Mapping Regulatory Determinants in Plants

Abstract

The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.

Keywords: chromatin; cis-regulatory regions; plant genomics; transcription factor binding; transcriptional regulation.

Figure 1

Plant transcriptional regulation (A) model of plant transcriptional regulation at gene X. Colored circles represent different TFs binding to three distinct cis-regulatory regions (CREs; light green bars) that can contact the core promoter via DNA looping. Motifs enriched within binding peaks for two TFs are shown for CRE3. (B) Conservation and variation of TF binding events among different lines or accessions. Colored peaks represent different TF binding events within CREs. mRNA expression levels, cell-type specific expression pattern, and resulting phenotype are shown. (C) Examples showing how single nucleotide polymorphisms (SNPs) and indels can result in expression and phenotypic changes. (D) Examples showing how transposon insertions can result in expression and phenotypic changes. (E) Examples showing how structural variants can result in expression changes.

Figure 2

Integration of various types of genomic regulatory data allows for the identification of CREs. Shown is a genome browser view of putative distal CRE (gray shaded region) located 40 kb upstream of the SBP8/UNBRANCHED2 gene in maize. Data obtained from Ricci et al., 2019.