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Editing inducer elements increases A-to-I editing efficiency in the mammalian transcriptome
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.ORCID iD: 0000-0002-6636-5841
Number of Authors: 42017 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 18, article id 195Article in journal (Refereed) Published
Abstract [en]

Background: Adenosine to inosine (A-to-I) RNA editing has been shown to be an essential event that plays a significant role in neuronal function, as well as innate immunity, in mammals. It requires a structure that is largely double-stranded for catalysis but little is known about what determines editing efficiency and specificity in vivo. We have previously shown that some editing sites require adjacent long stem loop structures acting as editing inducer elements (EIEs) for efficient editing. Results: The glutamate receptor subunit A2 is edited at the Q/R site in almost 100% of all transcripts. We show that efficient editing at the Q/R site requires an EIE in the downstream intron, separated by an internal loop. Also, other efficiently edited sites are flanked by conserved, highly structured EIEs and we propose that this is a general requisite for efficient editing, while sites with low levels of editing lack EIEs. This phenomenon is not limited to mRNA, as non-coding primary miRNAs also use EIEs to recruit ADAR to specific sites. Conclusions: We propose a model where two regions of dsRNA are required for efficient editing: first, an RNA stem that recruits ADAR and increases the local concentration of the enzyme, then a shorter, less stable duplex that is ideal for efficient and specific catalysis. This discovery changes the way we define and determine a substrate for A-to-I editing. This will be important in the discovery of novel editing sites, as well as explaining cases of altered editing in relation to disease.

Place, publisher, year, edition, pages
2017. Vol. 18, article id 195
Keywords [en]
RNA editing, Adenosine deamination, Glutamate receptor, ADAR, EIE, miRNA
National Category
Environmental Biotechnology Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-148990DOI: 10.1186/s13059-017-1324-xISI: 000413577600002PubMedID: 29061182OAI: oai:DiVA.org:su-148990DiVA, id: diva2:1160820
Available from: 2017-11-28 Created: 2017-11-28 Last updated: 2022-03-23Bibliographically approved
In thesis
1. Diversifying the transcriptome: Adenosine-to-inosine RNA editing in the mammalian brain
Open this publication in new window or tab >>Diversifying the transcriptome: Adenosine-to-inosine RNA editing in the mammalian brain
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Metazoan transcriptomes are extensively modified by adenosine-to-inosine (A-to-I) RNA editing, a process by which adenosines within double-stranded RNA are enzymatically deaminated to form inosines. Inosines has base-pairing characteristics similar to guanosine, meaning that A-to-I RNA editing results in functional rewriting of transcripts, affecting many biological processes. The aim of this thesis was to investigate the regulation and the function of RNA editing in the mammalian brain. We applied a novel method, in situ sequencing (ISS), to detect editing substrates in the developing mouse brain, which revealed regional and cell type-specific editing patterns emerging during development. Additionally, we characterized the structural requirements of site-selective editing and discovered an editing inducer elements (EIEs) as a general feature of efficiently edited substrates. Also edited microRNAs (miRNAs) were found to have EIEs, in the form of neighboring primary miRNA (pri-miRNA) hairpin structures. Site-selective editing has previously been found to increase during brain development. To investigate this developmental increase, we analyzed the regulation of ADAR2, one of the two editing enzymes, in an in vitro model system for neuronal maturation. Here, we observed increased nuclear import of ADAR2 during neuronal maturation, correlating to increased editing levels. Increased expression of the proteins importin-ɑ4 and Pin1 were found to contribute to this increased nuclear import. Finally, we studied editing of members of the miR-379-410 cluster, and we found that in general pri-miRNAs are more frequently edited than the corresponding mature miRNAs, which possibly indicates an inhibitory role of ADAR enzymes on miRNA biogenesis.. However, the opposite trend was observed for miR-376b-3p, which displayed higher editing in its mature form. Studying the editing and biogenesis of miR-376b-3p, we found that ADAR1 edits the miRNA while ADAR2 inhibits its maturation. Furthermore, the two enzymes compete in binding the pri-miRNA. Subsequently, we identified neuronal target genes of the edited miR-376b-3p. These included the 4-aminobutyrate aminotransferase (Abat), the enzyme responsible for the catabolism of the neurotransmitter GABA, and our results indicate that editing of miR-376b-3p can regulate GABAergic signaling.

Place, publisher, year, edition, pages
Stockholm: Department of Molecular Biosciences, the Wenner-Gren Institute, Stockholm University, 2021. p. 73
Keywords
RNA editing, ADAR, microRNA, brain development, neuron
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Bioscience
Identifiers
urn:nbn:se:su:diva-198116 (URN)978-91-7911-680-4 (ISBN)978-91-7911-681-1 (ISBN)
Public defence
2021-12-17, Vivi Täckholmsalen (Q-salen), NPQ-huset, Svante Arrhenius väg 20, also online via Zoom, public link is available at the department website, Stockholm, 10:00 (English)
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Supervisors
Available from: 2021-11-24 Created: 2021-10-27 Last updated: 2022-02-25Bibliographically approved

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Daniel, ChammiranWidmark, AlbinÖhman, Marie

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