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| Status |
Public on Apr 21, 2023 |
| Title |
Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (RNA-Seq) |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.
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| Overall design |
RNA-seq of either mESCs or NPCs of various genotypes (WT, Meteor promoter KO, Meteor promoter inversion) or perturbations (Ctrl, Meteor CRISPR/Cas9 KD).
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| Contributor(s) |
Ulitsky I, Gil N |
| Citation missing |
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| |
| Submission date |
Jan 22, 2023 |
| Last update date |
Apr 23, 2023 |
| Contact name |
Igor Ulitsky |
| E-mail(s) |
igor.ulitsky@weizmann.ac.il
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| Organization name |
Weizmann Institute of Science
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| Street address |
Hertzl St.
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (63)
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| This SubSeries is part of SuperSeries: |
| GSE223453 |
Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus |
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| Relations |
| BioProject |
PRJNA926338 |
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