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

Aktas, T., Ilik, I. A., Maticzka, D., Bhardwaj, V., Rodrigues, C. P., Mittler, G., et al. (2017). DHX9 Suppresses RNA processing defects originating from the Alu invasion of the human genome. Nature, 544, 115-119. doi:10.1038/nature21715.

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Aktas, Tugce1, Author
Ilik, Ibrahim Avsar1, Author              
Maticzka, Daniel2, Author
Bhardwaj, Vivek1, Author
Rodrigues , Celilia Pessoa1, Author
Mittler, Gerhard1, Author              
Manke, Thomas1, Author              
Backofen, Rolf2, Author
Akhtar, Asifa1, Author              
Affiliations:
1Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, 79108 Freiburg, DE, ou_2243640              
2Institute for Informatics, Albert-Ludwigs University Freiburg, Freiburg, Germany, ou_persistent22              

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 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.

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Language(s): eng - English
 Dates: 2017-04-06
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: DOI: 10.1038/nature21715
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Title: Nature
  Abbreviation : Nature
Source Genre: Journal
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Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: 544 Sequence Number: - Start / End Page: 115 - 119 Identifier: ISSN: 0028-0836
CoNE: https://pure.mpg.de/cone/journals/resource/954925427238