deletion of RIf1 in mammalian cells causes an initial alteration of three-dimensional chromatin organization which impacts first on replication timing and genome stability, but has long-term indirect repercussions also on gene expression.

2015-12-24 | E-MTAB-3502 | biostudies-arrayexpress

Replication timing profiles of Rif1 inducible knock-out embryonic stem cells

2015-12-24 | E-MTAB-3506 | biostudies-arrayexpress

Rif1 regulates the replication timing domains on the human genome

Project description:DNA replication is spatially and temporally regulated during S-phase. DNA replication timing is established in early G1-phase at a point referred to as TDP (timing decision point). We show that Rif1 (Rap1-interacting-factor1), originally identified as a telomere binding factor in yeast, is a critical determinant of the replication timing program in human cells. Depletion of Rif1 results in specific loss of mid-S replication foci profiles, stimulation of initiation events in early S-phase and changes in long-range replication timing domain structures. Overall replication timing is shifted toward mid-S in both directions, suggesting that replication timing regulation is abrogated in the absence of Rif1. Rif1 tightly binds to nuclear insoluble structures at late-M to early-G1 and regulates the chromatin-loop sizes. Furthermore, Rif1 colocalizes specifically with the mid-S replication foci. Thus, Rif1 establishes the mid-S replication domains that are restrained from being activated at early S-phase. Our results indicate that Rif1 plays crucial roles in determining the replication timing domain structures through regulating higher-order chromatin architecture. HeLa cells (ATCC), with a total of 4 individual replicates

2012-05-14 | E-GEOD-37971 | biostudies-arrayexpress

The role of Rif1 in ES cells

Project description:Purpose:The goals of this study are to understand the mechanisms underlying reduced self-renewal and loss of pluripotency by depletion of Rif1. Methods: We performed global gene expression analysis of Rif1 knockdown ES cell lines using Affymetrix 430 2.0 arrays, compared to shRNA controls. J1 ES cells were transfected with Control shRNA and Rif1 shRNA using lipofectamine 2000. Forty-eight hours after transfection, cells were collected for global gene expression analysis using Affymetrix mouse genome 430 2.0 array. Stable F1 Rif1 knockdown ES cells at passage 16 were used for long-term gene expression chip microarray using Affymetrix mouse genome 430 2.0 array.

2014-02-19 | E-GEOD-55129 | biostudies-arrayexpress

Mass spectrometry analysis of the impact of replication stress upon phosphorylation and protein interaction of human RIF1 protein

Project description:Wild-type or S2265A version of GFP-RIF1 protein (isoform 1) was over-expressed in Flp-In-T-REx cells (Watts et al. 2020. eLife 9:e58020) and immunopurified using GFP-Trap magnetic agarose beads. Proteins were subjected to on-beads trypsin digestion and resulting peptides were analysed by mass spectrometry for protein identification/quantification and identification of phosphorylated residues. Raw MS file names and descriptions: IP_RIF1_A.raw = GFP-RIF1-L immunoprecipitated from cells without aphidicolin treatment. IP_RIF1_B.raw = GFP-RIF1-L immunoprecipitated from cells treated with 1 µM aphidicolin for 24 hr before harvesting. IP_RIF1_C.raw = GFP-RIF1-L (S2265A) immunoprecipitated from cells treated with 1 µM aphidicolin for 24 hr before harvesting.

2022-04-14 | PXD032015 | Pride

Chromosome conformation capture in Rif1 null pMEFs

Project description:Mammalian Rif1 defines the architecture of replication-timing domains interactions through the three-dimensional organization of the nuclear volume.

2015-12-24 | E-MTAB-3505 | biostudies-arrayexpress

Chromosome conformation capture in mouse embryonic Rif1 null stem cells

2015-12-24 | E-MTAB-3500 | biostudies-arrayexpress

ASF1 acts with RIF1 to promote DNA end-joining in BRCA1 deficient cells

Project description:RIF1 acts downstream of 53BP1 to coordinate DNA double strand break repair pathway choice between non-homologous end joining (NHEJ) and homologous recombination (HR). Here we identified ASF1 as an endogenous RIF1-associated protein. We showed that ASF1 forms complex with RIF1 and regulates RIF1-dependent functions in DNA damage response.

2022-06-09 | PXD027727 | Pride

Gene expression profiles of Rif1 inducible knock-out embryonic stem cells

2015-12-24 | E-MTAB-3503 | biostudies-arrayexpress

ChIP-seq analysis of RNA polymerase II occupancy in wt, wee1-50 and cdc25-22 fission yeast cells

Project description:This experiment aimed at understanding the correlation between RNA polymerase II occupancy and cell size. For this, we used three strains of increasing average size (wee1-50 < wt < cdc25-22) and performed ChIP-seq experiments using anti-CTD antibodies.

2020-01-01 | E-MTAB-8522 | biostudies-arrayexpress

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