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
; 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.
(Less)
- author
- Emperle, Max
; Bangalore, Disha M
; Adam, Sabrina
; Kunert, Stefan
; Heil, Hannah S
LU
; Heinze, Katrin G
; Bashtrykov, Pavel
; Tessmer, Ingrid
and Jeltsch, Albert
- publishing date
- 2021-08-20
- 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
-
- scopus:85112854308
- pmid:34289056
- 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
- 2025-10-14 09:00:09
@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}},
}