The Xenopus animal cap transcriptome: building a mucociliary epithelium

Nucleic Acids Research
Alessandro AngerilliRalph Aw Rupp

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 ...Continue Reading

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Citations

Jun 30, 2019·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Anneke Kakebeen, Andrea Wills
Feb 13, 2021·Genesis : the Journal of Genetics and Development·Venkatramanan G Rao, Saurabh S Kulkarni

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Datasets Mentioned

BETA
SRR1795663

Methods Mentioned

BETA
RNA-Seq
PCR
dissection
RNAseq
PCA

Software Mentioned

DESeq2
RSEM
WEB
Xenbase
EctoMap
Refseq
cytoscape
- Tool
Mogrify
stringApp1

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