Abstract
BackgroundThe neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in order to migrate and differentiate throughout the developing embryo. The derivative cell types give rise to multiple tissues, including the craniofacial skeleton, peripheral nervous system and skin pigment cells. Several well-studied gene regulatory networks underpin NC development, which when disrupted can lead to various neurocristopathies such as craniofrontonasal dysplasia, DiGeorge syndrome and some forms of cancer. Small RNAs, such as microRNAs (miRNAs) are non-coding RNA molecules important in post-transcriptional gene silencing and critical for cellular regulation of gene expression.ResultsTo uncover novel small RNAs in NC development we used high definition adapters and next generation sequencing of libraries derived from ectodermal explants of Xenopus laevis embryos induced to form neural and NC tissue. Ectodermal and blastula animal pole (blastula) stage tissues were also sequenced. We show that miR-427 is highly abundant in all four tissue types though in an isoform specific manner and we define a set of 11 miRNAs that are enriched in the NC. In addition, we show miR-301a and miR-338 are highly expressed in both the NC and blastula suggesting a role for these miRNAs in maintaining the stem cell-like phenotype of NC cells.ConclusionWe have characterised the miRNAs expressed in Xenopus embryonic explants treated to form ectoderm, neural or NC tissue. This has identified novel tissue specific miRNAs and highlighted differential expression of miR-427 isoforms.
Highlights
The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos
Analysis of the 29 nt peak showed that of the four tissue types blastula had the least number of reads aligning to piwi-interacting RNAs (piRNAs) (3.38%) whilst neural had the most at 6% suggesting that the peak observed at 29 nt included other classes of small RNAs (sRNA)
Sequences of all the hairpins identified and alignments of sequences to hairpins are shown in Additional files 5 and 6. 106 previously described micro RNA (miRNA) families derived from 388 hairpins were expressed
Summary
The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. In the early stages of neurulation where the brain and central nervous system develops, several well-studied gene regulatory networks interact to establish a neural plate border (NPB) between the neural plate and nonneural ectoderm, and overlying the paraxial mesoderm [2]. The genetics of NC development have been reported extensively, and there are a few transcriptomic studies, to date the complement of small RNAs (sRNAs) has not been characterized. SRNAs, 19–33 nucleotides (nt) in length, are a diverse class of noncoding RNA molecules that are key regulators of gene expression. SRNAs such as microRNAs (miRNAs) regulate the expression of >60% of protein coding genes in. Previous reports suggest an important role for miRNAs in NC development, with Wnt1-Cre mediated knockouts of Dicer, a protein involved in miRNA biogenesis, displaying phenotypes consisting of various NC related abnormalities such as impaired craniofacial development [14,15,16]
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