Identification of gene regulatory elements in the sea anemone Nematostella vectensis

The genetic complexity, genomic organization, and the level of sequence conservation in Nematostella vectensis, a cnidarian model organism, was found to be more similar to vertebrates than to other bilaterian model organisms. This lead to the assumption that the development of more complex body plans is mainly due to differences in gene regulation, rather than to different gene content between species.

Cis-regulatory elements (CREs) (promoters, enhancers or silencers) are essential to regulate gene expression. They have been annotated in the genomes of bilaterian model organisms, but not in a single non-bilaterian metazoan genome.

As gene regulatory mechanisms in Nematostella remain unknown, we set out to annotate promoters and enhancers in the Nematostella genome. To this end, we performed chromatin immunoprecipitation (ChIP) of the transcriptional coactivator p300, components of the basal transcription machinery (RNA Pol2) and several histone modifications in different developmental stages followed by Illumina sequencing.

Quality of samples was assured and the locations of enrichments are conserved as expected and correlating with gene expression. We employed a supervised learning aproach using ChromHMM for prediction and annotation of putative CREs based on functional chromatin state segments genome-wide. Using this set, we validated some by testing CREs in vivo for their ability to drive expression of a reporter gene (shown in functional disection of Dpp region). The analysis of the different chromatin marks suggests that the genomic location, as well as the function of the different chromatin modifications in regulating gene expression, is conserved between bilaterian model organisms and Nematostella.

Our genome-wide map of CREs in a basal metazoan reveals much similarity with bilaterians  and proves usefull in the study of the evolution of gene regulation in animals.


Presented at the 2012 EvoNet Symposium in Vienna.