Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide occupancy of Rif1FH in mouse ESC

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Rossana Foti

PROVIDER: E-MTAB-3502 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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-3506 | biostudies-arrayexpress

Chromosome conformation capture in mouse embryonic Rif1 null stem cells

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

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

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

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

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

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

Project description:Analyzed histones modifications: H3K9 H3K4 H3K27 H4K20

2015-12-24 | E-MTAB-3743 | biostudies-arrayexpress

Gene expression profiles of Rif1 conditional knock-out large T immortalized mouse embryonic fibroblast

2015-12-24 | E-MTAB-3501 | biostudies-arrayexpress

Nuclear organization and replication timing are coupled through RIF1-PP1 interaction

Project description:Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing program and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. RIF1’s role in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing program and nuclear architecture.

2021-03-09 | GSE148244 | GEO

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

Taz1-Shelterin promotes facultative heterochromatin assembly at chromosome-internal sites containing late replication origins [Taz1]

Project description:Occupancy profiling of Shelterin components in fission yeast. Facultative heterochromatin regulates gene expression, but its assembly is poorly understood. Previously, we identified facultative heterochromatin islands in the fission yeast genome and found that RNA elimination machinery promotes island assembly at meiotic genes. Here, we report that Taz1, a component of the telomere protection complex Shelterin, is required to assemble heterochromatin islands at regions corresponding to late replication origins that are sites of double-strand break formation during meiosis. The loss of Taz1 and other Shelterin subunits, including Ccq1 that interacts with Clr4/Suv39h, abolishes heterochromatin at late origins and causes defective silencing of associated genes. Moreover, the late origin regulator Rif1 affects heterochromatin at Taz1-dependent islands and subtelomeric regions. We uncover a connection between heterochromatin and replication control, and show that heterochromatin factors affect timing of replication. These analyses implicate Shelterin in facultative heterochromatin assembly at late origins, which has important implications for the maintenance of genome stability and gene regulation. Whole cell extract DNA and DNA recovered from Taz1 or Rif1-immunoprecipitated chromatin of fission yeast were random-prime PCR amplified and labeled with Cy3 (whole cell extract DNA) or with Cy5 (IP DNA) and analyzed using custom 60mer Agilent array that tiles Schizosaccharomyces pombe genome in 300bp intervals alternately on both strands.

2016-06-09 | E-GEOD-78822 | 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