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

Shaofei Ji, Iwen Fu, Spandana Naldiga, Hongzhao Shao, Ashis K. Basu, Suse Broyde, Natalia Y. Tretyakova

Research output: Contribution to journalArticle

Abstract

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 and . 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 and 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.

Original languageEnglish (US)
Pages (from-to)6455-6469
Number of pages15
JournalNucleic Acids Research
Volume46
Issue number13
DOIs
StatePublished - Jan 1 2018

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DNA Replication
Mutation
DNA
Proteins
Peptides
Histones
5-formylcytosine
link protein
HEK293 Cells
DNA-Directed DNA Polymerase
Epigenomics
Base Pairing
Lysine
Digestion
Catalytic Domain
Plasmids
Kidney

ASJC Scopus subject areas

  • Genetics

Cite this

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.

In: Nucleic Acids Research, Vol. 46, No. 13, 01.01.2018, p. 6455-6469.

Research output: Contribution to journalArticle

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. In: Nucleic Acids Research. 2018 ; Vol. 46, No. 13. pp. 6455-6469.
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