Making sense of the natural antisense transcript puzzle

Abstract

In plants, thousands of genes are associated with antisense transcription, which often produces noncoding RNAs. Although widespread, sense-antisense pairs have been implicated in a limited variety of functions in plants and are often thought to form extensive dsRNA stretches triggering gene silencing. In this opinion, we show that evidence does not support gene silencing as a major role for antisense transcription. In fact, it is more likely that antisense transcripts play diverse functions in gene regulation. We propose a general framework for the initial functional dissection of antisense transcripts, suggesting testable hypotheses relying on an experiment-based decision tree. By moving beyond the gene silencing paradigm, we argue that a broad and diverse role for natural antisense transcription will emerge. Natural antisense transcripts in plantsNatural antisense transcripts (NATs) (see Glossary) are widespread in eukaryotic genomes. The bulk of our current knowledge on the role of NATs in gene regulation is for cis-NATs (i.e., NATs and sense transcripts are transcribed from the same genomic locus), which are the focus of this work. Early work based on strand-specific RNA sequencing (RNA-seq) using short-read RNA sequencing of polyA+ mRNA, revealed that approximately 30% of loci of arabidopsis (Arabidopsis thaliana) are associated with cis-NATs [1]. More recent analysis of arabidopsis transcriptomics based on strand-specific RNA seq of either polyA+ mRNAs [2] or RNAs transcriptionally engaged with RNA Polymerase II (RNAPII) [3], reported 4300 to 5400 distinct cis-NATs, indicating that approximately 15-20% of arabidopsis loci possess a cis-NAT. Work in rice (Oryza sativum) using single-molecule long-read RNA sequencing reported that nearly 60% of loci are associated with a cis-NAT [4]. Similar high levels of genes associated with cis-NATs are also found in mice and humans [5].

MATR3-antisense LINE1 RNA meshwork scaffolds higher-order chromatin organization

“…Moreover, there are a great number of natural antisense transcripts (NATs) in human cells which is almost equal to sense transcripts, most (>91%) of them are ncRNAs 60 . NATs were suggested to interfere with the expression of sense mRNA through gene silencing, nuclear retention, epigenetic silencing or other mechanisms 61, 62 . Further investigations are needed to reveal the independent role of NATs, especially in the process of 3D genome organization.…”

The Identification of MATE Antisense Transcripts in Soybean Using Strand-Specific RNA-Seq Datasets

“…Surprisingly, we found that the relative expression levels of many of the MATE NATs are positively correlated to the corresponding sense transcripts ( Figure 2 ). Whether NATs promote or reduce the target transcript stability has been a subject of debate [ 25 , 44 ]. Nevertheless, there has been accumulating evidence to support the synergy brought forth by cis -NATs on the sense mRNA [ 25 ].…”

“…Whether NATs promote or reduce the target transcript stability has been a subject of debate [ 25 , 44 ]. Nevertheless, there has been accumulating evidence to support the synergy brought forth by cis -NATs on the sense mRNA [ 25 ]. In the global identification of Arabidopsis long non-coding RNAs (lncRNAs), based on the Pearson correlation coefficients, the strong tendency of NATs to positively regulate the expression of their sense overlapping genes was suggested [ 27 ].…”

“…For example, in the model plant Arabidopsis , the antisense transcripts covering the entire FLOWERING LOCUS C ( FLC locus) were suggested to silence FLC transcripts [ 22 ]; the antisense transcript of DOG1 ( Delay of Germination 1 ) was reported to suppress the expression of the sense DOG1 transcript [ 23 ]; CDF5 ( CYCLING DOF FACTOR 5 ) transcript and its antisense pair transcript FLORE ( CDF5 LONG NONCODING RNA ) were reported to inhibit each other’s expression [ 24 ]. However, accumulated evidence suggested that NATs are not necessarily the negative regulators of their sense counterparts [ 25 ]. For example, also in the model plant Arabidopsis , in a global analysis of antisense and sense transcript pairs that result in elevated small RNA levels, in terms of expression, the transcript pairs could have negative correlations, no correlations, or positive correlations [ 26 ].…”

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

“…Several of these RNAs seem to have regulatory roles, positively [ 10 , 11 ] or negatively [ 12 ] regulating the expression of other genes, such as the natural antisense transcripts (NATs). NATs are transcribed in the opposite orientation and are complementary to the sense transcripts (with mismatches or perfect matching) in the same (cis-NAT) or another locus (trans-NAT) [ 13 ]. In general, cis-NATs are easily identified in transcriptome studies, and most of the well-known NATs belong to this class.…”