Effects of length and location on the cellular response to double-stranded RNA

Abstract

Since double-stranded RNA (dsRNA) has not until recently generally been thought to be deliberately expressed in cells, it has commonly been assumed that the major source of cellular dsRNA is viral infections. In this view, the cellular responses to dsRNA would be natural and perhaps ancient antiviral responses. While the cell may certainly react to some dsRNAs as an antiviral response, this does not represent the only response or even, perhaps, the major one. A number of recent observations have pointed to the possibility that dsRNA molecules are not seen only as evidence of viral infection or recognized for degradation because they cannot be translated. In some instances they may also play important roles in normal cell growth and function. The purpose of this review is to outline our current understanding of the fate of dsRNA in cells, with a focus on the apparent fact that their fates and functions appear to depend critically not only on where in the cell dsRNA molecules are found, but also on how long they are and perhaps on how abundant they are.

FIG. 1.

Signaling pathways of long dsRNAs in the cytoplasm. The major known pathways of signaling by long cytoplasmic dsRNAs are shown and are discussed in detail in the text. Most long cytoplasmic dsRNAs result from virus infections. Such dsRNAs can bind to and activate PKR and 2′,5′-AS as well as activating the interferon pathway. Activated PKR phosphorylates a number of targets, including the translation factor eIF2α and the IκB protein, leading to translation inhibition and effects on gene expression in the nucleus. Activated 2′,5′-AS leads to activation of RNase L, which degrades mRNAs. As discussed in the text, long dsRNAs can also lead to apoptosis.

FIG. 2.

Domain structures of some key proteins involved in the response of cells to dsRNA. The proteins are discussed in detail in the text, and the conserved domains are shown in colored boxes and identified at the bottom. The numbers refer to amino acid chain lengths.

FIG. 3.

Mechanism of RNAi. In mammalian cells, long dsRNAs are trimmed in the nucleus by Dicer to siRNAs of 21 to 23 bp, which are then assembled into RISCs. During or after the assembly process, the two siRNA strands are unwound, and only one remains in active RISCs. These recognize their cytoplasmic mRNA targets by complementarity base pairing and direct mRNA degradation. In the case of micro-RNAs, nuclear precursors are first trimmed by the Drosha enzyme into highly structured RNAs of about 70 nucleotides in length. In the cytoplasm, these are further processed by Dicer to yield mature micro-RNAs that assemble into complexes related to RISCs. In this case, target sequences in mRNA 3′ untranslated regions are recognized by imperfect base pairing (indicated as a yellow bar in the siRNA-mRNA hybrid at the bottom) and lead to translation inhibition by a still-unclear mechanism. See the text for details.

FIG. 4.

One fate of long dsRNAs in the nucleus. Duplex RNAs produced by antisense transcription or transcriptional readthrough are promiscuously edited by ADAR enzymes, generating RNAs with extensive adenosine-to-inosine modifications. These molecules are bound tightly and cooperatively to a nuclear matrix-associated complex of p54nrb, PTB-associated splicing factor, and matrin 3, which prevents their export to the cytoplasm (433). RNAs with only one or a few inosines are not tightly bound and are allowed to leave the nucleus.

FIG. 5.

Nuclear dsRNAs might also induce heterochromatin formation. Transcription from repetitive elements, retrotransposons, and DNA satellite sequences, such as in centromeres and telomeres, might generate dsRNAs. In one model, developed primarily from work with S. pombe (see the text for details), this RNA is processed by the RNAi machinery to generate siRNAs that, by an unknown mechanism, lead to histone methylation, DNA methylation, and ultimately heterochromatin. On the right, and discussed in the text, is suggested a hypothetical pathway by which the editing machinery could also influence the formation of heterochromatin, either by an independent mechanism or by modulating the RNAi-based pathway.