Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells
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PROVIDER: PRJNA1080412 | ENA |
REPOSITORIES: ENA
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Project description:Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells
| PRJNA1079217 | ENA
Project description:Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells
| PRJNA1079219 | ENA
Project description:Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells
| PRJNA1079220 | ENA
Project description:Liebenberg syndrome severity arises from variations in Pitx1 locus topology and ectopically transcribing cells
| PRJNA1079218 | ENA
Project description: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.
2024-03-04 | GSE256339 | GEO
Project description: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.
2024-03-04 | GSE256338 | GEO
Project description: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.
2024-03-04 | GSE256337 | GEO
Project description: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.
2024-03-04 | GSE256336 | GEO
Project description: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.
2024-03-04 | GSE259212 | GEO
Project description:To identify genes regulated by Pitx1 during early hindlimb development, we compared gene expression differences between hindlimb buds from E12.5 Pitx1+/+ and Pitx1-/- mice on the Illumina MouseRef-8 expression Bead Chip. Genes involved in muscle development GeneGO processes were highly enriched in our dataset, specifically in down-regulated genes. This data is consistent with the reduced muscle volumes that were observed in the clubfoot limbs of our adult mice. Hindlimb buds were collected from Pitx1+/- mated mice at embryonic day E12.5 and genotypes were determined by PCR of DNA isolated from tails.
2011-11-21 | E-GEOD-27363 | biostudies-arrayexpress