Genome wide analysis of Silurana (Xenopus) tropicalis development reveals dynamic expression using network enrichment analysis

Development involves precise timing of gene expression and coordinated pathways for organogenesis and morphogenesis. Functional and sub-network enrichment analysis provides an integrated approach for identifying networks underlying development. The objectives of this study were to characterize early gene regulatory networks over Silurana tropicalis development from NF stage 2 to 46 using a custom Agilent 4 × 44 K microarray. There were >8000 unique gene probes that were differentially expressed between Nieuwkoop–Faber (NF) stage 2 and stage 16, and >2000 gene probes differentially expressed between NF 34 and 46. Gene ontology revealed that genes involved in nucleosome assembly, cell division, pattern specification, neurotransmission, and general metabolism were increasingly regulated throughout development, consistent with active development. Sub-network enrichment analysis revealed that processes such as membrane hyperpolarisation, retinoic acid, cholesterol, and dopamine metabolic gene networks were activated/inhibited over time. This study identifies RNA transcripts that are potentially maternally inherited in an anuran species, provides evidence that the expression of genes involved in retinoic acid receptor signaling may increase prior to those involved in thyroid receptor signaling, and characterizes novel gene expression networks preceding organogenesis which increases understanding of the spatiotemporal embryonic development in frogs.

► A functionally annotated microarray of 44 K probes for Silurana tropicalis was designed. ► Gene expression network analyses of transcribed genes in early development. ► Novel insight into the molecular networks regulating in early S. tropicalis development. ► Membrane hyperpolarisation, cholesterol, and dopamine networks are differentially activated over time.