Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes

Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, opposed conventional binding sites of transcription factors, few methods have been proposed formally and automatically characterize them. We present here a computational approach named DExTER (Domain Exploration To Explain Regulation) dedicated the identification candidate LREs (cLREs) apply it analysis genomes P . falciparum other eukaryotes. Our analyses show that all tested contain several cLREs somewhat conserved along evolution, expression can be predicted with surprising accuracy on basis these long regions only. Regulation by exhibits very different behaviours depending species conditions. In Apicomplexan organisms well Dictyostelium discoideum , process appears highly dynamic, involved at phases life cycle. For multicellular organisms, same tissues, but dynamic behavior is observed embryonic development stages. whose genome known strongly depleted predictive an above 70%, our they associated both transcriptional post-transcriptional signals. Moreover, we assessed biological relevance one LRE discovered using vivo reporter assay. The source code (python) available https://gite.lirmm.fr/menichelli/DExTER