The RNA-induced Silencing Complex: A Versatile Gene-silencing Machine

Abstract

RNA interference is a powerful mechanism of gene silencing that underlies many aspects of eukaryotic biology. On the molecular level, RNA interference is mediated by a family of ribonucleoprotein complexes called RNA-induced silencing complexes (RISCs), which can be programmed to target virtually any nucleic acid sequence for silencing. The ability of RISC to locate target RNAs has been co-opted by evolution many times to generate a broad spectrum of gene-silencing pathways. Here ,we review the fundamental biochemical and biophysical properties of RISC that facilitate gene targeting and describe the various mechanisms of gene silencing known to exploit RISC activity. RISC2 is a generic term for a family of heterogeneous molecular complexes that can be programmed to target almost any gene for silencing. In general, RISC programming is triggered by the appearance of dsRNA in the cytoplasm of a eukaryotic cell (Fig. 1). The dsRNA is processed into small regulatory RNAs (20 -30 nucleotides in length) that assemble into RISC and guide the complex to complementary RNA targets through base-pairing interactions. Once programmed with a small RNA, RISC can silence targeted genes by one of several distinct mechanisms, working at (a) the level of protein synthesis through repression of translation, (b) the transcript level through mRNA degradation, or (c) the level of the genome itself through the formation of heterochromatin or by DNA elimination.Although the mechanisms used to control gene expression by RISC are quite diverse, two central themes are common to all. First, at its core, every RISC contains a member of the Argonaute protein family that binds to the small regulatory RNA. Second, in every RISC, the small regulatory RNA functions as a guide that leads RISC to its target through Watson-Crick base pairing with cognate RNA transcripts. The role of the Argonaute protein is to bind the small RNA and position it in a conformation that facilitates target recognition. Argonaute proteins can either cleave target RNAs directly or recruit other gene-silencing proteins to identified targets. Here, we review how Argonaute proteins use small RNAs to recognize target transcripts. We also examine how recruitment of different types of Argonaute and Argonaute-associated proteins produce distinct RISCs, which then dictate the mechanism of gene regulation. RISC and Small RNA NomenclatureAs in many fields of biology, the nomenclature commonly used to describe RNAi and RISC is not completely rational or intuitive. The small regulatory RNAs that guide RISC have been given a variety of similar sounding names. These include siRNA, miRNA, piRNA, rasiRNA, tasiRNA, tncRNA, hcRNA, and scnRNA. These classifications are generally based on either the biosynthetic pathway of the small RNA or the type of RISC in which the RNA is found (for a detailed review, see Ref.

Phospho-ΔNp63α/microRNA network modulates epigenetic regulatory enzymes in squamous cell carcinomas

“…[3][4][5][6] microRNAs repress the expression of a variety of target genes involved in a plethora of distinct signaling pathways in development and disease. 7,8 Primary microRNA transcripts are processed by the RNA-induced silencing complex to generate mature microRNAs; the latter form complexes with the specific sequences within mRNA targets based on complementarity. [7][8][9][10][11] The microRNA/mRNA complexes then cause an inhibition of protein translation and/or degradation of the mRNAs.…”

Toward a Systematic Understanding of mRNA 3' Untranslated Regions

“…These small RNAs associate with members of the Argonaute family of small RNA-binding proteins within larger RNA-induced silencing complexes (RISCs) (25). Base-pairing interactions between a small RNA in the RISC and a partially complementary sequence in the 39 UTR lead to specific interactions between mRNAs and RISCs (24). RISCs are heterogeneous, but may contain Argonaute family members and other proteins that can cleave small RNA:mRNA heteroduplexes, block translational initiation or elongation, recruit poly(A) deadenylating and mRNA decapping complexes, and direct mRNAs to P bodies (24).…”

“…Base-pairing interactions between a small RNA in the RISC and a partially complementary sequence in the 39 UTR lead to specific interactions between mRNAs and RISCs (24). RISCs are heterogeneous, but may contain Argonaute family members and other proteins that can cleave small RNA:mRNA heteroduplexes, block translational initiation or elongation, recruit poly(A) deadenylating and mRNA decapping complexes, and direct mRNAs to P bodies (24). In addition to AREs and small RNA/ RISC targets, many other 39 UTR cis elements can also affect mRNA stability (13).…”

“…Evidence suggests that AU-rich elements can affect protein production by altering mRNA stability, by sequestering mRNAs from ribosomes (e.g., by sequestration in P bodies), and by recruiting proteins that directly affect translation efficiency (22,23). Sequences that are recognized by microRNAs (miRNAs) and other small (20-30 nt) RNAs, including small interfering RNAs (siRNAs) and Piwiinteracting RNAs (piRNAs) (24), also tend to be found largely in 39 UTRs. These small RNAs associate with members of the Argonaute family of small RNA-binding proteins within larger RNA-induced silencing complexes (RISCs) (25).…”

The epigenetic regulation of Dicer and microRNA biogenesis by Panobinostat

“…17 The RISC is responsible for bringing the miR to its target mRNAs, where it binds to the 3 0 UTR and leads to translation inhibition or degradation of the target mRNA. 19 Dicer is essential for proper embryonic development, as well as organogenesis in vertebrates. An embryonic knockout of Dicer is lethal in mice.…”