DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome

Abstract

Transposable elements are viewed as 'selfish genetic elements', yet they contribute to gene regulation and genome evolution in diverse ways. More than half of the human genome consists of transposable elements. Alu elements belong to the short interspersed nuclear element (SINE) family of repetitive elements, and with over 1 million insertions they make up more than 10% of the human genome. Despite their abundance and the potential evolutionary advantages they confer, Alu elements can be mutagenic to the host as they can act as splice acceptors, inhibit translation of mRNAs and cause genomic instability. Alu elements are the main targets of the RNA-editing enzyme ADAR and the formation of Alu exons is suppressed by the nuclear ribonucleoprotein HNRNPC, but the broad effect of massive secondary structures formed by inverted-repeat Alu elements on RNA processing in the nucleus remains unknown. Here we show that DHX9, an abundant nuclear RNA helicase, binds specifically to inverted-repeat Alu elements that are transcribed as parts of genes. Loss of DHX9 leads to an increase in the number of circular-RNA-producing genes and amount of circular RNAs, translational repression of reporters containing inverted-repeat Alu elements, and transcriptional rewiring (the creation of mostly nonsensical novel connections between exons) of susceptible loci. Biochemical purifications of DHX9 identify the interferon-inducible isoform of ADAR (p150), but not the constitutively expressed ADAR isoform (p110), as an RNA-independent interaction partner. Co-depletion of ADAR and DHX9 augments the double-stranded RNA accumulation defects, leading to increased circular RNA production, revealing a functional link between these two enzymes. Our work uncovers an evolutionarily conserved function of DHX9. We propose that it acts as a nuclear RNA resolvase that neutralizes the immediate threat posed by transposon insertions and allows these elements to evolve as tools for the post-transcriptional regulation of gene expression.

Post-transcriptional regulation of LINE-1 retrotransposition by AID/APOBEC and ADAR deaminases

“…Finally, we have preliminary results showing that ADAR1 may repress Alu retrotransposition in vitro (Orecchini et al unpublished), and these results are in agreement with recently published data by Aktas and colleagues (Aktaş et al 2017), suggesting that ADAR1 p150 and DHX9 RNA helicase may protect cells from transposon insertions. Noteworthy, as mentioned above, the vast majority of known A-to-I editing events occur in the RNA duplex formed between adjacent inverted repetitive elements (in particular Alu; Bazak et al 2014;Ramaswami et al 2012), thus it will be of great interest to test whether ADAR1 editing activity is critical for the suppression of Alu retrotransposition in vivo or, as for L1 suppression, editing is dispensable.…”

Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer

“…To this end, through conducting an unbiased screening for ADARs-interacting proteins using immunoprecipitation (IP) coupled with mass spectrometry (co-IP/MS), DEAH box helicase 9 (DHX9), also known as RNA helicase A (RHA) or nuclear DNA helicase II (NDH II), was identified as a ADARs-binding partner which forms a complex with ADAR1 and ADAR2 in the nucleus. Specific to its roles in RNA metabolism, DHX9 is known to be involved in translation (21), short interfering RNA (siRNA) (22) and circular RNA processing (23). …”

Multifaceted roles of complementary sequences on circRNA formation

“…It should be noted though that some circRNAs are processed without the regulation of complementary sequences, Such as CDR1as [7]. Interestingly, trans-factors are also suggested to be involved in circRNA formation together with ciscomplementary sequences [33,34]. Finally, how circRNAs are exported and degraded also remains to be addressed.…”

“…Very recently, by using genome-wide siRNA screening and an efficient circRNA expression reporter, we have identified a series of protein factors as key regulators in circRNA biogenesis [33], including those involved in immune responses. Some protein factors regulate circRNA biogenesis in a combinatorial manner by especially associating with intronic Alu elements [33,34]. Interestingly, a number of previously-unannotated exons were identified in circRNAs, but not in their linear RNA counterparts [16].…”