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ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA

BACKGROUND: Reversible enzymatic methylation of mammalian mRNA is widespread and serves crucial regulatory functions, but little is known to what degree chemical alkylators mediate overlapping modifications and whether cells distinguish aberrant from canonical methylations. METHODS: Here we use quan...

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Autores principales: Wollen, Kristian Lied, Hagen, Lars, Vågbø, Cathrine B., Rabe, Renana, Iveland, Tobias S., Aas, Per Arne, Sharma, Animesh, Sporsheim, Bjørnar, Erlandsen, Hilde O., Palibrk, Vuk, Bjørås, Magnar, Fonseca, Davi M., Mosammaparast, Nima, Slupphaug, Geir
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254245/
https://www.ncbi.nlm.nih.gov/pubmed/34217309
http://dx.doi.org/10.1186/s12967-021-02948-6
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author Wollen, Kristian Lied
Hagen, Lars
Vågbø, Cathrine B.
Rabe, Renana
Iveland, Tobias S.
Aas, Per Arne
Sharma, Animesh
Sporsheim, Bjørnar
Erlandsen, Hilde O.
Palibrk, Vuk
Bjørås, Magnar
Fonseca, Davi M.
Mosammaparast, Nima
Slupphaug, Geir
author_facet Wollen, Kristian Lied
Hagen, Lars
Vågbø, Cathrine B.
Rabe, Renana
Iveland, Tobias S.
Aas, Per Arne
Sharma, Animesh
Sporsheim, Bjørnar
Erlandsen, Hilde O.
Palibrk, Vuk
Bjørås, Magnar
Fonseca, Davi M.
Mosammaparast, Nima
Slupphaug, Geir
author_sort Wollen, Kristian Lied
collection PubMed
description BACKGROUND: Reversible enzymatic methylation of mammalian mRNA is widespread and serves crucial regulatory functions, but little is known to what degree chemical alkylators mediate overlapping modifications and whether cells distinguish aberrant from canonical methylations. METHODS: Here we use quantitative mass spectrometry to determine the fate of chemically induced methylbases in the mRNA of human cells. Concomitant alteration in the mRNA binding proteome was analyzed by SILAC mass spectrometry. RESULTS: MMS induced prominent direct mRNA methylations that were chemically identical to endogenous methylbases. Transient loss of 40S ribosomal proteins from isolated mRNA suggests that aberrant methylbases mediate arrested translational initiation and potentially also no-go decay of the affected mRNA. Four proteins (ASCC3, YTHDC2, TRIM25 and GEMIN5) displayed increased mRNA binding after MMS treatment. ASCC3 is a binding partner of the DNA/RNA demethylase ALKBH3 and was recently shown to promote disassembly of collided ribosomes as part of the ribosome quality control (RQC) trigger complex. We find that ASCC3-deficient cells display delayed removal of MMS-induced 1-methyladenosine (m(1)A) and 3-methylcytosine (m(3)C) from mRNA and impaired formation of MMS-induced P-bodies. CONCLUSIONS: Our findings conform to a model in which ASCC3-mediated disassembly of collided ribosomes allows demethylation of aberrant m(1)A and m(3)C by ALKBH3. Our findings constitute first evidence of selective sanitation of aberrant mRNA methylbases over their endogenous counterparts and warrant further studies on RNA-mediated effects of chemical alkylators commonly used in the clinic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-021-02948-6.
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spelling pubmed-82542452021-07-06 ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA Wollen, Kristian Lied Hagen, Lars Vågbø, Cathrine B. Rabe, Renana Iveland, Tobias S. Aas, Per Arne Sharma, Animesh Sporsheim, Bjørnar Erlandsen, Hilde O. Palibrk, Vuk Bjørås, Magnar Fonseca, Davi M. Mosammaparast, Nima Slupphaug, Geir J Transl Med Research BACKGROUND: Reversible enzymatic methylation of mammalian mRNA is widespread and serves crucial regulatory functions, but little is known to what degree chemical alkylators mediate overlapping modifications and whether cells distinguish aberrant from canonical methylations. METHODS: Here we use quantitative mass spectrometry to determine the fate of chemically induced methylbases in the mRNA of human cells. Concomitant alteration in the mRNA binding proteome was analyzed by SILAC mass spectrometry. RESULTS: MMS induced prominent direct mRNA methylations that were chemically identical to endogenous methylbases. Transient loss of 40S ribosomal proteins from isolated mRNA suggests that aberrant methylbases mediate arrested translational initiation and potentially also no-go decay of the affected mRNA. Four proteins (ASCC3, YTHDC2, TRIM25 and GEMIN5) displayed increased mRNA binding after MMS treatment. ASCC3 is a binding partner of the DNA/RNA demethylase ALKBH3 and was recently shown to promote disassembly of collided ribosomes as part of the ribosome quality control (RQC) trigger complex. We find that ASCC3-deficient cells display delayed removal of MMS-induced 1-methyladenosine (m(1)A) and 3-methylcytosine (m(3)C) from mRNA and impaired formation of MMS-induced P-bodies. CONCLUSIONS: Our findings conform to a model in which ASCC3-mediated disassembly of collided ribosomes allows demethylation of aberrant m(1)A and m(3)C by ALKBH3. Our findings constitute first evidence of selective sanitation of aberrant mRNA methylbases over their endogenous counterparts and warrant further studies on RNA-mediated effects of chemical alkylators commonly used in the clinic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-021-02948-6. BioMed Central 2021-07-03 /pmc/articles/PMC8254245/ /pubmed/34217309 http://dx.doi.org/10.1186/s12967-021-02948-6 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Wollen, Kristian Lied
Hagen, Lars
Vågbø, Cathrine B.
Rabe, Renana
Iveland, Tobias S.
Aas, Per Arne
Sharma, Animesh
Sporsheim, Bjørnar
Erlandsen, Hilde O.
Palibrk, Vuk
Bjørås, Magnar
Fonseca, Davi M.
Mosammaparast, Nima
Slupphaug, Geir
ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA
title ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA
title_full ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA
title_fullStr ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA
title_full_unstemmed ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA
title_short ALKBH3 partner ASCC3 mediates P-body formation and selective clearance of MMS-induced 1-methyladenosine and 3-methylcytosine from mRNA
title_sort alkbh3 partner ascc3 mediates p-body formation and selective clearance of mms-induced 1-methyladenosine and 3-methylcytosine from mrna
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254245/
https://www.ncbi.nlm.nih.gov/pubmed/34217309
http://dx.doi.org/10.1186/s12967-021-02948-6
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