Changes in Gene Regulation and Pattern Formation to Morphological Changes

Sonic Hedgehog (SHH)

• a signaling molecule that regulates limb development

• a target of Hox genes

• a morphogen that acts downstream of Hox pathways in patterning of limbs

• this protein is critical for development of the central nervous system, brain and other organs

Given the role of Shh in body patterning, where would you find sequences changes in this gene in snakes? (no limbs)

• In the regulatory sequence for the Shh gene (not protein!)

• we need Shh for development of other systems (needs to be functional) → it can’t be mutated

  • altering the protein sequence would impact its ability to regulate other developmental pathways

Progressive loss of function in a limb enhancer during Snake Evolution

• ZRS is a limb-specific enhancer that regulates the expression of Shh

• it is highly conserved and found in many vertebrates

• there are substantial deletions of this enhancer in snakes (17bp or more)

• changes in cis regulatory elements controlling limb formation have led to morphological changes in snakes

• 933 conserved non-coding elements (CNEs) that regulate limb formation

  • these elements tend to be conserved in limbed organisms but diverge in snakes

Mice Swap Experiment

• in WT mice, HOX protein bind to the ZRS to induce expression of Shh. This results in the developmental of functional limbs

• exp: transgenic mice were generated by editing out the mZRS and replacing it w/ the ZRS sequences found in Cobras (cZRS)

  • results in truncated limbs (cobra ZRS is no longer functional)

• since ZRS element regulates other systems, why do other systems appear normal develop in snakes, there is other enhancer elements that direct expression of SHHH in the central nervous system, brain and other organism

• reversing the 17bp deletion restores limb-specific enhancer function

Maximizing the diversity or organisms from a limited number of genes

Summary of Alternative transcription control: combinatorial possibility of transcription factors

• a greater number of TFs mean that a greater number of unique combinations are possible, allowing for more complex control of gene expression

• related to the high number of TFs: expansion of regulatory regions allow for more TF binding sites (and ever more combinations)

• concentrations and ratios of the different activators and repressors determine whether any particular regulatory region is activated or repressed

• regulatory regions allow for modular control of gene expression

  • e.g. multiple enhancers, each regulating expression in a diff tissue

  • mutation of specific regulatory regions such that gene expression is only affected in some tissues, promoting a diversity of form