A study of cis-regulatory elements in Xenopus and planarians

Multicellular organisms have the ability to produce and maintain several cell types despite the DNA molecule being the same in all cells. For that, a complex network of cis-regulatory elements (CRE) and transcription factors is involved in controlling cellular fate. Among the different approaches that allow the identification of CREs, the novel ATAC-sequencing is becoming an increasingly used tool due to its easy-to-perform protocol. In this study, this technique has been optimized to beused in two species (Xenopus laevis and Schmidtea mediterranea) to elucidate (1) the epigenetic mechanism behind Xenopus neural crest (NC) specification and differentiation, and (2) the establishment of anteroposterior identity during planarian regeneration.ATAC-sequencing has been carried out on Xenopus animal caps induced to give rise to NC or neural tissue. Comparison of this data along with non-injected ectodermal animal caps has led to the characterization of the epigenome involved in Xenopus neural crest formation. Results show that 4,528 NC open regions or potential enhancers are present during specification whereas 852 NC potential enhancers are specific for differentiation. In these NC open regions, the transcription factors Zic, Meis and Sox10 play an important role. Five enhancers driving expression of key neural crest genes (cmyc, foxd3, id3, snai2 and sox10) have been identified. ATAC-sequencing has also been successfully validated on dissected blastemas from 48h regenerating planarians. The analysis has revealed nervous system-related transcription factor motifs such as Prep or NeuroD-1 present in anterior specific open regions whereas posterior polarity-related transcription factor binding sites such as Islet or HoxD3 are present in posterior open regions. Key words: ATAC-sequencing, enhancer, transcription factor, Xenopus neural crest, planarian, anteroposterior polarity