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| Status |
Public on Mar 04, 2024 |
| Title |
Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells |
| Organism |
Mus musculus |
| Experiment type |
Other
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| Summary |
Enhancer hijacking, a common cause of gene misregulation linked to disease, occurs when non-matching enhancers and promoters interact ectopically. This interaction is made possible by genetic changes that alter the arrangement or insulation of gene regulatory landscapes. While the concept of enhancer hijacking is well understood, the specific reasons behind the variation in phenotypic severity or the point at which those phenotypes become evident remain unexplored. In this work, we expand on the ectopic activation of the hindlimb-specific transcription factor Pitx1 by one of its own enhancers, Pen, in forelimb tissues that causes the Liebenberg syndrome. We combine a previously developed in-embryo cell-tracing approach to a series of inversions and relocations to show that reduction in Pitx1-Pen relative genomic positioning leads to increased proportions of Pitx1 forelimb-expressing cells and more severe phenotypical outcomes. We demonstrate that the Pitx1 locus assumes an active topology when enhancer-promoter contacts are required for transcription and that its promoter generates consistent transcription levels across different alleles. Finally, we show that changes in 3D chromatin structure and enhancer-promoter contacts are not the result of Pitx1 transcriptional activity. In summary, our work shows that variation in enhancer-promoter interactions can lead to pathogenic locus activation in variable proportions of cells which, in turn, define phenotypic severity.
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| Overall design |
We used capture Hi-C enriching a 3,3Mb region at the Pitx1 locus in Mus musculus. We analysed GFP postive and negative cells from Pitx1GFP;Inv1, Pitx1GFP;Inv2, Pitx1GFP;Rel1, Pitx1GFP;Rel2 and Pitx1GFP;Rel3 forelimbs; dCas9P300-Pitx1TSSsgRNAs and dCas9P300-noSgRNAs, Prx1-CRE, Eedflox/- and wildtype bulk forelimbs; and Pitx1GFP;Inv1, Pitx1GFP;Inv2 and Pitx1GFP mESC cells to compare the structural changes at the locus.
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| Contributor(s) |
Bompadre O, Andrey G |
| Citation missing |
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| |
| Submission date |
Feb 22, 2024 |
| Last update date |
Mar 05, 2024 |
| Contact name |
Guillaume Andrey |
| E-mail(s) |
guillaume.andrey@unige.ch
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| Phone |
+41223795703
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| Organization name |
University of Geneva
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| Department |
Department of Genetic Medicine and Development
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| Street address |
Rue Michel-Servet 1
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| City |
Geneva |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE259212 |
Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells |
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| Relations |
| BioProject |
PRJNA1079219 |
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