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SRX4044225: GSM3131791: Kieffer-Kwon-2017-HIC078; Mus musculus; Hi-C
4 ILLUMINA (Illumina HiSeq 2500) runs: 159.1M spots, 31.8G bases, 20.3Gb downloads

Submitted by: NCBI (GEO)
Study: Myc regulates chromatin decompaction and nuclear architecture during B cell activation
show Abstracthide Abstract
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
Sample: Kieffer-Kwon-2017-HIC078
SAMN09076479 • SRS3261663 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2500
Strategy: Hi-C
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads. standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, or HiSeq 2500 following the manufacturer's protocols
Experiment attributes:
GEO Accession: GSM3131791
Links:
Runs: 4 runs, 159.1M spots, 31.8G bases, 20.3Gb
Run# of Spots# of BasesSizePublished
SRR712311141,492,0788.3G5.3Gb2018-05-17
SRR712311239,282,5217.9G5Gb2018-05-17
SRR712311338,433,3477.7G4.9Gb2018-05-17
SRR712311439,852,0418G5.1Gb2018-05-17

ID:
5521321

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