AUTHOR=Rozière Julien , Guichard Cécile , Brunaud Véronique , Martin Marie-Laure , Coursol Sylvie 

TITLE=A comprehensive map of preferentially located motifs reveals distinct proximal cis-regulatory sequences in plants

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.976371

DOI=10.3389/fpls.2022.976371

ISSN=1664-462X

ABSTRACT=<p>Identification of <italic>cis</italic>-regulatory sequences controlling gene expression is an arduous challenge that is being actively explored to discover key genetic factors responsible for traits of agronomic interest. Here, we used a genome-wide <italic>de novo</italic> approach to investigate preferentially located motifs (PLMs) in the proximal <italic>cis</italic>-regulatory landscape of <italic>Arabidopsis thaliana</italic> and <italic>Zea mays</italic>. We report three groups of PLMs in both the 5’- and 3’-gene-proximal regions and emphasize conserved PLMs in both species, particularly in the 3’-gene-proximal region. Comparison with resources from transcription factor and microRNA binding sites shows 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 that differ from those derived from transcription factor and microRNA binding sites. Our study provides a comprehensive map of PLMs and demonstrates their potential utility for future characterization of orphan genes in plants.</p>