Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η

Suresh Pujari; Mingxuan Wu; Jenna R Thomforde; Zhipeng A. Wang; Christopher Chao; Noelle M Olson; Luke Erber; William C.K. Pomerantz; Philip Cole; Natalia Y. Tretyakova

doi:10.1002/anie.202109418

Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η

Suresh Pujari, Mingxuan Wu, Jenna R Thomforde, Zhipeng A. Wang, Christopher Chao, Noelle M Olson, Luke Erber, William C.K. Pomerantz, Philip Cole, Natalia Y. Tretyakova

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

DNA-protein cross-links (DPCs) between DNA epigenetic mark 5-formylC and lysine residues of histone proteins spontaneously form in human cells. Such conjugates are likely to influence chromatin structure and mediate DNA replication, transcription, and repair, but are challenging to study due to their reversible nature. Here we report the construction of site specific, hydrolytically stable DPCs between 5fdC in DNA and K4 of histone H3 and an investigation of their effects on DNA replication. Our approach employs oxime ligation, allowing for site-specific conjugation of histones to DNA under physiological conditions. Primer extension experiments revealed that histone H3-DNA crosslinks blocked DNA synthesis by hPol η polymerase, but were bypassed following proteolytic processing.

Original language	English (US)
Pages (from-to)	26489-26494
Number of pages	6
Journal	Angewandte Chemie - International Edition
Volume	60
Issue number	51
DOIs	https://doi.org/10.1002/anie.202109418
State	Published - Dec 13 2021

Bibliographical note

Funding Information:
We thank Professor Peter F. Guengerich (Vanderbilt University) for providing the expression vector for human polymerase η, Maram Essawy and Professor Colin Campbell (University of Minnesota) for expressing and purifying the enzyme, Yingchun Zhao (Analytical Biochemistry Shared Resource, Masonic Cancer Center, University of Minnesota) for his help with MS analysis, and Robert Carlson (University of Minnesota) for preparing the graphics for the manuscript. This research is supported by an R01 grant from NIEHS (ES‐023350), an R37 grant from NIGMS (GM‐062437), and an R35 grant from NIGMS (GM‐140837). N.M.O was supported by NIH Biotechnology training grant, (5T32GM00347‐23).

Funding Information:
We thank Professor Peter F. Guengerich (Vanderbilt University) for providing the expression vector for human polymerase ?, Maram Essawy and Professor Colin Campbell (University of Minnesota) for expressing and purifying the enzyme, Yingchun Zhao (Analytical Biochemistry Shared Resource, Masonic Cancer Center, University of Minnesota) for his help with MS analysis, and Robert Carlson (University of Minnesota) for preparing the graphics for the manuscript. This research is supported by an R01 grant from NIEHS (ES-023350), an R37 grant from NIGMS (GM-062437), and an R35 grant from NIGMS (GM-140837). N.M.O was supported by NIH Biotechnology training grant, (5T32GM00347-23).

Publisher Copyright:
© 2021 Wiley-VCH GmbH

Keywords

5-formyl-dC
DNA-protein cross-link
histone
oxime ligation
polymerase bypass

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10.1002/anie.202109418

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Pujari, S., Wu, M., Thomforde, J. R., Wang, Z. A., Chao, C., Olson, N. M., Erber, L., Pomerantz, W. C. K., Cole, P., & Tretyakova, N. Y. (2021). Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η. Angewandte Chemie - International Edition, 60(51), 26489-26494. https://doi.org/10.1002/anie.202109418

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title = "Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η",

abstract = "DNA-protein cross-links (DPCs) between DNA epigenetic mark 5-formylC and lysine residues of histone proteins spontaneously form in human cells. Such conjugates are likely to influence chromatin structure and mediate DNA replication, transcription, and repair, but are challenging to study due to their reversible nature. Here we report the construction of site specific, hydrolytically stable DPCs between 5fdC in DNA and K4 of histone H3 and an investigation of their effects on DNA replication. Our approach employs oxime ligation, allowing for site-specific conjugation of histones to DNA under physiological conditions. Primer extension experiments revealed that histone H3-DNA crosslinks blocked DNA synthesis by hPol η polymerase, but were bypassed following proteolytic processing.",

keywords = "5-formyl-dC, DNA-protein cross-link, histone, oxime ligation, polymerase bypass",

author = "Suresh Pujari and Mingxuan Wu and Thomforde, {Jenna R} and Wang, {Zhipeng A.} and Christopher Chao and Olson, {Noelle M} and Luke Erber and Pomerantz, {William C.K.} and Philip Cole and Tretyakova, {Natalia Y.}",

