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Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes

Trypanosome U-insertion/deletion RNA editing in mitochondrial mRNAs involves guide RNAs (gRNAs) and the auxiliary RNA editing substrate binding complex (RESC) and RNA editing helicase 2 complex (REH2C). RESC and REH2C stably copurify with editing mRNAs but the functional interplay between these comp...

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Autores principales: Kumar, Vikas, Ivens, Alasdair, Goodall, Zachary, Meehan, Joshua, Doharey, Pawan Kumar, Hillhouse, Andrew, Hurtado, Daniel Osorio, Cai, James J., Zhang, Xiuren, Schnaufer, Achim, Cruz-Reyes, Jorge
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668249/
https://www.ncbi.nlm.nih.gov/pubmed/32873716
http://dx.doi.org/10.1261/rna.076513.120
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author Kumar, Vikas
Ivens, Alasdair
Goodall, Zachary
Meehan, Joshua
Doharey, Pawan Kumar
Hillhouse, Andrew
Hurtado, Daniel Osorio
Cai, James J.
Zhang, Xiuren
Schnaufer, Achim
Cruz-Reyes, Jorge
author_facet Kumar, Vikas
Ivens, Alasdair
Goodall, Zachary
Meehan, Joshua
Doharey, Pawan Kumar
Hillhouse, Andrew
Hurtado, Daniel Osorio
Cai, James J.
Zhang, Xiuren
Schnaufer, Achim
Cruz-Reyes, Jorge
author_sort Kumar, Vikas
collection PubMed
description Trypanosome U-insertion/deletion RNA editing in mitochondrial mRNAs involves guide RNAs (gRNAs) and the auxiliary RNA editing substrate binding complex (RESC) and RNA editing helicase 2 complex (REH2C). RESC and REH2C stably copurify with editing mRNAs but the functional interplay between these complexes remains unclear. Most steady-state mRNAs are partially edited and include misedited “junction” regions that match neither pre-mRNA nor fully edited transcripts. Editing specificity is central to mitochondrial RNA maturation and function, but its basic control mechanisms remain unclear. Here we applied a novel nucleotide-resolution RNA-seq approach to examine ribosomal protein subunit 12 (RPS12) and ATPase subunit 6 (A6) mRNA transcripts. We directly compared transcripts associated with RESC and REH2C to those found in total mitochondrial RNA. RESC-associated transcripts exhibited site-preferential enrichments in total and accurate edits. REH2C loss-of-function induced similar substrate-specific and site-specific editing effects in total and RESC-associated RNA. It decreased total editing primarily at RPS12 5′ positions but increased total editing at examined A6 3′ positions. REH2C loss-of-function caused site-preferential loss of accurate editing in both transcripts. However, changes in total or accurate edits did not necessarily involve common sites. A few 5′ nucleotides of the initiating gRNA (gRNA-1) directed accurate editing in both transcripts. However, in RPS12, two conserved 3′-terminal adenines in gRNA-1 could direct a noncanonical 2U-insertion that causes major pausing in 3′–5′ progression. In A6, a noncanonical sequence element that depends on REH2C in a region normally targeted by the 3′ half of gRNA-1 may hinder early editing progression. Overall, we defined transcript-specific effects of REH2C loss.
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spelling pubmed-76682492021-12-01 Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes Kumar, Vikas Ivens, Alasdair Goodall, Zachary Meehan, Joshua Doharey, Pawan Kumar Hillhouse, Andrew Hurtado, Daniel Osorio Cai, James J. Zhang, Xiuren Schnaufer, Achim Cruz-Reyes, Jorge RNA Article Trypanosome U-insertion/deletion RNA editing in mitochondrial mRNAs involves guide RNAs (gRNAs) and the auxiliary RNA editing substrate binding complex (RESC) and RNA editing helicase 2 complex (REH2C). RESC and REH2C stably copurify with editing mRNAs but the functional interplay between these complexes remains unclear. Most steady-state mRNAs are partially edited and include misedited “junction” regions that match neither pre-mRNA nor fully edited transcripts. Editing specificity is central to mitochondrial RNA maturation and function, but its basic control mechanisms remain unclear. Here we applied a novel nucleotide-resolution RNA-seq approach to examine ribosomal protein subunit 12 (RPS12) and ATPase subunit 6 (A6) mRNA transcripts. We directly compared transcripts associated with RESC and REH2C to those found in total mitochondrial RNA. RESC-associated transcripts exhibited site-preferential enrichments in total and accurate edits. REH2C loss-of-function induced similar substrate-specific and site-specific editing effects in total and RESC-associated RNA. It decreased total editing primarily at RPS12 5′ positions but increased total editing at examined A6 3′ positions. REH2C loss-of-function caused site-preferential loss of accurate editing in both transcripts. However, changes in total or accurate edits did not necessarily involve common sites. A few 5′ nucleotides of the initiating gRNA (gRNA-1) directed accurate editing in both transcripts. However, in RPS12, two conserved 3′-terminal adenines in gRNA-1 could direct a noncanonical 2U-insertion that causes major pausing in 3′–5′ progression. In A6, a noncanonical sequence element that depends on REH2C in a region normally targeted by the 3′ half of gRNA-1 may hinder early editing progression. Overall, we defined transcript-specific effects of REH2C loss. Cold Spring Harbor Laboratory Press 2020-12 /pmc/articles/PMC7668249/ /pubmed/32873716 http://dx.doi.org/10.1261/rna.076513.120 Text en © 2020 Kumar et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Article
Kumar, Vikas
Ivens, Alasdair
Goodall, Zachary
Meehan, Joshua
Doharey, Pawan Kumar
Hillhouse, Andrew
Hurtado, Daniel Osorio
Cai, James J.
Zhang, Xiuren
Schnaufer, Achim
Cruz-Reyes, Jorge
Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes
title Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes
title_full Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes
title_fullStr Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes
title_full_unstemmed Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes
title_short Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes
title_sort site-specific and substrate-specific control of accurate mrna editing by a helicase complex in trypanosomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7668249/
https://www.ncbi.nlm.nih.gov/pubmed/32873716
http://dx.doi.org/10.1261/rna.076513.120
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