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SRX10008819: GSM5060465: CX-5461 ES; Mus musculus; Hi-C
1 ILLUMINA (Illumina HiSeq 2500) run: 410.6M spots, 123.2G bases, 40.1Gb downloads

Submitted by: NCBI (GEO)
Study: rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [Hi-C]
show Abstracthide Abstract
Nucleolus is the organelle for ribosome biogenesis and sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive two-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the liquid-liquid phase separation (LLPS) mediated by rRNA and nucleolar proteins maintains the formation of peri-nucleolar heterochromatin (PNH). When mES cells undergo rRNA biogenesis defect, the normal LLPS of nucleolus is disrupted, causing deconjugation of NCL/TRIM28 complex on PNH and changes of epigenetic state and 3D structure of PNH, which leads to Dux, a conserved multicopy retrogene defining the cleavage-specific transcriptional program in placental mammals, to be released from the PNH region, activation of 2C-like program and transition of mES cells to 2C-like cells. Embryos with rRNA biogenesis defect are incompatible to develop from 2-cell (2C) to blastocyte (BC) and appear to skew from the blastocyst to earlier cleavage embryo signatures. Our results highlight that nucleolar LLPS-mediated 3D chromatin structure reshaping of PNH compartment regulates the fate transition of mES cells to 2C-like cells. Our findings for the first time elucidate the novel roles of rRNA biogenesis in regulating the 2C-like and ES state homeostasis in cultured cells and suggest that rRNA biogenesis is a new molecular switch from nucleolus-unmatured 2C stage to nucleolus-matured BC stage during murine pre-implantation embryo development. Overall design: Examination of the difference of chromatin high-order structure in control ES cells and CX-5461 treated ES cells.
Sample: CX-5461 ES
SAMN17764768 • SRS8177790 • All experiments • All runs
Organism: Mus musculus
Instrument: Illumina HiSeq 2500
Strategy: Hi-C
Selection: other
Layout: PAIRED
Construction protocol: 10^6 cells were cross-linked for 10 min with 1% final concentration fresh formaldehyde and quenched by 0.2M glycine for 5 min. The cross-linked cells were subsequently lysed in lysis buffer. Extracted nuclei were re-suspended with 150 μl 0.1% SDS and incubated at 65°C for 10 min, then SDS were quenched by 120 μl water and 30 μl 10% Triton X-100, and incubated at 37 °C for 15 min. Purified DNA was sheared to a length of ~400 bp. Point ligation junctions were pulled down by Dynabeads MyOne Streptavidin C1(Thermofisher) according to manufacturers` instructions. The Hi-C library for Illumina sequencing was prepared by NEBNext Ultra II DNA library Prep Kit for Illumina (NEB) according to manufacturers` instructions. The final library was sequenced on the Illumina HiSeq X Ten platform (San Diego, CA, United States) with 150PEmode. Two replicates were generated for one group material.
Experiment attributes:
GEO Accession: GSM5060465
Runs: 1 run, 410.6M spots, 123.2G bases, 40.1Gb
Run# of Spots# of BasesSizePublished


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