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RNA polymerase I transcription is essential for establishing the chromatin architecture in mouse but not in human embryos [RNA-seq]

GSE236152 Mus musculus Expression profiling by high throughput sequencing 8 samples Submitted 2025/04/11 Platform GPL17021
Summary
The distinctions in 3D genome between humans and mice, as well as the mechanisms underlying de novo organization, remain unexplored. Our study revealed an extensive reorganization of the 3D genome from human oogenesis to early embryogenesis, displaying significant differences to the mouse, notably dramatically attenuated TADs at GV stage in human. The 3D genome reconstruction timing also differs between species, which it initiates at the 4-cell stage in human, while in mouse, it commences at the 2-cell stage in mouse. We discovered that RNA polymerase I (Pol I) is crucial for establishing the chromatin structures during mouse embryogenesis, but not in human embryos. Intriguingly, the absence of Pol I transcription weakens TAD structure in mouse female germline stem cells, whereas it fortifies it in human counterparts. Our findings provide valuable insights into chromatin organization during germ cell and embryonic development and have implications for fertility preservation and birth defect prevention.
Published in
RNA polymerase I is essential for driving the formation of 3D genome in early embryonic development in mouse, but not in human
Hou C, Tian GG, Hu S et al. · Genome medicine 2025 · PMID 40390095 · doi:10.1186/s13073-025-01476-y
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Direct links to NCBI, no account and no request form: the whole study as GSE236152_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 8 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA989143 and SRA study SRP446567. Searching any of these in the dataset finder brings you back here.

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