Design of Synthetic Mammalian Promoters Using Highly Palindromic Subsequences

To express transgenes in specific
cell types and states, promoters
for endogenous genes are commonly created by truncating the sequence
upstream of the transcriptional start site until the promoter is no
longer functional. In this paper, we developed a method to design
shorter synthetic mammalian promoters for endogenous genes by concatenating
only its highly palindromic subsequences with a minimal core promoter.
After developing metrics for palindromic density, analysis across
all the human and mouse promoters showed higher palindromic density
than expected by random. As experimental demonstrations, we applied
the method to the CMV promoter (reduced to 432 nucleotides) and the
mouse synapsin-1 promoter (383 nucleotides) to express fluorescent
protein as reporters. Remarkably, the highly palindromic subsequences
of these synthetic promoters contained sites important for strong
constitutive expression and neuron-specific expression. As a resource
to the community, we created enhancer sequences for all the human
and mouse promoters.