The signalling pathway of the vitamin A derivative all-trans retinoic acid (RA) has been widely studied in the past, and its relevance for normal embryonic development in a great conspicuous number of Deuterostome species is well known. Despite the thorough research on the gene regulatory networks that conform the early embryology of the model Echinoderm species Strongylocentrotus purpuratus, there is a gap of knowledge on the genetic machinery that controls RA action in this species. By means of chromatin accessibility (ATAC-seq) and gene expression analysis (RNA-seq) we describe the first genome wide in silico analysis of putative cis-regulatory modules within the RA pathway of S. purpuratus early embryonic stages. The RA hydroxylase enzyme coding gene Sp-Cyp26L showed promising potential for retinoic acid mediated regulation. The appliance of newly created bioinformatical pipelines with chromatin accessibility analysis (ATAC-seq) failed to increase the confidence on the putative cis-regulatory modules found and issues causing this outcome were revised. Additionally, new DNA motifs where the basic transcription factors of the RA machinery bind were searched, and 15 new putative motifs were found. Overall, the present work provides valuable knowledge base for the further analysis of the RA gene regulatory network of S. purpuratus.
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