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The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network

Figure 5

In silico evolution of functional photoreceptor cis-regulatory elements.

A, Flatmount and cross-sectional images of mouse Rho-CRE fused to DsRed co-electroporated with CAG-eGFP. All constructs were electroporated at P0, cultured as explants, and harvested at P8. The column labeled ‘CRE architecture’ shows the distribution of Crx (top half) and Nrl (bottom half) sites with the indicated ‘affinity’ as described in the legend at the top of the figure. The orientation of a given site is indicated by the direction of the triangle representing that site. The score on the y-axis is the log odds score for that site which reflects its closeness to consensus. Size bar = 500 µm for flatmount images and 100 µm for cross-sections B-D, Images of retinas electroporated with the indicated synthetic CREs. For example, ‘Syn1-G70’ indicates a sequence corresponding to the genome of the ‘fittest’ organism of generation 70 in evolutionary run 1. The CREs in B-D derive from three separate evolutionary runs. E, Graph of first 700 generations of evolutionary run 3. The four ‘organisms’ from this run whose genomes were tested for CRE activity are circled and images of their expression patterns are given in Fig. S4. F, Graph of expression strength of four synthetic CREs from evolutionary run 3.

Figure 5

doi: https://doi.org/10.1371/journal.pone.0000643.g005