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Nucleic Acids Res 2018 Sep 28;4617:8772-8787. doi: 10.1093/nar/gky771.
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The Xenopus animal cap transcriptome: building a mucociliary epithelium.

Angerilli A , Smialowski P , Rupp RA .

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.

PubMed ID: 30165493
PMC ID: PMC6158741
Article link: Nucleic Acids Res

Species referenced: Xenopus tropicalis Xenopus laevis
Genes referenced: acss2.1 acss2.2 actc1 actn3 atp2a1 atp6v0a2 atp6v1e1 bmp7.1 bmp7.2 cdx1 cdx2 cpne1 eomes evpl grhl1 klf4 krt12.4 mcidas myh1 myh2 ncam1 neb odc1 otogl2 pou5f3 pou5f3.3 rem2 rfx2 sox2 tnnt3 tp63 tuba1a vim
GO keywords: skin epidermis development [+]

GEO Series: GSE111171: NCBI

Article Images: [+] show captions
References [+] :
Asashima, In vitro organogenesis from undifferentiated cells in Xenopus. 2009, Pubmed, Xenbase