In the last decade, one of the most significant advances in RNA biology has been the discovery of small non-coding RNAs that inhibit gene expression in sequence-specific manner in the process known as RNA silencing and/or RNA interference (RNAi), which is conserved pathway in various kinds of eukaryotes. Remarkable progress has been made to understand the RNA silencing machinery from the standpoint of RNA-protein interactions. However, although RNA silencing is essentially executed by complementary base-pairing between guide RNA and target mRNA, the consequence of base-pairing on silencing efficacy is poorly understood.
Both of small interfering RNAs (siRNAs) and microRNA (miRNA) duplexes are ? 22-bp long double-stranded RNAs with 2-nt 3'overhangs. However, they are structurally different: siRNAs are perfectly complementary RNA duplexes, but miRNAs form generally imperfect duplexes containing mismatched bulges. Both of them are loaded onto nuclease-containing regulatory complexes referred to as RNA-induced silencing complexes (RISCs), and unwound into single-stranded RNAs. In RNAi, siRNA guide strand pairs with target mRNAs with perfect complementarities, and the targets are cleaved by nuclease activity of Argonaute (Ago) protein contained in the RISC. However, siRNAs can also down-regulate genes whose transcripts possess partial complementarities to 7-nt of siRNA seed region positioned 2-8-nt from 5’ end of the guide strands through translational repression. This is known as off-target side effect of siRNAs. In the similar mechanism, miRNAs might associate with Ago proteins to direct translational repression of mRNAs. However, in both pathways, sequence-dependent base-pairing of RNA is considered to be an essential factor to trigger RNA silencing.
The capability of siRNA off-target silencing is shown to be highly correlated with the calculated melting temperature or standard free-energy change for formation of protein-free seed-target duplex, indicating that thermodynamic stability of RNA duplex is one of the major factors in determining the degree of silencing effects. The intrinsic stability of RNA duplex might reflect RNA sequence. However, other aspects, such as mismatches in the siRNA/miRNA central regions, fork-structured siRNAs, or RNA secondary structures, are also considered to alter RNA stabilities leading to the changes in RNA silencing efficacies. Furthermore, chemical modifications of siRNAs, such as 2’-fluoro-modified RNA or DNA-RNA chimera modification, are also demonstrated to prescribe the efficiencies of RNA silencing. Actual silencing efficiencies of siRNAs/miRNAs might be fundamental indicators to understand their biological consequences or effectiveness in technical and/or therapeutic applications. Thus, we would like to propose this area as a Research Topic in the journal as determining and prescribing factors of RNA silencing activity by siRNA/miRNA.
In the last decade, one of the most significant advances in RNA biology has been the discovery of small non-coding RNAs that inhibit gene expression in sequence-specific manner in the process known as RNA silencing and/or RNA interference (RNAi), which is conserved pathway in various kinds of eukaryotes. Remarkable progress has been made to understand the RNA silencing machinery from the standpoint of RNA-protein interactions. However, although RNA silencing is essentially executed by complementary base-pairing between guide RNA and target mRNA, the consequence of base-pairing on silencing efficacy is poorly understood.
Both of small interfering RNAs (siRNAs) and microRNA (miRNA) duplexes are ? 22-bp long double-stranded RNAs with 2-nt 3'overhangs. However, they are structurally different: siRNAs are perfectly complementary RNA duplexes, but miRNAs form generally imperfect duplexes containing mismatched bulges. Both of them are loaded onto nuclease-containing regulatory complexes referred to as RNA-induced silencing complexes (RISCs), and unwound into single-stranded RNAs. In RNAi, siRNA guide strand pairs with target mRNAs with perfect complementarities, and the targets are cleaved by nuclease activity of Argonaute (Ago) protein contained in the RISC. However, siRNAs can also down-regulate genes whose transcripts possess partial complementarities to 7-nt of siRNA seed region positioned 2-8-nt from 5’ end of the guide strands through translational repression. This is known as off-target side effect of siRNAs. In the similar mechanism, miRNAs might associate with Ago proteins to direct translational repression of mRNAs. However, in both pathways, sequence-dependent base-pairing of RNA is considered to be an essential factor to trigger RNA silencing.
The capability of siRNA off-target silencing is shown to be highly correlated with the calculated melting temperature or standard free-energy change for formation of protein-free seed-target duplex, indicating that thermodynamic stability of RNA duplex is one of the major factors in determining the degree of silencing effects. The intrinsic stability of RNA duplex might reflect RNA sequence. However, other aspects, such as mismatches in the siRNA/miRNA central regions, fork-structured siRNAs, or RNA secondary structures, are also considered to alter RNA stabilities leading to the changes in RNA silencing efficacies. Furthermore, chemical modifications of siRNAs, such as 2’-fluoro-modified RNA or DNA-RNA chimera modification, are also demonstrated to prescribe the efficiencies of RNA silencing. Actual silencing efficiencies of siRNAs/miRNAs might be fundamental indicators to understand their biological consequences or effectiveness in technical and/or therapeutic applications. Thus, we would like to propose this area as a Research Topic in the journal as determining and prescribing factors of RNA silencing activity by siRNA/miRNA.