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Series GSE145873 Query DataSets for GSE145873
Status Public on Jun 02, 2020
Title Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III [Hi-C]
Organism Mus musculus
Experiment type Other
Summary Genome binding/occupancy profiling by high throughput sequencing | Expression profiling by high throughput sequencing | Other
We analyzed Hi-C, HiChIP, Ocean-C, RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to provide the most comprehensive evidence to date to demonstrate that transcription plays a marginal role in organizing the 3D genome in mammalian cells: 1) degraded Pol I, Pol II and Pol III proteins in mESCs, and showed their loss results in little or no changes of global 3D chromatin structures for the first time; 2) selected RNA polymerases high abundance binding sites-associated interactions and found they still persist after the degradation; 3) generated higher resolution chromatin interaction maps and revealed that transcription inhibition mildly alters small loop domains; 4) identified Pol II bound but CTCF and Cohesin unbound loops and disclosed that they are largely resistant to transcription inhibition
Interestingly, we found that Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting RNA polymerases are capable of affecting the 3D genome indirectly. So, the direct and indirect effects of transcription inhibition explain the previous confusing effects on the 3D genome. We conclude that Pol I, Pol II, and Pol III loss only mildly alter chromatin interactions in mammalian cells, suggesting the 3D chromatin structures are preestablished and relatively stable.
 
Overall design We have finished the Hi-C, HiChIP, Ocean-C, RNA-seq, ATAC-seq, ChIP-seq and 4C-seq to investigate the roles of Pol I, Pol II and Pol III in 3D genome organization and transcription. The V6.5 mouse ES (mES) cell line was used to perform all the high-throughput analysis. Degron mES cells were treated with 1 μg/ml Doxycycline for different hours refer to individual Series.
 
Contributor(s) Jiang Y, Huang J, Lun K, Li B
Citation(s) 32616013
BioProject PRJNA607400
Submission date Feb 25, 2020
Last update date Jul 13, 2020
Contact name Xiong Ji
E-mail(s) xiongji@pku.edu.cn
Organization name Peking University
Department School of Life Sciences
Lab Jilab
Street address Haidian District, Beijing Summer Palace Road No. 5
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (22)
GSM4338289 Untreated_Pol1_Hi-C_rep1
GSM4338290 Untreated_Pol1_Hi-C_rep2
GSM4338291 IAA_24h_Pol1_Hi-C_rep1
This SubSeries is part of SuperSeries:
GSE145874 Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III
Relations
SRA SRP250063

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
GSE145873_Pol1_IAA_24h_downsampled_75mi_allValidPairs.hic 273.4 Mb (ftp)(http) HIC
GSE145873_Pol1_untreated_downsampled_75mi_allValidPairs.hic 263.2 Mb (ftp)(http) HIC
GSE145873_Pol2_IAA_1h_downsampled_55mi_allValidPairs_2nd.hic 689.0 Mb (ftp)(http) HIC
GSE145873_Pol2_IAA_6h_Mitotic_downsampled_75mi_allValidPairs.hic 291.0 Mb (ftp)(http) HIC
GSE145873_Pol2_IAA_6h_downsampled_55mi_allValidPairs_2nd.hic 731.5 Mb (ftp)(http) HIC
GSE145873_Pol2_IAA_6h_downsampled_75mi_allValidPairs.hic 291.6 Mb (ftp)(http) HIC
GSE145873_Pol2_untreated_Mitotic_downsampled_75mi_allValidPairs.hic 278.9 Mb (ftp)(http) HIC
GSE145873_Pol2_untreated_downsampled_55mi_allValidPairs_2nd.hic 691.4 Mb (ftp)(http) HIC
GSE145873_Pol2_untreated_downsampled_75mi_allValidPairs.hic 284.0 Mb (ftp)(http) HIC
GSE145873_Pol3_IAA_24h_downsampled_75mi_allValidPairs.hic 262.9 Mb (ftp)(http) HIC
GSE145873_Pol3_untreated_downsampled_75mi_allValidPairs.hic 257.2 Mb (ftp)(http) HIC
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Raw data are available in SRA
Processed data are available on Series record

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