From yeast to mice to chicks to stem cells – 4 ways RNA-Seq analysis sheds light on the world around us (a four part series)- Part II

In my previous blog post, I had walked you through a yeast paper where the authors had mapped its mitochondrial trancriptome. They had used the RNA-Seq analysis tool from Avadis NGS in clever ways to figure out details about the transcriptome that played a key role in piecing together the final map. In this week’s post, I briefly describe how gene expression data was used to show how evolutionarily, the partially bony tongues of birds were transformed into a muscular tongue in mammals.

Briefly, Liu H. et. al in their PNAS paper, demonstrated the importance of the Odd skipped related 1 (Osr-1) transcription factor in causing morphological differences between the tongues of birds and those of mammals. This paper is a thorough compilation of details that illustrate how differences in gene expression patterns can cause differences in the way an appendage or organ develops in different species- or in this particular case different classes of organisms.

In mammals, the tongue is just striated muscle, while in birds it is mostly cartilaginous. Liu H. et. al approach this problem from a developmental angle. Since the tongue skeleton and framework is formed at the time of embryogenesis, specifically during neural crest mesenchyme differentiation, the authors looked at changes in gene expression in mouse and chick embryos. The Osr-1 and Osr-2 genes are implicated in embryogenesis and organogenesis and are thus investigated for their role in tongue development in this paper. Most of the paper dealt with histologically mapping Osr-1 and Osr-2 expression in embryos at different times during embryogenesis, as well as in embryos that had increased/ reduced expression of these genes, and checking for morphological changes in developing tongue tissue. They were able to show that the presence of Osr-1 at the wrong moment in chick tongue development (embryonic day- D5) impaired chondrogenesis or cartilage formation, while its tissue-specific absence in mice (with neural-crest inactivated Osr-1) caused the formation of ectopic cartilage in the anterior tongue (on embryonic day E12.5).

The authors of this paper used the RNA-Seq workflow from Avadis NGS as one of the tools to demonstrate differential expression of genes during tongue morphogenesis at day E12 between mice with neural-crest specific inactivation of the Osr-1 gene and their control littermates. They demonstrated that the expression of genes involved in chondrogenesis such as the SRY-box containing gene-9 (Sox9), Sox5, (and their downstream target genes) and a number of chondrocyte collagens were up-regulated in the central tongue region, while Osr-1 mRNA levels were down-regulated in these mice with neural-crest inactivated Osr-1 compared to those in control mice. With RT-PCR data and in-situ hybridization results to corroborate their RNA-Seq data, the authors were able to prove that Osr-1 is a negative regulator of Sox9 and hence cartilage formation.

This paper provides an elegant answer to the question of how tongue morphogenesis changed evolutionarily with the expression of an extra gene (here Osr-1) at a specific developmental stage. RNA-Seq analysis was thus similarly used in this second paper to elucidate differential expression of genes in a given experimental system.

Next time, I will discuss how Microarray data analysis and RNA-Seq analysis fared in a head to head contest when they were used to map changes in gene expression after mice with Gaucher’s disease were treated with 2 different bio-similars. So don’t forget to log back in……