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5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells

5-Formylcytosine (5fC) is an epigenetic DNA modification introduced via TET protein-mediated oxidation of 5-methyl-dC. We recently reported that 5fC form reversible DNA–protein conjugates (DPCs) with histone proteins in living cells (Ji et al. (2017) Angew. Chem. Int. Ed., 56:14130–14134). We now ex...

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Autores principales: Ji, Shaofei, Fu, Iwen, Naldiga, Spandana, Shao, Hongzhao, Basu, Ashis K, Broyde, Suse, Tretyakova, Natalia Y
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061883/
https://www.ncbi.nlm.nih.gov/pubmed/29905846
http://dx.doi.org/10.1093/nar/gky444
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author Ji, Shaofei
Fu, Iwen
Naldiga, Spandana
Shao, Hongzhao
Basu, Ashis K
Broyde, Suse
Tretyakova, Natalia Y
author_facet Ji, Shaofei
Fu, Iwen
Naldiga, Spandana
Shao, Hongzhao
Basu, Ashis K
Broyde, Suse
Tretyakova, Natalia Y
author_sort Ji, Shaofei
collection PubMed
description 5-Formylcytosine (5fC) is an epigenetic DNA modification introduced via TET protein-mediated oxidation of 5-methyl-dC. We recently reported that 5fC form reversible DNA–protein conjugates (DPCs) with histone proteins in living cells (Ji et al. (2017) Angew. Chem. Int. Ed., 56:14130–14134). We now examined the effects of 5fC mediated DPCs on DNA replication. Synthetic DNA duplexes containing site-specific DPCs between 5fC and lysine-containing proteins and peptides were subjected to primer extension experiments in the presence of human translesion synthesis DNA polymerases η and κ. We found that DPCs containing histones H2A or H4 completely inhibited DNA replication, but the replication block was removed when the proteins were subjected to proteolytic digestion. Cross-links to 11-mer or 31-mer peptides were bypassed by both polymerases in an error-prone manner, inducing targeted C→T transitions and –1 deletions. Similar types of mutations were observed when plasmids containing 5fC-peptide cross-links were replicated in human embryonic kidney (HEK) 293T cells. Molecular simulations of the 11-mer peptide-dC cross-links bound to human polymerases η and κ revealed that the peptide fits well on the DNA major groove side, and the modified dC forms a stable mismatch with incoming dATP via wobble base pairing in the polymerase active site.
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spelling pubmed-60618832018-08-07 5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells Ji, Shaofei Fu, Iwen Naldiga, Spandana Shao, Hongzhao Basu, Ashis K Broyde, Suse Tretyakova, Natalia Y Nucleic Acids Res Chemical Biology and Nucleic Acid Chemistry 5-Formylcytosine (5fC) is an epigenetic DNA modification introduced via TET protein-mediated oxidation of 5-methyl-dC. We recently reported that 5fC form reversible DNA–protein conjugates (DPCs) with histone proteins in living cells (Ji et al. (2017) Angew. Chem. Int. Ed., 56:14130–14134). We now examined the effects of 5fC mediated DPCs on DNA replication. Synthetic DNA duplexes containing site-specific DPCs between 5fC and lysine-containing proteins and peptides were subjected to primer extension experiments in the presence of human translesion synthesis DNA polymerases η and κ. We found that DPCs containing histones H2A or H4 completely inhibited DNA replication, but the replication block was removed when the proteins were subjected to proteolytic digestion. Cross-links to 11-mer or 31-mer peptides were bypassed by both polymerases in an error-prone manner, inducing targeted C→T transitions and –1 deletions. Similar types of mutations were observed when plasmids containing 5fC-peptide cross-links were replicated in human embryonic kidney (HEK) 293T cells. Molecular simulations of the 11-mer peptide-dC cross-links bound to human polymerases η and κ revealed that the peptide fits well on the DNA major groove side, and the modified dC forms a stable mismatch with incoming dATP via wobble base pairing in the polymerase active site. Oxford University Press 2018-07-27 2018-06-14 /pmc/articles/PMC6061883/ /pubmed/29905846 http://dx.doi.org/10.1093/nar/gky444 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://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 Chemical Biology and Nucleic Acid Chemistry
Ji, Shaofei
Fu, Iwen
Naldiga, Spandana
Shao, Hongzhao
Basu, Ashis K
Broyde, Suse
Tretyakova, Natalia Y
5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells
title 5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells
title_full 5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells
title_fullStr 5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells
title_full_unstemmed 5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells
title_short 5-Formylcytosine mediated DNA–protein cross-links block DNA replication and induce mutations in human cells
title_sort 5-formylcytosine mediated dna–protein cross-links block dna replication and induce mutations in human cells
topic Chemical Biology and Nucleic Acid Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061883/
https://www.ncbi.nlm.nih.gov/pubmed/29905846
http://dx.doi.org/10.1093/nar/gky444
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