Endogenous Double-Stranded RNA

Abstract

The birth of long non-coding RNAs (lncRNAs) is closely associated with the presence and activation of repetitive elements in the genome. The transcription of endogenous retroviruses as well as long and short interspersed elements is not only essential for evolving lncRNAs but is also a significant source of double-stranded RNA (dsRNA). From an lncRNA-centric point of view, the latter is a minor source of bother in the context of the entire cell; however, dsRNA is an essential threat. A viral infection is associated with cytoplasmic dsRNA, and endogenous RNA hybrids only differ from viral dsRNA by the 5' cap structure. Hence, a multi-layered defense network is in place to protect cells from viral infections but tolerates endogenous dsRNA structures. A first line of defense is established with compartmentalization; whereas endogenous dsRNA is found predominantly confined to the nucleus and the mitochondria, exogenous dsRNA reaches the cytoplasm. Here, various sensor proteins recognize features of dsRNA including the 5' phosphate group of viral RNAs or hybrids with a particular length but not specific nucleotide sequences. The sensors trigger cellular stress pathways and innate immunity via interferon signaling but also induce apoptosis via caspase activation. Because of its central role in viral recognition and immune activation, dsRNA sensing is implicated in autoimmune diseases and used to treat cancer.

Keywords: antisense transcript; double-stranded RNA (dsRNA); innate immunity; repetitive DNA elements (RE).

Figure 1

Schematic representation of repetitive elements in the human genome associated with double-stranded RNA (dsRNA) formation. LINE 1 and endogenous retroviruses (ERVs) give potential rise to long dsRNA structures formed from convergent transcripts or hairpin structures from read-through transcription of head-to-head/tail-to-tail arranged elements. Alu elements are much shorter and form hairpin structures as well as “open” dsRNA hybrids, though the intermolecular duplexes are rare. Alu elements are the predominant target for adenosine deaminase acting on RNA (ADAR)-mediated adenosine-to-inosine (A-to-I) editing. LTRs function as bi-directional promoters. ORF, open reading frame; GAG (group specific antigen), POL (reverse transcriptase), ENV (envelope protein), retroviral proteins; UTR, untranslated region; LTR, long terminal repeat. Figure created with Biorender.com.

Figure 2

Double-stranded RNA (dsRNA) formation from sense–antisense transcripts. Natural antisense transcripts are processed and potentially reach the cytoplasm, where they interact with the sense transcript. In somatic cells, the level of sense–antisense hybrids is low, and there is no evidence of ADAR editing, for example, nor is dsRNA immune signaling triggered. Various mechanisms (RNA interference, RNA masking, RNA editing and dsRNA signaling) are potentially triggered by the dsRNA, depending on the cellular context. In male germ cells and during early embryogenesis, sense–antisense dsRNA formation may play a general, system-relevant role. Figure created with Biorender.com.

Figure 3

Double-stranded RNA (dsRNA) sensor proteins and activation of innate immunity. Viral dsRNA (including 5′ phosphorylation) or dsRNA from mitochondria and repetitive elements in the cytoplasm are recognized by dsRNA sensors retinoic acid-inducible gene I (RIG1), melanoma differentiation-associated gene 5 (MDA5), protein kinase R (PKR) and ADAR. RIG1 requires the 5′ phosphate group to initiate oligomerization, and MDA5 forms long dsRNA-dependent polymers. Both structures induce mitochondrial antiviral signaling (MAVS) polymerization and, eventually, caspase and interferon signaling. PKR binds short dsRNA molecules, dimerizes and becomes activated through autophosphorylation. Activated PKR dissociates from dsRNA, phosphorylates eukaryotic initiation factor 2α (eIF2α) (which, in turn, inhibits translation globally) and triggers an interferon response. ADAR is present in both the nucleus and cytoplasm and antagonizes dsRNA signaling by melting the RNA hybrid. Figure created with Biorender.com.