Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane

Abstract

Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.

Long non-coding RNAs regulate the expression of cell surface receptors in plants

“…The regulation of sense gene expression by associated cis-NATs can be positive or negative and can occur via numerous mechanisms(5, 7). The overexpression of BRI1_NAT , CLV1_NAT , and SOBIR1_NAT in Arabidopsis resulted in striking phenotypes, suggesting that cis-NAT dosage can modify sense gene function (Figure 2).…”

“…The regulation by cis-NATs provides an elegant example of the evolution of a shared regulatory mechanism to control the activity of a large family of LRR-RLKs with diverse functions, distinct expression patterns, and varied targets. This investigation of NAT-derived regulation of an entire gene family greatly expands on our limited understanding of cis-NAT regulatory mechanisms in plants(5, 7), and provides an ideal system to understand better the complex pathways through which cis-NATs regulate their cognate genes. Having demonstrated that this relationship between cis-NATs and LRR-RLKs is conserved across plant evolution also raises the possibility of engineering improved crop performance through cis-NAT modification, as they have been shown to control critical agronomic traits in other contexts(18, 21, 58, 59, 61).…”

“…An emerging class of lncRNAs are natural antisense transcript lncRNAs (NAT lncRNAs, hereafter NATs) that are transcribed from the antisense strand of coding genes and are widespread in plants and animals (4)(5)(6)(7)(8). NATs are grouped into two categories, cis-NATs and trans-NATs, based on their locus of action (4,9).…”

Genome-Wide Identification and Characterization of miRNAs and Natural Antisense Transcripts Show the Complexity of Gene Regulatory Networks for Secondary Metabolism in Aristolochia contorta

“…Based on genomic locations, lncRNAs are generally divided into three types, including long intergenic ncRNAs (lincRNAs), intronic ncRNAs, and non-coding natural antisense transcripts (NATs) [ 20 ]. Among them, NATs are transcribed from the opposite strand of a protein-coding gene or another lncRNA and often overlap or are partially complementary to their sense counterparts [ 21 , 22 , 23 ]. They can interact with their sense partners through base pairing to inhibit the transcription of sense genes or can mediate in chromatin modification [ 24 ], where the interaction is complex.…”