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Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase

DNMT3A/3L heterotetramers contain two active centers binding CpG sites at 12 bp distance, however their interaction with DNA not containing this feature is unclear. Using randomized substrates, we observed preferential co-methylation of CpG sites with 6, 9 and 12 bp spacing by DNMT3A and DNMT3A/3L....

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Autores principales: Emperle, Max, Bangalore, Disha M, Adam, Sabrina, Kunert, Stefan, Heil, Hannah S, Heinze, Katrin G, Bashtrykov, Pavel, Tessmer, Ingrid, Jeltsch, Albert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8373138/
https://www.ncbi.nlm.nih.gov/pubmed/34289056
http://dx.doi.org/10.1093/nar/gkab600
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author Emperle, Max
Bangalore, Disha M
Adam, Sabrina
Kunert, Stefan
Heil, Hannah S
Heinze, Katrin G
Bashtrykov, Pavel
Tessmer, Ingrid
Jeltsch, Albert
author_facet Emperle, Max
Bangalore, Disha M
Adam, Sabrina
Kunert, Stefan
Heil, Hannah S
Heinze, Katrin G
Bashtrykov, Pavel
Tessmer, Ingrid
Jeltsch, Albert
author_sort Emperle, Max
collection PubMed
description DNMT3A/3L heterotetramers contain two active centers binding CpG sites at 12 bp distance, however their interaction with DNA not containing this feature is unclear. Using randomized substrates, we observed preferential co-methylation of CpG sites with 6, 9 and 12 bp spacing by DNMT3A and DNMT3A/3L. Co-methylation was favored by AT bases between the 12 bp spaced CpG sites consistent with their increased bending flexibility. SFM analyses of DNMT3A/3L complexes bound to CpG sites with 12 bp spacing revealed either single heterotetramers inducing 40° DNA bending as observed in the X-ray structure, or two heterotetramers bound side-by-side to the DNA yielding 80° bending. SFM data of DNMT3A/3L bound to CpG sites spaced by 6 and 9 bp revealed binding of two heterotetramers and 100° DNA bending. Modeling showed that for 6 bp distance between CpG sites, two DNMT3A/3L heterotetramers could bind side-by-side on the DNA similarly as for 12 bp distance, but with each CpG bound by a different heterotetramer. For 9 bp spacing our model invokes a tetramer swap of the bound DNA. These additional DNA interaction modes explain how DNMT3A and DNMT3A/3L overcome their structural preference for CpG sites with 12 bp spacing during the methylation of natural DNA.
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spelling pubmed-83731382021-08-19 Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase Emperle, Max Bangalore, Disha M Adam, Sabrina Kunert, Stefan Heil, Hannah S Heinze, Katrin G Bashtrykov, Pavel Tessmer, Ingrid Jeltsch, Albert Nucleic Acids Res Nucleic Acid Enzymes DNMT3A/3L heterotetramers contain two active centers binding CpG sites at 12 bp distance, however their interaction with DNA not containing this feature is unclear. Using randomized substrates, we observed preferential co-methylation of CpG sites with 6, 9 and 12 bp spacing by DNMT3A and DNMT3A/3L. Co-methylation was favored by AT bases between the 12 bp spaced CpG sites consistent with their increased bending flexibility. SFM analyses of DNMT3A/3L complexes bound to CpG sites with 12 bp spacing revealed either single heterotetramers inducing 40° DNA bending as observed in the X-ray structure, or two heterotetramers bound side-by-side to the DNA yielding 80° bending. SFM data of DNMT3A/3L bound to CpG sites spaced by 6 and 9 bp revealed binding of two heterotetramers and 100° DNA bending. Modeling showed that for 6 bp distance between CpG sites, two DNMT3A/3L heterotetramers could bind side-by-side on the DNA similarly as for 12 bp distance, but with each CpG bound by a different heterotetramer. For 9 bp spacing our model invokes a tetramer swap of the bound DNA. These additional DNA interaction modes explain how DNMT3A and DNMT3A/3L overcome their structural preference for CpG sites with 12 bp spacing during the methylation of natural DNA. Oxford University Press 2021-07-21 /pmc/articles/PMC8373138/ /pubmed/34289056 http://dx.doi.org/10.1093/nar/gkab600 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Nucleic Acid Enzymes
Emperle, Max
Bangalore, Disha M
Adam, Sabrina
Kunert, Stefan
Heil, Hannah S
Heinze, Katrin G
Bashtrykov, Pavel
Tessmer, Ingrid
Jeltsch, Albert
Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase
title Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase
title_full Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase
title_fullStr Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase
title_full_unstemmed Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase
title_short Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase
title_sort structural and biochemical insight into the mechanism of dual cpg site binding and methylation by the dnmt3a dna methyltransferase
topic Nucleic Acid Enzymes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8373138/
https://www.ncbi.nlm.nih.gov/pubmed/34289056
http://dx.doi.org/10.1093/nar/gkab600
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