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Series GSE228878 Query DataSets for GSE228878
Status Public on Jun 13, 2023
Title RIF1 regulates replication origin activity and early replication timing in B cells [Repli-Seq]
Organism Mus musculus
Experiment type Other
Summary The mammalian DNA replication timing (RT) program is crucial for the proper functioning and integrity of the genome. The best-known mechanism for controlling RT is the suppression of late origins of replication in heterochromatin by RIF1. Here, we report that in antigen-activated, hypermutating B lymphocytes, RIF1 binds predominantly to early-replicating active chromatin, regulates early origin firing and promotes early replication. However, RIF1 has a minor role in gene expression and genome organization in B cells. Furthermore, we find that RIF1 functions in a complementary and non-epistatic manner with minichromosome maintenance (MCM) proteins to establish early RT signatures genome-wide and, specifically, to ensure the early replication of highly transcribed genes. These findings reveal a new layer of regulation within the B cell RT program, driven by the coordinated activity of RIF1 and MCM proteins.
 
Overall design Repli-seq in LacZ and Mcm infected CH12 and Rif-/- CH12 cells cells
Web link https://www.biorxiv.org/content/10.1101/2023.03.31.535086v2.full
 
Contributor(s) Malzl D, Peycheva M, Rahjouei A, Gnan S, Klein KN, Nazarova M, Schoeberl UE, Gilbert DM, Buonomo SC, Di Virgilio M, Neumann T, Pavri R
Citation(s) 38081811
Submission date Apr 03, 2023
Last update date Dec 14, 2023
Contact name Tobias Neumann
Organization name IMP
Street address Campus-Vienna-Biocenter 1
City Vienna
ZIP/Postal code 1030
Country Austria
 
Platforms (1)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (36)
GSM7140992 CH12_Repliseq_Rif1KO_shLacZ_early_rep1
GSM7140993 CH12_Repliseq_Rif1KO_shLacZ_early_rep2
GSM7140994 CH12_Repliseq_Rif1KO_shLacZ_late_rep1
This SubSeries is part of SuperSeries:
GSE228880 RIF1 regulates early replication timing in murine B cells.
Relations
BioProject PRJNA951772

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE228878_CH12_Repliseq_Rif1KO_shLacZ_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_Rif1KO_shLacZ_RT_20kb_loess.bw 1.8 Mb (ftp)(http) BW
GSE228878_CH12_Repliseq_Rif1KO_shLacZ_RT_5kb_loess.bedGraph.gz 6.6 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_Rif1KO_shLacZ_RT_5kb_loess.bw 7.0 Mb (ftp)(http) BW
GSE228878_CH12_Repliseq_Rif1KO_shMcm6_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_Rif1KO_shMcm6_RT_20kb_loess.bw 1.9 Mb (ftp)(http) BW
GSE228878_CH12_Repliseq_Rif1KO_shMcm6_RT_5kb_loess.bedGraph.gz 6.7 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_Rif1KO_shMcm6_RT_5kb_loess.bw 7.1 Mb (ftp)(http) BW
GSE228878_CH12_Repliseq_shLacZ_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_shLacZ_RT_20kb_loess.bw 1.8 Mb (ftp)(http) BW
GSE228878_CH12_Repliseq_shLacZ_RT_5kb_loess.bedGraph.gz 6.6 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_shLacZ_RT_5kb_loess.bw 7.0 Mb (ftp)(http) BW
GSE228878_CH12_Repliseq_shLacZ_RT_domains.bed.gz 25.6 Kb (ftp)(http) BED
GSE228878_CH12_Repliseq_shMcm6_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_shMcm6_RT_20kb_loess.bw 1.8 Mb (ftp)(http) BW
GSE228878_CH12_Repliseq_shMcm6_RT_5kb_loess.bedGraph.gz 6.6 Mb (ftp)(http) BEDGRAPH
GSE228878_CH12_Repliseq_shMcm6_RT_5kb_loess.bw 7.0 Mb (ftp)(http) BW
GSE228878_MEF_Repliseq_WT_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_MEF_Repliseq_WT_RT_20kb_loess.bw 1.8 Mb (ftp)(http) BW
GSE228878_MEF_Repliseq_WT_RT_5kb_loess.bedGraph.gz 6.6 Mb (ftp)(http) BEDGRAPH
GSE228878_MEF_Repliseq_WT_RT_5kb_loess.bw 6.9 Mb (ftp)(http) BW
GSE228878_MEF_Repliseq_WT_RT_domains.bed.gz 21.3 Kb (ftp)(http) BED
GSE228878_priB_Repliseq_Rif1Het_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_priB_Repliseq_Rif1Het_RT_20kb_loess.bw 1.8 Mb (ftp)(http) BW
GSE228878_priB_Repliseq_Rif1Het_RT_5kb_loess.bedGraph.gz 6.6 Mb (ftp)(http) BEDGRAPH
GSE228878_priB_Repliseq_Rif1Het_RT_5kb_loess.bw 7.0 Mb (ftp)(http) BW
GSE228878_priB_Repliseq_Rif1KO_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_priB_Repliseq_Rif1KO_RT_20kb_loess.bw 1.8 Mb (ftp)(http) BW
GSE228878_priB_Repliseq_Rif1KO_RT_5kb_loess.bedGraph.gz 6.7 Mb (ftp)(http) BEDGRAPH
GSE228878_priB_Repliseq_Rif1KO_RT_5kb_loess.bw 7.0 Mb (ftp)(http) BW
GSE228878_priB_Repliseq_WT_RT_20kb_loess.bedGraph.gz 1.7 Mb (ftp)(http) BEDGRAPH
GSE228878_priB_Repliseq_WT_RT_20kb_loess.bw 1.8 Mb (ftp)(http) BW
GSE228878_priB_Repliseq_WT_RT_5kb_loess.bedGraph.gz 6.6 Mb (ftp)(http) BEDGRAPH
GSE228878_priB_Repliseq_WT_RT_5kb_loess.bw 7.0 Mb (ftp)(http) BW
GSE228878_priB_Repliseq_WT_RT_domains.bed.gz 26.0 Kb (ftp)(http) BED
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