Ptbp1 and Exosc9 knockdowns trigger skin stability defects through different pathways

Abstract

In humans, genetic diseases affecting skin integrity (genodermatoses) are generally caused by mutations in a small number of genes that encode structural components of the dermal-epidermal junctions. In this article, we first show that inactivation of both exosc9, which encodes a component of the RNA exosome, and ptbp1, which encodes an RNA-binding protein abundant in Xenopus embryonic skin, impairs embryonic Xenopus skin development, with the appearance of dorsal blisters along the anterior part of the fin. However, histological and electron microscopy analyses revealed that the two phenotypes are distinct. Exosc9 morphants are characterized by an increase in the apical surface of the goblet cells, loss of adhesion between the sensorial and peridermal layers, and a decrease in the number of ciliated cells within the blisters. Ptbp1 morphants are characterized by an altered goblet cell morphology. Gene expression profiling by deep RNA sequencing showed that the expression of epidermal and genodermatosis-related genes is also differentially affected in the two morphants, indicating that alterations in post-transcriptional regulations can lead to skin developmental defects through different routes. Therefore, the developing larval epidermis of Xenopus will prove to be a useful model for dissecting the post-transcriptional regulatory network involved in skin development and stability with significant implications for human diseases.

Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis

“…Finding these processes enriched is not surprising given the phenotype of ptbp1 morphants, with the appearance of dorsal blisters revealing defective structure or adhesion of the epidermis cells to their substrate (Noiret et al, 2016). Taken together, these data show that a large part of the differential splicing events revealed by the exon-centric approach are also identified by the junction-centric approaches, but that the junction-centric approaches identify numerous additional splicing events.…”

“…Our initial aim when we undertook this piece of work was to understand the molecular reasons of the specific phenotype of ptbp1 morphants, namely the appearance of blisters on the dorsal fin revealing epidermis instability (Noiret et al, 2016). It is therefore highly encouraging to find that many Ptbp1-controlled genes that we discover are linked to cell shape or adhesion.…”

“…We have described the construction and deep sequencing of 6 libraries from pools of non-injected X.laevis embryos and ptbp1 morphants (Noiret et al, 2016) (Figure 2A). We have obtained on average 56 millions of reads per condition ( Figure 2B).…”

“…We mapped them is two successive passes using the STAR mapper (Dobin et al, 2013) and the most recent genome assembly (v9.1) as shown in Figure 1A. With this procedure, 93 % of the reads on average were mapped ( Figure 2B), to be compared with 85 % attained with TopHat2 and the v7.1 genome assembly (Noiret et al, 2016). We identified differential junctions and exons as above.…”

“…Down-regulating ptbp1 in Xenopus, either directly (by injecting morpholino antisense oligonucleotides against ptbp1 mRNA) or indirectly (with morpholino antisense oligonucleotides against esrp1) leads to embryonic skin defects with the appearance of blisters developing along the dorsal fin of the embryos Méreau et al, 2015). We recently used deep RNA sequencing (RNAseq) to identify molecular events potentially responsible for the skin defects (Noiret et al, 2016). Initially, we had looked for RNAs with different abundances in control embryos and ptbp1 morphants.…”