Navigating the Multiverse of Antisense RNAs: The Transcription- and RNA-Dependent Dimension

Abstract

Evidence accumulated over the past decades shows that the number of identified antisense transcripts is continuously increasing, promoting them from transcriptional noise to real genes with specific functions. Indeed, recent studies have begun to unravel the complexity of the antisense RNA (asRNA) world, starting from the multidimensional mechanisms that they can exert in physiological and pathological conditions. In this review, we discuss the multiverse of the molecular functions of asRNAs, describing their action through transcription-dependent and RNA-dependent mechanisms. Then, we report the workflow and methodologies to study and functionally characterize single asRNA candidates.

Keywords: RNA-dependent mechanism; antisense RNA (asRNA); functional study; long non-coding RNA (lncRNA); transcription-dependent mechanism.

Figure 1

asRNA classification based on their genomic position and direction of transcription with respect to the sense genes. asRNAs are divided into two major categories: convergent overlapping asRNAs, which include (a) head-to-head, (b) tail-to-tail, (c) intronic and (d) embedded transcripts, and divergent non-overlapping asRNAs, which can (e) share a bidirectional promoter with their sense gene or (f) have an independent one. Created with BioRender.com accessed on 25 October 2022.

Figure 2

Transcription-dependent mechanisms of asRNAs. In the figure, the transcription-dependent modes of action of asRNAs are reported. In cases of non-overlapping asRNAs (a), the transcription or the binding of a transcription factor (TF) at the asRNA locus promote the transcription at the sense RNA (sRNA) locus. In cases of overlapping asRNAs (b,c), the transcriptional overlap (b) interferes with the recruitment of the RNA polymerase II (Pol II), causing sRNA locus silencing, or (c) leads to collision of the concomitant and convergent progression of bulky Pol II on opposite strands. Created with BioRender.com accessed on 25 October 2022.

Figure 3

RNA-dependent mechanisms of asRNAs. In the figure, the different RNA-dependent modalities of asRNAs are depicted. asRNAs can act through base pairing with other RNAs by affecting the (a) mRNA stability and translation or (b) the alternative splicing of target genes; (c) they can also act as sponges to sequester miRNAs or (d) form R-loop with the DNA helix. On the other hand, asRNAs can act through sequence motifs and RNA structure, allowing them to bind to (e) DNA and (f) proteins, respectively. ADA: adenosine deaminase; RBP: RNA binding protein; miRNA: microRNA; Pol II: RNA Polymerase II; TF: transcription factor; EE: epigenetic enzyme. Created with BioRender.com accessed on 25 October 2022.

Figure 4

Experimental workflow for asRNA identification and functional study. Techniques and tools are reported in light blue boxes; obtained results are reported in orange boxes. Created with BioRender.com accessed on 25 October 2022.