Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress

Abstract

Abiotic stresses such as nutritional imbalance, salt, light intensity, and high and low temperatures negatively affect plant growth and development. Through the course of evolution, plants developed multiple mechanisms to cope with environmental variations, such as physiological, morphological, and molecular adaptations. Epigenetic regulation, transcription factor activity, and post-transcriptional regulation operated by RNA molecules are mechanisms associated with gene expression regulation under stress. Epigenetic regulation, including histone and DNA covalent modifications, triggers chromatin remodeling and changes the accessibility of transcription machinery leading to alterations in gene activity and plant homeostasis responses. Soybean is a legume widely produced and whose productivity is deeply affected by abiotic stresses. Many studies explored how soybean faces stress to identify key elements and improve productivity through breeding and genetic engineering. This review summarizes recent progress in soybean gene expression regulation through epigenetic modifications and circRNAs pathways, and points out the knowledge gaps that are important to study by the scientific community. It focuses on epigenetic factors participating in soybean abiotic stress responses, and chromatin modifications in response to stressful environments and draws attention to the regulatory potential of circular RNA in post-transcriptional processing.

Figure 1 -. Histone epigenetic marks. Histone modifications associated with gene activation (left) and with gene repression (right). Histone acetylation involves histone acetyltransferase (HAT) that mediates the ligation of acetyl groups (Ac) to lysine residues (K⁺) of histones that form the nucleosome (light-blue circles), and as a result an open configuration of the chromatin. Readers as Bromodomain proteins (BROMO) are needed to mediate downstream biological responses. Histone deacetylation involves histone deacetylases (HDAC) to remove acetyl groups of histones (Ac) increasing their affinity to DNA and a close configuration of the chromatin. Histone methylation and demethylation occur through the activity of histone methyl transferases (HMT) and demethylases (HDM), respectively. Tri-methylation of the fourth lysine of histone 3 (H3K4me3) and demethylation of lysine 27 of histone 3 (H3K27) results in gene activation, whereas trimethylation of lysine 27 of histone 3 (H3K27me3) and demethylation of the fourth lysine of histone 3 (H3K4) results in gene repression.

Figure 2 -. DNA methylation and demethylation. DNA methylation occurs in cytosine (C) and adenine (A) bases mediated by DNA methylase proteins (DNA MTase), and results in gene repression or gene activation, respectively. Methyl binding domain proteins (MBD) have been identified as readers of methylated cytosine to initiate a transcription response. Demethylation occurs through base excision and repair (an active process) or by DNA replication (passive process).

Figure 3 -. Histone acetylation/deacetylation as epigenetic regulators in soybean under abiotic stress. (A) HDAC gene expression under multiple stresses can be either up or downregulated. Under salt stress: (B) acetylation H3K9Ac has been found in the promoter regions of stress responsive transcription factors (TF), such as MYB, b-ZIP, AP2/DREB. This epigenetic mark was correlated with their differential expression after stress. It has been proposed that GmNFYA forms a complex with GmFVE to bind CCAA box promoters, preventing HDA13 from reaching the promoter and preserving acetylation; (C) MIR482b gene expression is regulated by histone deacetylation, leading to the reduction of its expression and increasing its target gene (HEC1) expression.

Figure 4 -. Methylation as epigenetic regulators in soybean under abiotic stress. (A) Histone methyltransferases (HMT) and demethylases (HDM) can be either increased or reduced under stress. Under salt stress: activation of transcription factors (TFs) was correlated with a higher level of histone H3K4me3 and gene inactivation with the H3K27me3. Under cold stress H3K4me3 activation and H3K9me2 repression mark were observed. Plant homeodomain fingers 6 (PHD6) reads low methylated histone H3K4me0/1/2 but not H3K4me3. Upon binding to low methylated histones, the amino-terminal region of PHD6 interacts with its LHP1-1/2 coactivator to form a transcriptional activation complex. (B) Promoter regions of TFs genes are differentially methylated on DNA under salt stress. Differential DNA methylation was observed in soybean under cold, heat, cadmium, brassinosteroids, low-phosphorus, radioactivity, continuous cropping stress and domestication.

Figure 5 -. Summary of epigenetic factor identified in soybean under abiotic stress. Epigenetic factors and marks are described in pink for histone acetylation and deacetylation, in blue for histone methylation and demethylation and green for DNA methylation. They are also grouped by salt or other abiotic stresses. The percentages of studies reviewed in each type of modification are presented.

Figure 6 -. The microRNAs and circRNAs as non-coding RNAs that modulate gene expression in soybean. Different microRNAs have their expression modulated by abiotic stresses and can regulate post-transcriptionally the expression of target genes. Additionally, microRNA can be sponged by circRNAs, molecules that act as repressors of microRNA inhibition.