Analysis of the dynamics of limb transcriptomes during mouse development

Istvan Gyurján,Bernhard Sonderegger,Felix Naef,Denis Duboule

doi:10.1186/1471-213x-11-47

Istvan Gyurján, Bernhard Sonderegger + Show 2 more

Open Access

https://doi.org/10.1186/1471-213x-11-47

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Abstract

BackgroundThe development of vertebrate limbs has been a traditional system to study fundamental processes at work during ontogenesis, such as the establishment of spatial cellular coordinates, the effect of diffusible morphogenetic molecules or the translation between gene activity and morphogenesis. In addition, limbs are amongst the first targets of malformations in human and they display a huge realm of evolutionary variations within tetrapods, which make them a paradigm to study the regulatory genome.ResultsAs a reference resource for future biochemical and genetic analyses, we used genome-wide tiling arrays to establish the transcriptomes of mouse limb buds at three different stages, during which major developmental events take place. We compare the three time-points and discuss some aspects of these datasets, for instance related to transcriptome dynamics or to the potential association between active genes and the distribution of intergenic transcriptional activity.ConclusionsThese datasets provide a valuable resource, either for research projects involving gene expression and regulation in developing mouse limbs, or as examples of tissue-specific, genome-wide transcriptional activities.

Highlights

The development of vertebrate limbs has been a traditional system to study fundamental processes at work during ontogenesis, such as the establishment of spatial cellular coordinates, the effect of diffusible morphogenetic molecules or the translation between gene activity and morphogenesis
E11.5 limb buds consist of a rather poorly differentiated inner mesenchyme, located within an epidermal envelope. Mesenchymal cells at this stage can be already differentiated as belonging to denser, centrally located regions where condensation of the future cartilage rods starts to occur [2]
After careful curation, which removed all potential 3’untranslated regions (UTR), pseudogenes and non-coding isoforms of coding genes, we identified 49 long Non-coding RNAs (ncRNAs) that were differentially expressed in our samples (Table 3)

Summary

Introduction

The development of vertebrate limbs has been a traditional system to study fundamental processes at work during ontogenesis, such as the establishment of spatial cellular coordinates, the effect of diffusible morphogenetic molecules or the translation between gene activity and morphogenesis. Limb development has fascinated biologists for a century, mostly because of the importance of these structures in the evolution of land vertebrates and due to their spectacular morphological diversity. Speaking, limb phenotypes can be detected and usually do not impair survival too strongly. For all these reasons, limbs have been excellent model structures to study vertebrate patterning and morphogenesis. Tetrapods limbs bud out from the lateral plate mesoderm and establish early on the bases of a three-dimensional pattern.

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