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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 LU orcid ; Heinze, Katrin G ; Bashtrykov, Pavel ; Tessmer, Ingrid and Jeltsch, Albert (2021) In Nucleic Acids Research 49(14). p.8294-8308
Abstract

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... (More)

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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author
; ; ; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
keywords
Binding Sites/genetics, CpG Islands/genetics, DNA/genetics, DNA (Cytosine-5-)-Methyltransferases/genetics, DNA Methylation/genetics, DNA Methyltransferase 3A, DNA Modification Methylases/genetics, Humans, Protein Domains/genetics
in
Nucleic Acids Research
volume
49
issue
14
pages
8294 - 8308
publisher
Oxford University Press
external identifiers
  • pmid:34289056
  • scopus:85112854308
ISSN
1362-4962
DOI
10.1093/nar/gkab600
language
English
LU publication?
no
additional info
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
id
8f02105a-499d-483b-96dc-0e29da484c14
date added to LUP
2025-04-26 12:08:56
date last changed
2025-05-25 07:01:46
@article{8f02105a-499d-483b-96dc-0e29da484c14,
  abstract     = {{<p>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.</p>}},
  author       = {{Emperle, Max and Bangalore, Disha M and Adam, Sabrina and Kunert, Stefan and Heil, Hannah S and Heinze, Katrin G and Bashtrykov, Pavel and Tessmer, Ingrid and Jeltsch, Albert}},
  issn         = {{1362-4962}},
  keywords     = {{Binding Sites/genetics; CpG Islands/genetics; DNA/genetics; DNA (Cytosine-5-)-Methyltransferases/genetics; DNA Methylation/genetics; DNA Methyltransferase 3A; DNA Modification Methylases/genetics; Humans; Protein Domains/genetics}},
  language     = {{eng}},
  month        = {{08}},
  number       = {{14}},
  pages        = {{8294--8308}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase}},
  url          = {{http://dx.doi.org/10.1093/nar/gkab600}},
  doi          = {{10.1093/nar/gkab600}},
  volume       = {{49}},
  year         = {{2021}},
}