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Series GSE82144 Query DataSets for GSE82144
Status Public on Aug 10, 2017
Title Myc regulates chromatin decompaction and nuclear architecture during B cell activation
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Expression profiling by high throughput sequencing
Summary 50 years ago, Vincent Allfrey and colleagues discovered that lymphocyte activation triggers massive acetylation of chromatin. However, the molecular mechanisms driving epigeneticaccessibility are still unknown. We here show that stimulated lymphocytes decondense chromatin by three differentially regulated steps. First, chromatin is repositioned away from the nuclear periphery in response to global acetylation. Second, histone nanodomainclusters decompact into mononucleosome fibers through a mechanism that requires Mycand continual energy input. Single-molecule imaging shows that this step lowers transcription factor residence time and non-specific collisions during sampling for DNA targets. Third, chromatin interactions shift from long range to predominantly short range, and CTCF-mediated loops and contact domains double in numbers. This architectural change facilitates cognate promoter-enhancer contacts and also requires Myc and continual ATPproduction. Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells.
 
Overall design Chip-Seq of 36 histone modifications, Gro-Seq, Mnase-Seq, ATAC-seq and Hi-C from mouse resting, activated B cells and various conditions on B cells
 
Contributor(s) Kieffer-Kwon K, Nimura K, Rao S, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang S, Ricci M, Baranello L, Zheng Y, Ardori F, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, Johnson S, Dubois W, Cosma M, Batchelor E, Levens D, Phair R, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Lieberman-Aiden E, Casellas R
Citation(s) 29706548, 29555645
Submission date Jun 01, 2016
Last update date Sep 29, 2019
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab Casellas lab
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (258)
GSM2184221 aB3h_wt_H3K27Ac
GSM2184222 aB48h_wt_H3K27Ac
GSM2184223 aB_wt_H3K27Ac
Relations
BioProject PRJNA324130
SRA SRP075985

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
GSE82144_Kieffer-Kwon-2017-activated_B_cells_24_hours_MYC_KO.hic 20.1 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-activated_B_cells_24_hours_MYC_KO_30.hic 18.7 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-activated_B_cells_24_hours_oligomycin.hic 20.7 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-activated_B_cells_24_hours_oligomycin_30.hic 19.2 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT.hic 15.6 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30.hic 14.3 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-mES_WT.hic 9.1 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-mES_WT_30.hic 8.3 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-resting_B_cells_TSA.hic 13.3 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-resting_B_cells_TSA_30.hic 12.5 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-resting_B_cells_WT.hic 21.8 Gb (ftp)(http) HIC
GSE82144_Kieffer-Kwon-2017-resting_B_cells_WT_30.hic 20.2 Gb (ftp)(http) HIC
GSE82144_RAW.tar 451.2 Gb (http)(custom) TAR (of BW, HIC)
GSE82144_Series-level_HIC_readme.txt 1.9 Kb (ftp)(http) TXT
GSE82144_aB_loops.txt.gz 272.1 Kb (ftp)(http) TXT
GSE82144_aB_wt_ATAC.bw 395.3 Mb (ftp)(http) BW
GSE82144_aBminusrB.bw 8.4 Gb (ftp)(http) BW
GSE82144_rB_loops.txt.gz 112.3 Kb (ftp)(http) TXT
GSE82144_rB_wt_ATAC.bw 428.9 Mb (ftp)(http) BW
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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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