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Series GSE154051 Query DataSets for GSE154051
Status Public on Oct 10, 2020
Title Calcium Signaling Prompts NIPBL Recruitment at Active Enhancers and Promoters via Distinct Mechanisms to Reconstruct Genome Compartmentalization
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary During developmental progression the genomes of immune cells undergo large-scale changes in chromatin folding. However, insights into the signals and epigenetics that induce alterations in nuclear architecture remain rudimentary. Here, we found that calcium influx rapidly recruited the cohesin-loading factor NIPBL to thousands of binding sites to dictate widespread changes in compartment segregation. The induction of NIPBL-binding was coordinate with increased P300, BRG1 and RNA Polymerase II co-occupancy, via different kinetics at active enhancers and promoters. Through acute degradation system, we found that enhancers, rather than promoters, are dependent on BAF complexes to induce NIPBL recruitment. Finally, we found that calcium signaling acts universally to orchestrate rapid redistribution of NIPBL in both primary innate and adaptive immune cells. Collectively, these data reveal how calcium signaling regulates NIPBL occupancy to orchestrate nuclear architecture.
 
Overall design Performed in situ Hi-C, ChIP-Seq, GRO-Seq and ATAC-Seq to pinpoint the underlying molecular mechanisms by which calcium signaling modulates nuclear architecture.
 
Contributor(s) Zhu Y, Denholtz M, Lu H, Murre C
Citation(s) 33334824
Submission date Jul 08, 2020
Last update date Jan 09, 2021
Contact name Cornelis Murre
E-mail(s) cmurre@ucsd.edu
Phone 8585348796
Organization name UCSD
Department Molecular Biology
Lab Murre
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92039
Country USA
 
Platforms (4)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (165)
GSM4663201 HiC Neutrophils replicate 1 [re-analysis]
GSM4663202 HiC Progenitors replicate 1 [re-analysis]
GSM4663203 HiC Neutrophils replicate 2 [re-analysis]
Relations
BioProject PRJNA644932
SRA SRP270993

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
GSE154051_GSE93127_NeuUT_mapq1_allValidPairs.hic.bz2 1.7 Gb (ftp)(http) HIC
GSE154051_GSE93127_NeuUT_mapq1_hicpro2homer.25x50kb.PC1.bedGraph.bz2 1.1 Mb (ftp)(http) BEDGRAPH
GSE154051_GSE93127_NeuUT_mapq1_hicpro2homer.25x50kb.PC1.txt.bz2 1.3 Mb (ftp)(http) TXT
GSE154051_GSE93127_NeuUT_mapq1_negativeDomain.new.txt.bz2 25.5 Kb (ftp)(http) TXT
GSE154051_GSE93127_NeuUT_mapq1_positiveDomain.new.txt.bz2 23.6 Kb (ftp)(http) TXT
GSE154051_GSE93127_Pro_mapq1_allValidPairs.hic.bz2 1.2 Gb (ftp)(http) HIC
GSE154051_GSE93127_Pro_mapq1_hicpro2homer.25x50kb.PC1.bedGraph.bz2 1.1 Mb (ftp)(http) BEDGRAPH
GSE154051_GSE93127_Pro_mapq1_hicpro2homer.25x50kb.PC1.txt.bz2 1.3 Mb (ftp)(http) TXT
GSE154051_RAW.tar 24.8 Gb (http)(custom) TAR (of BEDGRAPH, BW, HIC, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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