| 1. |
- Chammiran, Daniel, et al.
(författare)
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A distant cis acting intronic element induces site-selective RNA editing
- 2012
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 40:19, s. 9876-9886
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 2. |
- Daniel, Chammiran, et al.
(författare)
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Adenosine-to-Inosine RNA Editing Affects Trafficking of the γ-Aminobutyric Acid Type A (GABAA) Receptor
- 2011
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 286:3, s. 2031-2040
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Tidskriftsartikel (refereegranskat)abstract
- Recoding by adenosine-to-inosine RNA editing plays an important role in diversifying proteins involved in neurotransmission. We have previously shown that the Gabra-3 transcript, coding for the α3 subunit of the GABAA receptor is edited in mouse, causing an isoleucine to methionine (I/M) change. Here we show that this editing event is evolutionarily conserved from human to chicken. Analyzing recombinant GABAA receptor subunits expressed in HEK293 cells, our results suggest that editing at the I/M site in α3 has functional consequences on receptor expression. We demonstrate that I/M editing reduces the cell surface and the total number of α3 subunits. The reduction in cell surface levels is independent of the subunit combination as it is observed for α3 in combination with either the β2 or the β3 subunit. Further, an amino acid substitution at the corresponding I/M site in the α1 subunit has a similar effect on cell surface presentation, indicating the importance of this site for receptor trafficking. We show that the I/M editing during brain development is inversely related to the α3 protein abundance. Our results suggest that editing controls trafficking of α3-containing receptors and may therefore facilitate the switch of subunit compositions during development as well as the subcellular distribution of α subunits in the adult brain.
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| 3. |
- Daniel, Chammiran, et al.
(författare)
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Alu elements shape the primate transcriptome by cis-regulation of RNA editing
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:2
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Tidskriftsartikel (refereegranskat)abstract
- Background: RNA editing by adenosine to inosine deamination is a widespread phenomenon, particularly frequent in the human transcriptome, largely due to the presence of inverted Alu repeats and their ability to form double-stranded structures - a requisite for ADAR editing. While several hundred thousand editing sites have been identified within these primate-specific repeats, the function of Alu-editing has yet to be elucidated. Results: We show that inverted Alu repeats, expressed in the primate brain, can induce site-selective editing in cis on sites located several hundred nucleotides from the Alu elements. Furthermore, a computational analysis, based on available RNA-seq data, finds that site-selective editing occurs significantly closer to edited Alu elements than expected. These targets are poorly edited upon deletion of the editing inducers, as well as in homologous transcripts from organisms lacking Alus. Sequences surrounding sites near edited Alus in UTRs, have been subjected to a lesser extent of evolutionary selection than those far from edited Alus, indicating that their editing generally depends on cis-acting Alus. Interestingly, we find an enrichment of primate-specific editing within encoded sequence or the UTRs of zinc finger-containing transcription factors. Conclusions: We propose a model whereby primate-specific editing is induced by adjacent Alu elements that function as recruitment elements for the ADAR editing enzymes. The enrichment of site-selective editing with potentially functional consequences on the expression of transcription factors indicates that editing contributes more profoundly to the transcriptomic regulation and repertoire in primates than previously thought.
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| 4. |
- Daniel, Chammiran, et al.
(författare)
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Editing inducer elements increases A-to-I editing efficiency in the mammalian transcriptome
- 2017
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 18
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Daniel, Chammiran, 1968-
(författare)
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Regulation and Function of RNA Editing in the Mammalian Brain
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Adenosine (A) to inosine (I) RNA editing is a widespread post-transcriptional mechanism in eukaryotes that increases the protein diversity. Adenosine deaminases acting on RNA (ADARs) are the enzymes that catalyze this conversion. The diversity generated by ADAR enzymes occurs mainly in the brain where they target transcripts coding for proteins in the central nervous system (CNS).We have determined the editing frequency of known ADAR substrates during development of the mouse brain using the large-scale 454-sequencing method. We show in paper I that editing is regulated during development of the brain, where it increases along with the maturation of the brain. We propose that the unedited isoform of proteins are required for the undeveloped brain while the edited isoforms are more suitable for the mature brain.In paper II we show that substrates with multiple editing sites, one specific principle adenosine is favored for initial editing. We demonstrate that within these substrates, editing is coupled when adenosines are located in multiples of twelve nucleotides. These edited adenosines reside on the same side in the tertiary RNA helical structure. A model is suggested where kinetically favored structures at principle editing sites attract ADAR to the substrate, followed by editing at sites that are structurally adjacent to the initiation site.Editing of the mammalian Gabra-3 transcripts coding for the GABAA receptor α3 subunits recodes an isoleucine (I) to a methionine (M) referred as the I/M site. In paper III we demonstrate that receptors containing edited α3 subunits have altered trafficking properties compared to receptors containing unedited α3 subunits. We suggest that the amino acid residue change, affects protein interactions required for stability and trafficking of GABAA receptors. We propose that the biological function of editing is to reduce the number of α3 subunits in favor of other α subunits.The dsRNA structure at the I/M site in the Gabra-3 transcript is formed within the exon 9 sequence. We show in paper IV that a conserved intronic dsRNA structure in the downstream intron is required for editing to occur at the I/M site. We demonstrate that in the context of this intronic duplex also non-ADAR substrates can be edited. We propose that the intronic dsRNA stabilize the short I/M stem structure, thereby increasing the ability of ADAR to bind and edit the I/M site. These discoveries have expanded the knowledge in how ADAR editing is employed to supply the development of the brain as well as the RNA structure requirement for editing to occur.
