Enhancers as potential targets for engineering salinity stress tolerance in crop plants

Abstract

Enhancers represent noncoding regulatory regions of the genome located distantly from their target genes. They regulate gene expression programs in a context-specific manner via interacting with promoters of one or more target genes and are generally associated with transcription factor binding sites and epi(genomic)/chromatin features, such as regions of chromatin accessibility and histone modifications. The enhancers are difficult to identify due to the modularity of their associated features.Although enhancers have been studied extensively in human and animals, only a handful of them has been identified in few plant species till date due to nonavailability of plant-specific experimental and computational approaches for their discovery. Being an important regulatory component of the genome, enhancers represent potential targets for engineering agronomic traits, including salinity stress tolerance in plants. Here, we provide a review of the available experimental and computational approaches along with the associated sequence and chromatin/epigenetic features for the discovery of enhancers in plants. In addition, we provide insights into the challenges and future prospects of enhancer research in plant biology with emphasis on potential applications in engineering salinity stress tolerance in crop plants.

Natural and induced variations in transcriptional regulator genes result in low‐nicotine phenotypes in tobacco

“…Moreover, we identified no stretch of homologous sequences in the genomic region around ERF189 at the NIC2 locus, suggesting this mode of gene regulation is specific to the NIC1 locus. How the deleted genomic sequence, apart from ERF199 itself, regulates nicotine‐controlling genes is not known, but it may entail chromatin‐based mechanisms (Grosveld et al., 2021; Jain & Garg, 2021; Miele & Dekker, 2008). Notably, we detected no significant increase in DNA methylation in nic1‐1 within the ERF199 promoter region (Figure 2b), indicating that the epigenetic regulation is not involved in this process.…”

Genomic and Transcriptomic Approaches to Developing Abiotic Stress-Resilient Crops

“…Precise elimination of SlHyPRP1 negative-response domain(s) using CRISPR-Cas9 has led to high salinity tolerance at the germination and vegetative stages [26]. The ARGOS8 gene, which acts as a negative regulator in the ethylene response pathway, has been found to induce drought tolerance genes in maize [27]. Although numerous natural genotypes displaying drought resistance have been identified, the expression of ARGOS8 therein has been observed to be very low.…”

“…Although numerous natural genotypes displaying drought resistance have been identified, the expression of ARGOS8 therein has been observed to be very low. To overcome this limitation, CRISPR-Cas9 was used with a less-restrictive constitutive promoter called GOS2 to enhance the expression of ARGOS8 [27]. This led to increased drought tolerance in maize.…”

Identification of Barley Enhancers across Genome via STARR-seq

“…These common elements act in upstream or downstream of genes, and they are always located in distal promoter regions [2]. In recent years, a number of enhancers have been found to regulate developmental or tolerance processes, such as the inflorescence architecture, phosphate homeostasis, shoot regeneration, floral transition, and salinity stress tolerance [3–7]; thus, these elements show good potential in regulating various functional genes. However, enhancers are difficult to identify because their position and orientation are uncertain.…”