Noncoding RNAs: key molecules in understanding and treating pain

Abstract

Although noncoding RNAs (ncRNAs) were initially considered to be transcriptional byproducts, recent technological advances have led to a steady increase in our understanding of their importance in gene regulation and disease pathogenesis. In keeping with these developments, pain research is also experiencing rapid growth in the investigation of links between ncRNAs and pathological pain. Although the initial focus was on analyzing expression and dysregulation of candidate miRNAs, elucidation of other ncRNAs and ncRNA-mediated functional mechanisms in pain modulation has just commenced. Here we review the major ncRNA literature available to date with respect to pain modulation and discuss tools and opportunities available for testing the impact of other types of ncRNA on pain.

Keywords: chronic pain; lncRNA; miRNA; ncRNA; pain mechanisms.

Figure 1

miRNA biosynthetic pathway and tools available for miRNA functional analysis. Primary miRNA (pri-miRNA) transcripts are produced by RNA polymerase II (RNA pol-II) and processed by the endonuclease Drosha and its cofactors in the nucleus. The resulting hairpin-shaped precursor miRNA (pre-miRNA) is transported to the cytoplasm via Exportin-5 for further processing by Dicer, an RNase-like enzyme, creating a 21-nucleotide miRNA duplex (miRNA5p–miRNA3p). The mature single-stranded miRNA is assembled into the miRNA-induced silencing effector complex (RISC). The RISC is then guided by the miRNA to complementary mRNA target sequences. Perfect sequence complementarity to the target mRNA results in mRNA degradation. Translational repression is initiated in cases of imperfect seed-region pairing. Modes of action of available tools to study miRNA-mediated functional aspects are also depicted. Lenti- or adeno-associated viral particles carrying pre-miRNA or coding sequences for either miRNA inhibitors or miRNA sponges are used to circumvent the problems of cellular uptake and to achieve long-term expression. miRNA mimics are synthetic double-stranded oligos; following cellular uptake one of the strands (the active strand) is incorporated into the RISC and directs downstream mechanisms to downregulate the mRNA target. The other strand (the passive strand) is degraded. miRNA inhibitors are single-stranded chemically modified oligonucleotides containing a sequence complementary to either the seed region or the complete sequence of the targeted miRNA. miRNA sponges are also like inhibitors but contain multiple sequences in tandem. Following cellular uptake of inhibitors or sponges, the endogenous miRNA is scavenged and cannot be incorporated into the RISC and contribute to mRNA cleavage or translational repression. miRNA target protectors work at the target mRNA level. Following cellular uptake, the target protectors bind to and block the miRNA-binding sites of the target mRNA from the RISC, ultimately resulting in bypass of RISC-associated mRNA cleavage or translational repression.

Figure 2

Representation of miRNA–mRNA functional pairs involved in nociceptive modulation along the somatosensory pain pathway. miRNA–mRNA functional pairs studied in the context of nociceptive modulation in the dorsal root ganglion (DRG), spinal cord dorsal horn (SDH), and brain are represented. mRNA targets that are functionally characterized in pain modulation are represented in bold.

Figure 3

Mechanisms of action of long noncoding RNAs (lncRNAs). Several studies have described different modes of action for the functioning of lncRNAs in different model systems. It has been suggested that the primary sequence, secondary structure, and genomic position with respect to coding genes (intragenic, exonic, intronic, or overlapping) decides the mode of action of lncRNAs. Some lncRNAs function as RNA decoys at the genetic level by directly scavenging transcription factors . Competitive endogenous RNAs (ceRNAs) function at the post-transcriptional level by scavenging miRNA functional effectors and thereby limiting miRNA availability for their mRNA targets, and provide another level of post-transcriptional gene regulation [103–105]. Some lncRNAs act as ‘RNA scaffolds’ for regulatory protein binding, which can lead to chromatin remodelling . Some other lncRNAs result in the generation of endogenous small interfering RNAs (endo-siRNAs) via Dicer-mediated cleavage in the cytoplasm and thus inhibit target mRNA expression. Some lncRNAs are known directly to modulate target mRNA expression levels by translational repression, transcriptional activation, modulation of splicing patterns, or degradation [107–109].