Cis-regulatory elements and regulatory landscapes are essential for evolution, defining how and
where the genes should be expressed. Despite their obvious importance, they have been the
least understood DNA regulatory elements, until recently. One of our main questions is how Cis-
Regulatory elements (CREs) appear and are modified during evolution. Here we aim to elucidate
how the regulatory information impacts on the phenotypic adaptation to new environments at a
micro evolutionary level. For that purpose, we will use Astyanax mexicanus as a model organism.
This fish presents two well morphologically differentiated populations, Surface Fish and Cavefish.
For instance, Cavefish has lost pigmentation, the eyes, and has developed an increased number
and size of neuromasts. Therefore, the comparison of the activity of CREs during development in
both surface and cavefish could provide us with new insights about the relationship between a
certain phenotype and the underlying gene-regulatory network. Also, this approach could be
fundamental for modeling some human diseases in cavefish, like age-related macular
degeneration or Retinitis pigmentosa. In order to identify CREs in Surface Fish and Cavefish, we
have used ATAC-seq to determine open chromatin data at different developmental stages in both
populations. This approach allowed the successful identification of CREs that show differential
activity near genes that are important for eye development and other cave-specific traits.
Furthermore, we aim to integrate this information with chromosome architecture. For that purpose,
we generated HiChIP data for H3K4me3, which provides a genome-wide map of chromatin
contacts from all active promoters helping us to connect CREs to target genes. Together, our
ATAC-seq and H3K4me3 HiChIP data will allow us to determine how regulatory landscapes of
critical developmental genes has been modified during the cave life adaptation of Astyanax