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