Along with discovering new genes, the experiment also identified Shh affecting transcription of other already known genes. These genes were divided into categories of positively regulated and negatively regulated. Multiple genes in each category were grouped together based off of common effects on development. One group of genes found to be positively regulated by Shh was follistatin and follistatin-like2. These genes are known to work on the Bone Morphogenic Protein (BMP) pathway. The fact that increased levels of Shh also increase the levels of these two proteins provides a link between Shh and BMP. It had been previously shown that BMP signalling had an effect on Hh signalling, but this experiment is the first evidence of Shh regulating follistatin. Other groups of genes were found which suggest Hh plays a role in development of different neural areas in the brain, modify expression in specific locations, and interact with other signalling pathways such as the iroquois (irx) genes.
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