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| 6. |
- Daniel, Chammiran, et al.
(författare)
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RNA editing and its impact on GABAa receptor function
- 2009
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Ingår i: Biochemical Society Transactions. - : Biochemical Society. - 0300-5127 .- 1470-8752. ; 37, s. 1399-1403
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Tidskriftsartikel (refereegranskat)abstract
- A-to-I (adenosine-to-inosine) RNA editing catalysed by the ADARs (adenosine deaminases that act on RNA) is a post-transcriptional event that contributes to protein diversity in metazoans. In mammalian neuronal ion channels, editing alters functionally important amino acids and creates receptor subtypes important for the development of the nervous system. The excitatory AMPA (α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid) and kainate glutamate receptors, as well as the inhibitory GABAA [GABA (γ-aminobutyric acid) type A] receptor, are subject to A-to-I RNA editing. Editing affects several features of the receptors, including kinetics, subunit assembly and cell-surface expression. Here, we discuss the regulation of editing during brain maturation and the impact of RNA editing on the expression of different receptor subtypes.
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| 7. |
- Daniel, Chammiran, et al.
(författare)
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RNA editing of non-coding RNA and its role in gene regulation
- 2015
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Ingår i: Biochimie. - : Elsevier BV. - 0300-9084 .- 1638-6183. ; 117, s. 22-27
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Forskningsöversikt (refereegranskat)abstract
- It has for a long time been known that repetitive elements, particularly Alu sequences in human, are edited by the adenosine deaminases acting on RNA, ADAR, family. The functional interpretation of these events has been even more difficult than that of editing events in coding sequences, but today there is an emerging understanding of their downstream effects. A surprisingly large fraction of the human transcriptome contains inverted Alu repeats, often forming long double stranded structures in RNA transcripts, typically occurring in introns and UTRs of protein coding genes. Alu repeats are also common in other primates, and similar inverted repeats can frequently be found in non-primates, although the latter are less prone to duplex formation. In human, as many as 700,000 Alu elements have been identified as substrates for RNA editing, of which many are edited at several sites. In fact, recent advancements in transcriptome sequencing techniques and bioinformatics have revealed that the human editome comprises at least a hundred million adenosine to inosine (A-to-I) editing sites in Alu sequences. Although substantial additional efforts are required in order to map the editome, already present knowledge provides an excellent starting point for studying cis-regulation of editing. In this review, we will focus on editing of long stem loop structures in the human transcriptome and how it can effect gene expression.
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| 8. |
- Daniel, Chammiran, et al.
(författare)
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The role of Alu elements in the cis-regulation of RNA processing
- 2015
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Ingår i: Cellular and Molecular Life Sciences (CMLS). - : Springer Science and Business Media LLC. - 1420-682X .- 1420-9071. ; 72:21, s. 4063-4076
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Forskningsöversikt (refereegranskat)abstract
- The human genome is under constant invasion by retrotransposable elements. The most successful of these are the Alu elements; with a copy number of over a million, they occupy about 10 % of the entire genome. Interestingly, the vast majority of these Alu insertions are located in gene-rich regions, and one-third of all human genes contains an Alu insertion. Alu sequences are often embedded in gene sequence encoding pre-mRNAs and mature mRNAs, usually as part of their intron or UTRs. Once transcribed, they can regulate gene expression as well as increase the number of RNA isoforms expressed in a tissue or a species. They also regulate the function of other RNAs, like microRNAs, circular RNAs, and potentially long non-coding RNAs. Mechanistically, Alu elements exert their effects by influencing diverse processes, such as RNA editing, exonization, and RNA processing. In so doing, they have undoubtedly had a profound effect on human evolution.
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| 9. |
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| 10. |
- Ensterö, Mats, et al.
(författare)
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Recognition and coupling af A-to-I edited sites are determined by the tertiary structure of the RNA
- 2009
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 37:20, s. 6916-6926
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Tidskriftsartikel (refereegranskat)abstract
- Adenosine-to-inosine (A-to-I) editing has been shown to be an important mechanism that increases protein diversity in the brain of organisms from human to fly. The family of ADAR enzymes converts some adenosines of RNA duplexes to inosines through hydrolytic deamination. The adenosine recognition mechanism is still largely unknown. Here, to investigate it, we analyzed a set of selectively edited substrates with a cluster of edited sites. We used a large set of individual transcripts sequenced by the 454 sequencing technique. On average, we analyzed 570 single transcripts per edited region at four different developmental stages from embryogenesis to adulthood. To our knowledge, this is the first time, large-scale sequencing has been used to determine synchronous editing events. We demonstrate that edited sites are only coupled within specific distances from each other. Furthermore, our results show that the coupled sites of editing are positioned on the same side of a helix, indicating that the three-dimensional structure is key in ADAR enzyme substrate recognition. Finally, we propose that editing by the ADAR enzymes is initiated by their attraction to one principal site in the substrate.
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