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| Status |
Public on Jan 25, 2023 |
| Title |
Reduced representation bisulfite sequencing (RRBS) of the retina of crumbs 2a (crb2a m289/m289) zebrafish model of Leber congenital amaurosis and retinitis pigmentosa. |
| Organism |
Danio rerio |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
The crumbs cell polarity complex plays a crucial role in apical-basal epithelial polarity. When human CRB1 is mutated, it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa, with no established genotype-phenotype correlation. Using the oko meduzym289/m289 (crb2a-/-) zebrafish model, we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient-derived retinal organoids, with disruption to cell cycle modulation and epigenetic transcriptional control. Hence, using reduced representation bisulphite sequencing (RRBS) we explored differential DNA methylation, identifying hypermethylated pathways involving biological adhesion, Hippo and transforming growth factor beta (TGFbeta) signalling. Functional epigenetic modules (FEM) were highlighted through the integration of RNA-seq and RRBS, confirming cell cycle involvement and disturbance of TGFbeta, BMP, Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development.
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| Overall design |
We used RRBS to identify differentially methylated regions/genes between the zebrafish model of CRB, crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a-/- and control wildtype. Biological replicates were taken.
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| Contributor(s) |
Owen N, Toms M, Tian Y, Moosajee M |
| Citation(s) |
36656098 |
| |
| Submission date |
Jun 24, 2021 |
| Last update date |
Jan 28, 2023 |
| Contact name |
Mariya Moosajee |
| Organization name |
UCL
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| Department |
Institute of Ophthalmology
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| Street address |
11-43 Bath Street
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| City |
London |
| ZIP/Postal code |
EC1V 9EL |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA741229 |
| SRA |
SRP325504 |
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