cis-Regulatory Elements in Plant Development, Adaptation, and Evolution

Abstract

cis-Regulatory elements encode the genomic blueprints that ensure the proper spatiotemporal patterning of gene expression necessary for appropriate development and responses to the environment. Accumulating evidence implicates changes to gene expression as a major source of phenotypic novelty in eukaryotes, including acute phenotypes such as disease and cancer in mammals. Moreover, genetic and epigenetic variation affecting cis-regulatory sequences over longer evolutionary timescales has become a recurring theme in studies of morphological divergence and local adaptation. Here, we discuss the functions of and methods used to identify various classes of cis-regulatory elements, as well as their role in plant development and response to the environment. We highlight opportunities to exploit cis-regulatory variants underlying plant development and environmental responses for crop improvement efforts. Although a comprehensive understanding of cis-regulatory mechanisms in plants has lagged behind that in animals, we showcase several breakthrough findings that have profoundly influenced plant biology and shaped the overall understanding of transcriptional regulation in eukaryotes.

Keywords: adaptation; chromatin; cis-regulatory elements; development; stress response; transcription regulation.

Figure 1

Identification and classification of cis-regulatory elements. (a) Exemplary chromatin and cis-element landscape of actively transcribed and silenced genes. (b) Schematic of two cases of higher-order chromatin architecture resulting in distinct gene expression outcomes. Chromatin architecture in plants is predicted to be mediated by TCP transcription factors (CTCF in metazoans). (c) Illustration of chromatin accessibility profiling methods in a chromatin (top) and sequence fragment (bottom) context. (d) Schematic of ChIP-seq and DAP-seq approaches for mapping in vivo and in vitro transcription factor binding sites genome-wide, respectively. (e) STARR-seq experimental and computation workflow. Abbreviations: ATAC-seq, assay for transposase-accessible chromatin using sequencing; ChIP-seq, chromatin immunoprecipitation and sequencing; CTCF, CCCTC-binding transcription factor; DAP-seq, DNA affinity purification and sequencing; DNase-seq, DNase I digestion coupled with high-throughput sequencing; gDNA, genomic DNA; H3K27ac, acetylation of histone H3 lysine 27; H3K4me3, trimethylation of histone 3 lysine 4; MNase-seq, micrococcal nuclease sequencing; mRNA, messenger RNA; ORF, open reading frame; PRC2, Polycomb repressive complex 2; RNA Pol II, RNA polymerase II; STARR-seq, self-transcribing active regulatory region sequencing; TCP, teosinte branched 1/cycloidea/proliferating cell factor 1; TF, transcription factor; TFBS, transcription factor binding site; TSS, transcription start site.

Figure 2

Dynamic and static chromatin accessibility can underlie differential gene expression. Rapid, environmentally induced transcriptional changes are infrequently associated with widespread chromatin accessibility variation (a-c), in contrast to developmentally associated gene expression changes (d-f), which are more frequently attributed to chromatin remodeling. (a) A hypothetical locus with a strong TF affinity and/or TF nuclear concentration leads to greater chromatin accessibility and increased transcription. (b) Differential gene transcription arises due to differences in concentrations for competing TFs but causes no changes to chromatin accessibility. (c) Posttranslational modifications, such as phosphorylation or acetylation, to TFs can result in differential activation of transcription but cause no changes to chromatin accessibility. (d) The emergence of a shoulder peak in a broadly accessible domain due to TF binding leads to increased transcription. (e) The expression and binding of a silencing TF (blue) leads to nucleosome shifting and displacement of an activating TF (pink), resulting in gene silencing. There is novel chromatin accessibility in the non-expressed scenario. (f) An activating pioneer TF (pink) binds to nucleosomal DNA, leading to nucleosome eviction and activated transcription. There is novel chromatin accessibility in the transcribed scenario. Abbreviations: H3K27me3, histone 3 lysine 27 trimethylation; mRNA, messenger RNA; TF, transcription factor; TFBS, transcription factor binding site; TSS, transcription start site.

Figure 3

Evolution of CRMs and chromatin accessibility. (a) Hypothetical ancestral (top) and derived (bottom) haplotypes are shown. The ancestral haplotype has several ACRs (turquoise) over CRMs (green) and is moderately but broadly expressed. The derived haplotype has genetic variation including SNPs and a transposon insertion containing a novel CRM (purple and green rectangle), resulting in enhanced cell-type-specific expression. The size of the transcription arrow shows the relative expression level. (b) A tissue-constitutive CRE (c3) has lost activity because it no longer interacts with the promoter. There is a novel ACR/CRM located within the transposon (c5), as well as a quantitative gain of accessibility in another ACR (c2) due to a SNP that increases TF binding stability within the CRM. (c) These changes result in distinct spatiotemporal patterns of transcription. Abbreviations: ACR, accessible chromatin region; CRE, cis-regulatory element; CRM, cis-regulatory module; SNP, single-nucleotide polymorphism; TF, transcription factor.