Plant-PLMview: a database for identifying cis-regulatory sequences with preferential positions in gene-proximal regions of plants

Background Establishing relationships between transcription factors and target genes is essential for understanding the mechanisms regulating gene expression, which play a fundamental role in plant adaptation to the local environment. Despite the importance of this research area and the tremendous progress in sequencing methods such as ChIP-seq and DAP-seq, we are still far from a complete reconstruction of the cis-regulatory landscape. Only a small number of transcription factors can be assessed from experimental data to identify their cis-regulatory binding sites. This highlights the role that in silico approaches can play to complement experimental data. Results We have developed Plant-PLMview, a web-accessible database for detecting preferentially cis-regulatory sequences in the gene-proximal regions of 20 plant species. Users of Plant-PLMview can (i) access the proximal regions of controlled genes from 20 plant species, (ii) query their own DNA motifs or access 840 cis-regulatory sequences from various plant resources, and (iii) use a tool called PLMdetect to search for preferentially located motifs in the gene-proximal regions of a list of genes. Results are displayed via a web interface with a list of DNA motifs preferentially located in a region near the start or end of genes, the distribution of these motifs and associated annotations. In addition, a graphical map of the preferential locations of the motifs in the 5’ and 3’-proximal regions of genes provides an overview of all motifs and genes examined. Conclusion Plant-PLMview provides the opportunity to study the proximal landscape of gene regulation in 20 plant genomes. The originality of the database lies in its ease of use thanks to the curated data (cis-regulatory sequences and proximal regions of genes) and the possibility to search through PLMdetect in the 5’-gene-proximal region, but also in the 3’-gene-proximal region, which is rarely explored. The web interface provides numerous graphical views that allow the users to get an overview and interpret the results more easily.