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A-to-I RNA editing: Function and consequences during brain development
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The aim of my thesis has been to study how A-to-I RNA editing of miRNAs is regulated during brain development and the biological function of these editing events.

Using high throughput RNA sequencing, we performed an unbiased search for edited, mature miRNAs in total mouse brain tissue from three developmental stages. We searched for known and novel editing sites within short RNA sequences approximately resembling the length of mature miRNAs.

We can conclude that the gradual increase in editing efficiency seen for most selectively edited sites in transcripts encoding neurotransmission proteins, also applies to miRNAs during development of the mammalian brain. The most striking editing events all occur in the crucial seed sequence, essential for target recognition. These results indicate that A-to-I editing is utilized to diversify target recognition by the miRNAs during development.

Furthermore, our data suggests that specific transcripts, targeted by either non-edited or edited miRNAs, are regulated in a manner that is consistent with the developmental shifts in editing frequencies. One example of this is the developmentally regulated editing of miR-381, targeting the Pum2 transcript in the brain. Pum2 is a translational repressor that regulates many mRNAs shown to be important for neurological functions, including memory formation and learning.

We have further analyzed what determines a substrate to be edited by the ADAR enzymes, specifically in the context of the mammalian GABAA receptor. We found that long stem loop structures located close to exon sequences function as inducers of exonic editing.

Taken together, my research demonstrate the power of combining, RNA-Seq, bioinformatics and specific experimental verifications in order to shed light on the impact of A-to-I editing on the process of RNA interference. Furthermore, we have expanded the knowledge of RNA structure requirements for ADAR editing to occur. 

Place, publisher, year, edition, pages
Stockholm: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University , 2013. , 54 p.
Keyword [en]
RNA editing, miRNAs, Brain development
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-93137ISBN: 978-91-7447-739-9 (print)OAI: oai:DiVA.org:su-93137DiVA: diva2:646229
Public defence
2013-10-11, Nordenskiöldsalen, Geovetenskapens hus, Svante Arrhenius väg 12, Stockholm, 13:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defence the following paper was unpublished and had a status as follows: Paper 3: Manuscript

Available from: 2013-09-19 Created: 2013-09-03 Last updated: 2013-09-10Bibliographically approved
List of papers
1. A-to-I editing of microRNAs in the mammalian brain increases during development
Open this publication in new window or tab >>A-to-I editing of microRNAs in the mammalian brain increases during development
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2012 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 22, no 8, 1477-1487 p.Article in journal (Refereed) Published
Abstract [en]

Adenosine-to-inosine (A-to-I) RNA editing targets double-stranded RNA stem-loop structures in the mammalian brain. It has previously been shown that miRNAs are substrates for A-to-I editing. For the first time, we show that for several definitions of edited miRNA, the level of editing increases with development, thereby indicating a regulatory role for editing during brain maturation. We use high-throughput RNA sequencing to determine editing levels in mature miRNA, from the mouse transcriptome, and compare these with the levels of editing in pri-miRNA. We show that increased editing during development gradually changes the proportions of the two miR-376a isoforms, which previously have been shown to have different targets. Several other miRNAs that also are edited in the seed sequence show an increased level of editing through development. By comparing editing of pri-miRNA with editing and expression of the corresponding mature miRNA, we also show an editing-induced developmental regulation of miRNA expression. Taken together, our results imply that RNA editing influences the miRNA repertoire during brain maturation.

National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:su:diva-81732 (URN)10.1101/gr.131912.111 (DOI)000307090300010 ()
Note

AuthorCount:5;

Available from: 2012-10-30 Created: 2012-10-30 Last updated: 2017-05-08Bibliographically approved
2. A distant cis acting intronic element induces site-selective RNA editing
Open this publication in new window or tab >>A distant cis acting intronic element induces site-selective RNA editing
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2012 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no 19, 9876-9886 p.Article in journal (Refereed) Published
Abstract [en]

Transcripts have been found to be site selectively edited from adenosine-to-inosine (A-to-I) in the mammalian brain, mostly in genes involved in neurotransmission. While A-to-I editing occurs at double-stranded structures, other structural requirements are largely unknown. We have investigated the requirements for editing at the I/M site in the Gabra-3 transcript of the GABA(A) receptor. We identify an evolutionarily conserved intronic duplex, 150 nt downstream of the exonic hairpin where the I/M site resides, which is required for its editing. This is the first time a distant RNA structure has been shown to be important for A-to-I editing. We demonstrate that the element also can induce editing in related but normally not edited RNA sequences. In human, thousands of genes are edited in duplexes formed by inverted repeats in non-coding regions. It is likely that numerous such duplexes can induce editing of coding regions throughout the transcriptome.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:su:diva-83006 (URN)10.1093/nar/gks691 (DOI)000310377200048 ()
Note

AuthorCount:5;

Available from: 2012-12-05 Created: 2012-12-03 Last updated: 2017-12-07Bibliographically approved
3. Complex post-transcriptional regulation of Pumilio 2 fine-tunes the neuron
Open this publication in new window or tab >>Complex post-transcriptional regulation of Pumilio 2 fine-tunes the neuron
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Highly polarized cells, such as differentiated

neurons, requires a sophisticated network of

regulatory events to control gene expression

in response to different environmental as

well as developmental conditions. In this

study we show how different RNA processing

events can work in concert to regulate gene

expression of Pumillio 2 (Pum2), a

translational repressor important for

neuronal homeostasis as well as memory and

learning. We have previously shown that

miRNAs, encoded within the miR379-410

cluster, which regulate the Pum2 expression

in turn are regulated by A-to-I editing. Here,

we identify an alternative splicing event

within the Pum2 3’UTR that facilitates the

escape of targeting by many of these

miRNAs. We propose that splicing and

editing are two RNA processing events that

can work in concert to fine-tune the

expression of Pum2 and have different

effects depending on the neuronal

subcellular localization of the transcript.

This enables a differential gene expression in

different compartments of the cell such as

cell body and synaptic buds.

National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:su:diva-93321 (URN)
Available from: 2013-09-06 Created: 2013-09-06 Last updated: 2013-09-10

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