Purifying selection of long dsRNA is the first line of defense against false activation of innate immunity

Abstract

Background: Mobile elements comprise a large fraction of metazoan genomes. Accumulation of mobile elements is bound to produce multiple putative double-stranded RNA (dsRNA) structures within the transcriptome. These endogenous dsRNA structures resemble viral RNA and may trigger false activation of the innate immune response, leading to severe damage to the host cell. Adenosine to inosine (A-to-I) RNA editing is a common posttranscriptional modification, abundant within repetitive elements of all metazoans. It was recently shown that a key function of A-to-I RNA editing by ADAR1 is to suppress the immunogenic response by endogenous dsRNAs.Results: Here, we analyze the transcriptomes of dozens of species across the Metazoa and identify a strong genomic selection against endogenous dsRNAs, resulting in their purification from the canonical transcriptome. This purifying selection is especially strong for long and nearly perfect dsRNAs. These are almost absent from mRNAs, but not pre-mRNAs, supporting the notion of selection due to cytoplasmic processes. The few long and nearly perfect structures found in human transcripts are weakly expressed and often heavily edited. Conclusion: Purifying selection of long dsRNA is an important defense mechanism against false activation of innate immunity. This newly identified principle governs the integration of mobile elements into the genome, a major driving force of genome evolution. Furthermore, we find that most ADAR1 activity is not required to prevent an immune response to endogenous dsRNAs. The critical targets of ADAR1 editing are, likely, to be found mostly in non-canonical transcripts.

Immune Sensing Mechanisms that Discriminate Self from Altered Self and Foreign Nucleic Acids

“…However, recent research indicates that the absence of endogenous cytosolic dsRNA is not coincidental. Our genome contains a large number of complementarily inverted mobile elements, particularly Alu elements, which could potentially form long dsRNA ( Reich and Bass, 2019 ), and their overwhelming absence in the cytosol results from both strong purifying transcriptomic selection ( Barak et al., 2020 ) and A-to-I editing of the remaining transcripts by ADAR1 ( Ahmad et al., 2018 ; Chung et al., 2018 ). In addition, mitochondria utilize an RNA helicase, SUV3, and polynucleotide phosphorylase (PNPase) to actively eliminate dsRNA species resulting from bidirectional transcription thus preventing innate immune activation ( Dhir et al., 2018 ; Pajak et al., 2019 ).…”

Increased RNA editing in maternal immune activation model of neurodevelopmental disease

“…The ADAR family of enzymes carry out the common post-transcriptional modification, A-to-I RNA editing, in which ADAR deaminases adenosine to inosine 22 – 24 . This editing is applied to long double-stranded RNA transcripts, which are recognized by MDA5 in the cytoplasm 25 , or to RNA elements in the nucleus. Since inosine is recognized by the ribosome as guanosine during translation, editing can alter the proteome outcome.…”

What do editors do? Understanding the physiological functions of A-to-I RNA editing by adenosine deaminase acting on RNAs

“…As these are spliced before nuclear export, editing by either ADAR1 or ADAR2 at these sites likely does not contribute to the potential immunogenicity of the RNA when cytosolic. Furthermore, many of the repetitive elements do not form ideal substrates for MDA5 (less than 300 bp and imperfect dsRNA structures) and are lowly edited, so the lack of editing is unlikely to directly activate an immune response [ 87 ]. There is evidence for strong purifying selection over evolution against long perfect dsRNA within mature mRNAs, providing further evidence that those within introns are less deleterious and may be more likely to be stochastically edited [ 87 ].…”

“…Furthermore, many of the repetitive elements do not form ideal substrates for MDA5 (less than 300 bp and imperfect dsRNA structures) and are lowly edited, so the lack of editing is unlikely to directly activate an immune response [ 87 ]. There is evidence for strong purifying selection over evolution against long perfect dsRNA within mature mRNAs, providing further evidence that those within introns are less deleterious and may be more likely to be stochastically edited [ 87 ]. The second factor that probably contributes to the ADAR1-specific requirement to suppress immune activation is cellular compartmentalization.…”

“…Barak et al . [ 87 ] studied the transcriptomes of 49 organisms and compared selection for inverted duplicated sequences (that can form long dsRNA) compared with tandem duplicated sequences (which do not form long dsRNA). There was evidence for very strong selection specifically against the inverted sequences in mRNAs.…”