Skip to Main content Skip to Navigation
Journal articles

Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example

Abstract : Abstract The identification of functional elements encoded in plant genomes is necessary to understand gene regulation. Although much attention has been paid to model species like Arabidopsis (Arabidopsis thaliana), little is known about regulatory motifs in other plants. Here, we describe a bottom-up approach for de novo motif discovery using peach (Prunus persica) as an example. These predictions require pre-computed gene clusters grouped by their expression similarity. After optimizing the boundaries of proximal promoter regions, two motif discovery algorithms from RSAT::Plants (http://plants.rsat.eu) were tested (oligo and dyad analysis). Overall, 18 out of 45 co-expressed modules were enriched in motifs typical of well-known transcription factor (TF) families (bHLH, bZip, BZR, CAMTA, DOF, E2FE, AP2-ERF, Myb-like, NAC, TCP, and WRKY) and a few uncharacterized motifs. Our results indicate that small modules and promoter window of [–500 bp, +200 bp] relative to the transcription start site (TSS) maximize the number of motifs found and reduce low-complexity signals in peach. The distribution of discovered regulatory sites was unbalanced, as they accumulated around the TSS. This approach was benchmarked by testing two different expression-based clustering algorithms (network-based and hierarchical) and, as control, genes grouped for harboring ChIPseq peaks of the same Arabidopsis TF. The method was also verified on maize (Zea mays), a species with a large genome. In summary, this article presents a glimpse of the peach regulatory components at genome scale and provides a general protocol that can be applied to other species. A Docker software container is released to facilitate the reproduction of these analyses.
Document type :
Journal articles
Complete list of metadata

https://hal-amu.archives-ouvertes.fr/hal-03243277
Contributor : Lionel Spinelli Connect in order to contact the contributor
Submitted on : Monday, May 31, 2021 - 4:51:59 PM
Last modification on : Tuesday, October 19, 2021 - 10:50:12 PM

File

kiaa091.pdf
Publication funded by an institution

Licence


Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives 4.0 International License

Identifiers

Collections

Citation

Najla Ksouri, Jaime Castro-Mondragón, Francesc Montardit-Tarda, Jacques van Helden, Bruno Contreras-Moreira, et al.. Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example. Plant Physiology, American Society of Plant Biologists, 2021, 185 (3), pp.1242-1258. ⟨10.1093/plphys/kiaa091⟩. ⟨hal-03243277⟩

Share

Metrics

Record views

32

Files downloads

29