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| Status |
Public on Jul 08, 2022 |
| Title |
Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [ChIP-seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Hmga2 KO pluripotent stem cells fail to develop into epiblast-like stem cells (EpiLCs). By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in stabilized epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. As nuclear lamina is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of HiC data in wt and Hmga2 KO cells allowed us to observe that inter-TAD interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina.
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| Overall design |
Genome binding/occupancy profiling of Hmga2 in EpiLCs by high throughput sequencing.
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| Contributor(s) |
Parisi S, Zoppoli P |
| Citation(s) |
35918713 |
| Submission date |
Apr 12, 2022 |
| Last update date |
Oct 07, 2022 |
| Contact name |
Pietro Zoppoli |
| Organization name |
Università degli Studi di Napoli Federico II
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| Department |
DMMBM
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| Lab |
NGS facility
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| Street address |
via S.Pansini,5
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| City |
Napoli |
| State/province |
Napoli |
| ZIP/Postal code |
80131 |
| Country |
Italy |
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| Platforms (1) |
| GPL16173 |
Illumina HiScanSQ (Mus musculus) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE200673 |
Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment |
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| Relations |
| BioProject |
PRJNA825829 |
