Error-prone replication of a 5-formylcytosine-mediated DNA-peptide cross-link in human cells

Spandana Naldiga, Shaofei Ji, Jenna Thomforde, Claudia M. Nicolae, Marietta Lee, Zhongtao Zhang, George Lucian Moldovan, Natalia Y. Tretyakova, Ashis K. Basu

Research output: Contribution to journalArticle

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Abstract

DNA–protein cross-links can interfere with chromatin architecture, block DNA replication and transcription, and interfere with DNA repair. Here we synthesized a DNA 23-mer containing a site-specific DNA–peptide cross-link (DpC) by cross-linking an 11-mer peptide to the DNA epigenetic mark 5-formylcytosine in synthetic DNA and used it to generate a DpC-containing plasmid construct. Upon replication of the DpC-containing plasmid in HEK 293T cells, approximately 9% of progeny plasmids contained targeted mutations and 5% semitargeted mutations. Targeted mutations included C3 T transitions and C deletions, whereas semitargeted mutations included several base substitutions and deletions near the DpC lesion. To identify DNA polymerases involved in DpC bypass, we comparatively studied translesion synthesis (TLS) efficiency and mutagenesis of the DpC in a series of cell lines with TLS polymerase knockouts or knockdowns. Knockdown of either hPol or hPol reduced the mutation frequency by nearly 50%. However, the most significant reduction in mutation frequency (50%–70%) was observed upon simultaneous knockout of hPol and hPol with knockdown of hPol , suggesting that these TLS polymerases play a critical role in error-prone DpC bypass. Because TLS efficiency of the DpC construct was not significantly affected in TLS polymerase–deficient cells, we examined a possible role of replicative DNA polymerases in their bypass and determined that hPol and hPol can accurately bypass the DpC. We conclude that both replicative and TLS polymerases can bypass this DpC lesion in human cells but that mutations are induced mainly by TLS polymerases.

Original languageEnglish (US)
Pages (from-to)10619-10627
Number of pages9
JournalJournal of Biological Chemistry
Volume294
Issue number27
DOIs
StatePublished - Jan 1 2019

Fingerprint

Cells
Peptides
Mutation
DNA
Plasmids
Mutation Rate
DNA-Directed DNA Polymerase
HEK293 Cells
DNA Replication
Epigenomics
Mutagenesis
DNA Repair
Chromatin
Transcription
5-formylcytosine
Cell Line
Repair
Substitution reactions

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Naldiga, Spandana ; Ji, Shaofei ; Thomforde, Jenna ; Nicolae, Claudia M. ; Lee, Marietta ; Zhang, Zhongtao ; Moldovan, George Lucian ; Tretyakova, Natalia Y. ; Basu, Ashis K. / Error-prone replication of a 5-formylcytosine-mediated DNA-peptide cross-link in human cells. In: Journal of Biological Chemistry. 2019 ; Vol. 294, No. 27. pp. 10619-10627.
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abstract = "DNA–protein cross-links can interfere with chromatin architecture, block DNA replication and transcription, and interfere with DNA repair. Here we synthesized a DNA 23-mer containing a site-specific DNA–peptide cross-link (DpC) by cross-linking an 11-mer peptide to the DNA epigenetic mark 5-formylcytosine in synthetic DNA and used it to generate a DpC-containing plasmid construct. Upon replication of the DpC-containing plasmid in HEK 293T cells, approximately 9{\%} of progeny plasmids contained targeted mutations and 5{\%} semitargeted mutations. Targeted mutations included C3 T transitions and C deletions, whereas semitargeted mutations included several base substitutions and deletions near the DpC lesion. To identify DNA polymerases involved in DpC bypass, we comparatively studied translesion synthesis (TLS) efficiency and mutagenesis of the DpC in a series of cell lines with TLS polymerase knockouts or knockdowns. Knockdown of either hPol or hPol reduced the mutation frequency by nearly 50{\%}. However, the most significant reduction in mutation frequency (50{\%}–70{\%}) was observed upon simultaneous knockout of hPol and hPol with knockdown of hPol , suggesting that these TLS polymerases play a critical role in error-prone DpC bypass. Because TLS efficiency of the DpC construct was not significantly affected in TLS polymerase–deficient cells, we examined a possible role of replicative DNA polymerases in their bypass and determined that hPol and hPol can accurately bypass the DpC. We conclude that both replicative and TLS polymerases can bypass this DpC lesion in human cells but that mutations are induced mainly by TLS polymerases.",
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Error-prone replication of a 5-formylcytosine-mediated DNA-peptide cross-link in human cells. / Naldiga, Spandana; Ji, Shaofei; Thomforde, Jenna; Nicolae, Claudia M.; Lee, Marietta; Zhang, Zhongtao; Moldovan, George Lucian; Tretyakova, Natalia Y.; Basu, Ashis K.

In: Journal of Biological Chemistry, Vol. 294, No. 27, 01.01.2019, p. 10619-10627.

Research output: Contribution to journalArticle

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AU - Naldiga, Spandana

AU - Ji, Shaofei

AU - Thomforde, Jenna

AU - Nicolae, Claudia M.

AU - Lee, Marietta

AU - Zhang, Zhongtao

AU - Moldovan, George Lucian

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AU - Basu, Ashis K.

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AB - DNA–protein cross-links can interfere with chromatin architecture, block DNA replication and transcription, and interfere with DNA repair. Here we synthesized a DNA 23-mer containing a site-specific DNA–peptide cross-link (DpC) by cross-linking an 11-mer peptide to the DNA epigenetic mark 5-formylcytosine in synthetic DNA and used it to generate a DpC-containing plasmid construct. Upon replication of the DpC-containing plasmid in HEK 293T cells, approximately 9% of progeny plasmids contained targeted mutations and 5% semitargeted mutations. Targeted mutations included C3 T transitions and C deletions, whereas semitargeted mutations included several base substitutions and deletions near the DpC lesion. To identify DNA polymerases involved in DpC bypass, we comparatively studied translesion synthesis (TLS) efficiency and mutagenesis of the DpC in a series of cell lines with TLS polymerase knockouts or knockdowns. Knockdown of either hPol or hPol reduced the mutation frequency by nearly 50%. However, the most significant reduction in mutation frequency (50%–70%) was observed upon simultaneous knockout of hPol and hPol with knockdown of hPol , suggesting that these TLS polymerases play a critical role in error-prone DpC bypass. Because TLS efficiency of the DpC construct was not significantly affected in TLS polymerase–deficient cells, we examined a possible role of replicative DNA polymerases in their bypass and determined that hPol and hPol can accurately bypass the DpC. We conclude that both replicative and TLS polymerases can bypass this DpC lesion in human cells but that mutations are induced mainly by TLS polymerases.

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