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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 16, 2022 |
| Title |
Chromatin condensation is independent from nuclear condensation in late-stage terminal erythropoiesis revealed from the dynamic three-dimensional genomic organizations [Hi-C] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Mammalian terminal erythropoiesis involves chromatin and nuclear condensation followed by enucleation. Late-stage erythroblasts undergo caspase-mediated nuclear opening formation that is important for nuclear condensation through partial release of histones. It remains unknown whether nuclear opening and histone release influence the three-dimensional (3D) genomic organization during terminal erythropoiesis. Here, we compared the genome wide 3D organization, chromatin accessibility, and transcriptome of the cultured mouse erythroid progenitors with and without the blocking of nuclear opening during differentiation. We found that terminal differentiation from the basophilic to orthochromatic stages of erythroblasts involves compaction and establishment of long-range interactions of the heterochromatin regions, which is associated with globally increased accessibility and upregulation of erythroid-related genes. Surprisingly, blocking of nuclear opening did not have a significant impact on 3D genomic organization, chromatin accessibility, or transcriptome despite the inhibition of histone release and nuclear condensation. Inhibition of nuclear opening also significantly affected enucleation. We further demonstrated this through a caspase-3 and 7 double knockout mouse model, which showed significant defects in nuclear opening and condensation with a compromise of enucleation in fetal erythroid progenitors. However, loss of these effector caspases had minimal effects on the red cell indices and survival of the recipient animals in a fetal liver cell transplantation model. Overall, these results indicate that nuclear opening and histone release may not be necessary for chromatin condensation and global transcriptome but are critical for nuclear condensation and efficient enucleation. These data also underline the robustness of enucleation despite the dysplastic or less condensed nucleus.
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| Overall design |
RNA-Seq, ATAC-seq and genome-wide chromatin conformation capture (Hi-C) in mouse erythroblast precursors cells collected at time 0 and compared to cells treated with Z-VAD or DMSO at 24 h and collected at 30 h.
This submission contains Hi-C data.
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| Contributor(s) |
Bi H, Wang D, Wang J, Liu Y, Bao H, Han X, Yue F, Ji P |
| Citation(s) |
36465116 |
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| Submission date |
Sep 29, 2021 |
| Last update date |
Dec 17, 2022 |
| Contact name |
Feng Yue |
| E-mail(s) |
yue@northwestern.edu
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| Organization name |
Northwestern University Feinberg School of Medicine
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| Street address |
303 E. Superior Simpson Querrey
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| City |
CHICACO |
| State/province |
ILLINOIS |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA767263 |
| SRA |
SRP339264 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE184974_RAW.tar |
3.7 Gb |
(http)(custom) |
TAR (of COOL) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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