Lack of Vsx TFs in the forming retina is buffered by genetic redundancy. (a) Volcano plots illustrating chromatin accessibility variations upon vsx1 and vsx2 mutation in zebrafish retina at 18hpf. Each dot corresponds to an ATAC-seq peak, that is an open chromatin region. Grey dots indicate not significant variations, whereas colored dots point out significant differentially open chromatin regions. (b). Frequency of DOCRs’ fold change values. (c). Transcriptome variations in vsxKO retina at 18hpf. The genes reported in the plot are the only known retinal regulators whose transcriptional levels are affected by the loss of Vsx factors, with a very modest fold change. Essentially, RNA-seq experiments did not highlight a remarkable change of the levels of the main TFs governing the retinal GRN. (d). Correspondence between genes associated with DOCRs from ATAC-seq and DEGs from RNA-seq. (e). qPCR of the main retinal TFs confirming the stability of the eye gene network expression after vsx1 and vsx2 loss (n=3). **p<0.001, *p<0.01 using one-way ANOVA. Data is shown as mean ± SD. DOCR: differentially open chromatin regions, DEG: differentially expressed genes.
|
