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| Status |
Public on Mar 28, 2024 |
| Title |
The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain’s imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse embryonic stem cells (mESCs) that carry an ectopic poly(A) signal, reducing RNA levels along the polycistron, and generated Rian-/- mESCs as well. Upon ESC differentiation, we found that Meg3 lncRNA (but not Rian) is required for Dlk1 repression on the maternal chromosome. Biallelic Meg3 expression acquired through CRISPR-mediated demethylation of the paternal Meg3 promoter led to biallelic Dlk1 repression, and to loss of Rtl1 expression. lncRNA expression also correlated with DNA hypomethylation and CTCF binding at the 5’-side of Meg3. Using Capture Hi-C, we found that this creates a Topologically Associating Domain (TAD) organization that brings Meg3 close to Dlk1 on the maternal chromosome. The requirement of Meg3 for gene repression and TAD structure may explain how aberrant MEG3 expression at the human DLK1-DIO3 locus associates with imprinting disorders.
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| Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for CTCF in F1-hybrid mouse embryonic stem cells (BJ1 cells = C57BL/6J x JF1; JB1 cells = JF1 x C57BL/6J). Cells are described in Kota et al. (2014). Input is also provided
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| Contributor(s) |
Moindrot B, Noordermeer D |
| Citation(s) |
38613389 |
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| Submission date |
Jun 29, 2022 |
| Last update date |
Jun 27, 2024 |
| Contact name |
Benoit Moindrot |
| E-mail(s) |
benoit.moindrot@i2bc.paris-saclay.fr
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| Organization name |
Institute for Integrative Biology of the Cell
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| Street address |
1, avenue de la terrasse
|
| City |
Gif-sur-Yvette |
| ZIP/Postal code |
91198 |
| Country |
France |
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| Platforms (1) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA854075 |
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