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Visualizing adenosine-to-inosine RNA editing in single mammalian cells.

ABSTRACT: Conversion of adenosine to inosine is a frequent type of RNA editing, but important details about the biology of this conversion remain unknown because of a lack of imaging tools. We developed inoFISH to directly visualize and quantify adenosine-to-inosine-edited transcripts in situ. We found that editing of the GRIA2, EIF2AK2, and NUP43 transcripts is uncorrelated with nuclear localization and paraspeckle association. Further, NUP43 exhibits constant editing levels between single cells, while GRIA2 editing levels vary.

SUBMITTER: Mellis IA

PROVIDER: S-EPMC5542810 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Visualizing adenosine-to-inosine RNA editing in single mammalian cells.

Mellis Ian A IA Gupte Rohit R Raj Arjun A Rouhanifard Sara H SH

Nature methods 20170612 8

Conversion of adenosine to inosine is a frequent type of RNA editing, but important details about the biology of this conversion remain unknown because of a lack of imaging tools. We developed inoFISH to directly visualize and quantify adenosine-to-inosine-edited transcripts in situ. We found that editing of the GRIA2, EIF2AK2, and NUP43 transcripts is uncorrelated with nuclear localization and paraspeckle association. Further, NUP43 exhibits constant editing levels between single cells, while G ...[more]

PMID: 28604724

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Increased adenosine-to-inosine RNA editing in rheumatoid arthritis.

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| S-EPMC7479519 | biostudies-literature

Identification of Adenosine-to-Inosine RNA Editing with Acrylonitrile Reagents.

Project description:New chemical probes have been designed to facilitate the identification of adenosine-to-inosine (A-to-I) edited RNAs. These reagents combine a conjugate acceptor for selective inosine covalent modification with functional groups for bioorthogonal biotinylation. The resulting biotinylated RNA was enriched and verified with RT-qPCR. This powerful chemical approach provides new opportunities to identify and quantify A-to-I editing sites.

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Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Project description:A-to-I RNA editing by ADARs is a post-transcriptional mechanism for expanding the proteomic repertoire. Genetic recoding by editing was so far observed for only a few mammalian RNAs that are predominantly expressed in nervous tissues. However, as these editing targets fail to explain the broad and severe phenotypes of ADAR1 knockout mice, additional targets for editing by ADARs were always expected. Using comparative genomics and expressed sequence analysis, we identified and experimentally verified four additional candidate human substrates for ADAR-mediated editing: FLNA, BLCAP, CYFIP2 and IGFBP7. Additionally, editing of three of these substrates was verified in the mouse while two of them were validated in chicken. Interestingly, none of these substrates encodes a receptor protein but two of them are strongly expressed in the CNS and seem important for proper nervous system function. The editing pattern observed suggests that some of the affected proteins might have altered physiological properties leaving the possibility that they can be related to the phenotypes of ADAR1 knockout mice.

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Adenosine-to-inosine RNA editing shapes transcriptome diversity in primates.

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Identification of Diverse Adenosine-to-Inosine RNA Editing Subtypes in Colorectal Cancer.

Project description:PurposeRNA editing generates protein diversity by altering RNA sequences in coding regions without changing the overall DNA sequence. Adenosine-to-inosine (A-to-I) RNA editing events have recently been reported in some types of cancer, but they are rare in human colorectal cancer (CRC). Therefore, this study was conducted to identify diverse RNA editing in CRC.Materials and methodsWe compared transcriptome data of 39 CRC samples and paired adjacent tissues from The Cancer Genome Atlas database to identify RNA editing patterns in CRC, focusing on canonical A-to-I RNA edits in coding sequence regions. We investigated nonsynonymous RNA editing patterns by comparing tumor and normal tissue transcriptome data.ResultsThe number of RNA edits varied from 12 to 42 per sample. We also observed that hypoand hyper-RNA editing patterns were distinguishable within the samples. We found 10 recurrent nonsynonymous RNA editing candidates in nine genes (PDLIM, NEIL1, SRP9, GLI1, APMAP, IGFBP7, ZNF358, COPA, and ZNF587B) and validated some by Sanger sequencing and the inosine chemical erasing assay. We further showed that editing at these positions was performed by the adenosine deaminase acting on RNA 1 enzyme. Most of these genes are hypoedited in CRC, but editing of GLI1 was increased in cancer tissues compared with normal tissues.ConclusionOur results show that nonsynonymous RNA editing patterns can be used to identify CRC patients and could serve as novel biomarkers for CRC.

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Proteogenomics of adenosine-to-inosine RNA editing in fruit fly

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2018-10-25 | PXD009590 | Pride

Proteogenomics of adenosine-to-inosine RNA editing in fruit fly

2019-03-13 | PXD004949 | Pride

Testicular adenosine to inosine RNA editing in the mouse

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2016-12-24 | GSE92870 | GEO

Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis.

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