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bioRxiv · 10.1101/2022.01.17.476590

Genome-wide identification of preferentially located motifs in gene-proximal regions provides new insights into cis-regulatory sequences in plants

Roziere, J.·Guichard, C.·Brunaud, V.·Martin, M.-L.·Coursol, S.
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Abstract

The identification of cis-regulatory elements controlling gene expression is an arduous challenge that is being actively explored to discover the key genetic factors responsible for traits of agronomic interest. Here, we have used a de novo and genome-wide approach for preferentially located motif (PLM) detection to investigate the proximal cis-regulatory landscape of Arabidopsis thaliana and Zea mays. We report three groups of PLMs in each gene-proximal region and emphasize conserved PLMs in both species, particularly in the 3-gene-proximal region. Comparison with resources of transcription factor and microRNA binding sites indicates that 79% of the identified PLMs are unassigned, although some are supported by MNase-defined cistrome occupancy analysis. Enrichment analyses further reveal that unassigned PLMs provide functional predictions distinct from those inferred by transcription factor and microRNA binding sites. Our study provides a comprehensive map of PLMs and points at their potential utility for future characterization of orphan genes in plants.

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Roziere, J., Guichard, C., Brunaud, V., Martin, M.-L., Coursol, S.. 2022-01-18. Genome-wide identification of preferentially located motifs in gene-proximal regions provides new insights into cis-regulatory sequences in plants. https://doi.org/10.1101/2022.01.17.476590

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