PLMdetect : de novo mapping of functional cis-regulatory motifs in 5'-and 3'proximal regions from Arabidopsis and maize

International audience

英语. Identifying cis-regulatory motifs controlling gene expression is an arduous challenge that is actively explored to discover key genetic factors responsible for traits of agronomic interest. The Preferentially Located Motif detection (PLMdetect) method was developed to identify over-represented motifs (PLMs) in promoters at a preferred distance from the transcription start site in the model plant Arabidopsis [1]. Here, we expanded the PLMdetect method to comprehensively analyze de novo the promoters as well as the untranslated transcribed regions of Arabidopsis and the important crop maize. We sought to determine how their differences in genome content and architecture would be reflected in features of their PLMs in 5’- and 3’-proximal regions of each gene locus. We have currently identified three groups of PLMs for each species in each targeted region. An assessment of these PLMs using known plant transcription factor (TF) binding site (TFBS) data [2] revealed that a subset of these PLMs (9.4% and 7.3% in Arabidopsis and maize, respectively) are previously characterized TFBSs (tPLMs), while the others represent novel and uncharacterized motifs (uPLMs), not captured by the current collection of plant TFBSs. Positional analyses of the tPLMs revealed positional preferences of TFBSs from several TF families as previously reported in Arabidopsis [3]. Furthermore, GO term enrichment analyses showed that 15.3% of the uPLMs are able to infer functional predictions which are not provided by tPLMs. In the near future, we will add comparisons between the datasets obtained from each species. Additionally, the development of the interactive PLMviewer website will provide the plant community with a valuable resource of PLM datasets for exploitation to investigate user-specific sequences.