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| 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
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| 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.
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| 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
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| 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 |
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| Submission date |
Jun 01, 2016 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Seolkyoung Jung |
| Organization name |
NIH
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| Department |
NIAMS
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| Lab |
biodata mining and discovery section
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| Street address |
10 Center Dr
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| City |
bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (3) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21273 |
HiSeq X Ten (Mus musculus) |
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| Samples (258)
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| Relations |
| BioProject |
PRJNA324130 |
| SRA |
SRP075985 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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