The Xenopus animal cap transcriptome: building a mucociliary epithelium

Abstract

With the availability of deep RNA sequencing, model organisms such as Xenopus offer an outstanding opportunity to investigate the genetic basis of vertebrate organ formation from its embryonic beginnings. Here we investigate dynamics of the RNA landscape during formation of the Xenopus tropicalis larval epidermis. Differentiation of non-neural ectoderm starts at gastrulation and takes about one day to produce a functional mucociliary epithelium, highly related to the one in human airways. To obtain RNA expression data, uncontaminated by non-epidermal tissues of the embryo, we use prospective ectodermal explants called Animal Caps (ACs), which differentiate autonomously into a ciliated epidermis. Their global transcriptome is investigated at three key timepoints, with a cumulative sequencing depth of ∼108 reads per developmental stage. This database is provided as online Web Tool to the scientific community. In this paper, we report on global changes in gene expression, an unanticipated diversity of mRNA splicing isoforms, expression patterns of repetitive DNA Elements, and the complexity of circular RNAs during this process. Computationally we derive transcription factor hubs from this data set, which may help in the future to define novel genetic drivers of epidermal differentiation in vertebrates.

Combinatorial transcription factor activities on open chromatin induce embryonic heterogeneity in vertebrates

“…Within the animal cap at early gastrula stages, ectoderm primarily consists of a superficial (epithelial) layer, and an attached deep (sensorial) layer (Chalmers et al, 2002), which diverge to goblet cells, multiciliated cells, ionocytes, and small secretary cells in the epidermal ectoderm by larval stages (Angerilli et al, 2018). In addition, the animal cap cells are competent to form mesoderm, but can also be induced to neural ectoderm by underlying mesoderm during gastrulation.…”

Histone H4K20 methylation synchronizes cytoskeletal dynamics with cell cycle phases during epidermal differentiation

“…ACs are prospective ectodermal explants that recapitulate the differentiation of the embryonic epidermis (Angerilli et al, 2018). We injected embryos radially at the 2-cell stage with either control or suv4-20h1/h2 Mos.…”

“…We injected embryos radially at the 2-cell stage with either control or suv4-20h1/h2 Mos. We then cut ACs at the blastula stage and performed RNA-Seq analysis at three key developmental stages (gastrula, neurula and tailbud; see (Angerilli et al, 2018) (Deblandre et al, 1999).…”

Advancing genetic and genomic technologies deepen the pool for discovery in Xenopus tropicalis

“…Transcriptomic profiling using RNA‐Seq gained immediate traction in X. tropicalis as soon as a draft genome was available, and in the years following publication of the genome, deep sequencing has been used to define the transcriptome across developmental stages and tissues, during processes such as regeneration, and under a multitude of molecular perturbations too numerous to detail. The genome assembly is now available at chromosome‐level (version 9.1 as of this writing) and gene models and annotations are well‐suited to RNA‐Seq analysis.…”