note = "Funding Information: We thank Professor Peter F. Guengerich (Vanderbilt University) for providing the expression vector for human polymerase η, Maram Essawy and Professor Colin Campbell (University of Minnesota) for expressing and purifying the enzyme, Yingchun Zhao (Analytical Biochemistry Shared Resource, Masonic Cancer Center, University of Minnesota) for his help with MS analysis, and Robert Carlson (University of Minnesota) for preparing the graphics for the manuscript. This research is supported by an R01 grant from NIEHS (ES‐023350), an R37 grant from NIGMS (GM‐062437), and an R35 grant from NIGMS (GM‐140837). N.M.O was supported by NIH Biotechnology training grant, (5T32GM00347‐23). Funding Information: We thank Professor Peter F. Guengerich (Vanderbilt University) for providing the expression vector for human polymerase ?, Maram Essawy and Professor Colin Campbell (University of Minnesota) for expressing and purifying the enzyme, Yingchun Zhao (Analytical Biochemistry Shared Resource, Masonic Cancer Center, University of Minnesota) for his help with MS analysis, and Robert Carlson (University of Minnesota) for preparing the graphics for the manuscript. This research is supported by an R01 grant from NIEHS (ES-023350), an R37 grant from NIGMS (GM-062437), and an R35 grant from NIGMS (GM-140837). N.M.O was supported by NIH Biotechnology training grant, (5T32GM00347-23). Publisher Copyright: {\textcopyright} 2021 Wiley-VCH GmbH",

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T2 - Synthesis and Polymerase Bypass by Human DNA Polymerase η

AU - Pujari, Suresh

AU - Wu, Mingxuan

AU - Thomforde, Jenna R

AU - Wang, Zhipeng A.

AU - Chao, Christopher

AU - Olson, Noelle M

AU - Erber, Luke

AU - Pomerantz, William C.K.

AU - Cole, Philip

AU - Tretyakova, Natalia Y.

N1 - Funding Information: We thank Professor Peter F. Guengerich (Vanderbilt University) for providing the expression vector for human polymerase η, Maram Essawy and Professor Colin Campbell (University of Minnesota) for expressing and purifying the enzyme, Yingchun Zhao (Analytical Biochemistry Shared Resource, Masonic Cancer Center, University of Minnesota) for his help with MS analysis, and Robert Carlson (University of Minnesota) for preparing the graphics for the manuscript. This research is supported by an R01 grant from NIEHS (ES‐023350), an R37 grant from NIGMS (GM‐062437), and an R35 grant from NIGMS (GM‐140837). N.M.O was supported by NIH Biotechnology training grant, (5T32GM00347‐23). Funding Information: We thank Professor Peter F. Guengerich (Vanderbilt University) for providing the expression vector for human polymerase ?, Maram Essawy and Professor Colin Campbell (University of Minnesota) for expressing and purifying the enzyme, Yingchun Zhao (Analytical Biochemistry Shared Resource, Masonic Cancer Center, University of Minnesota) for his help with MS analysis, and Robert Carlson (University of Minnesota) for preparing the graphics for the manuscript. This research is supported by an R01 grant from NIEHS (ES-023350), an R37 grant from NIGMS (GM-062437), and an R35 grant from NIGMS (GM-140837). N.M.O was supported by NIH Biotechnology training grant, (5T32GM00347-23). Publisher Copyright: © 2021 Wiley-VCH GmbH

PY - 2021/12/13

Y1 - 2021/12/13

N2 - DNA-protein cross-links (DPCs) between DNA epigenetic mark 5-formylC and lysine residues of histone proteins spontaneously form in human cells. Such conjugates are likely to influence chromatin structure and mediate DNA replication, transcription, and repair, but are challenging to study due to their reversible nature. Here we report the construction of site specific, hydrolytically stable DPCs between 5fdC in DNA and K4 of histone H3 and an investigation of their effects on DNA replication. Our approach employs oxime ligation, allowing for site-specific conjugation of histones to DNA under physiological conditions. Primer extension experiments revealed that histone H3-DNA crosslinks blocked DNA synthesis by hPol η polymerase, but were bypassed following proteolytic processing.

AB - DNA-protein cross-links (DPCs) between DNA epigenetic mark 5-formylC and lysine residues of histone proteins spontaneously form in human cells. Such conjugates are likely to influence chromatin structure and mediate DNA replication, transcription, and repair, but are challenging to study due to their reversible nature. Here we report the construction of site specific, hydrolytically stable DPCs between 5fdC in DNA and K4 of histone H3 and an investigation of their effects on DNA replication. Our approach employs oxime ligation, allowing for site-specific conjugation of histones to DNA under physiological conditions. Primer extension experiments revealed that histone H3-DNA crosslinks blocked DNA synthesis by hPol η polymerase, but were bypassed following proteolytic processing.

KW - 5-formyl-dC

KW - DNA-protein cross-link

KW - histone

KW - oxime ligation

KW - polymerase bypass

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AN - SCOPUS:85118997643

SN - 1433-7851

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JO - Angewandte Chemie - International Edition

JF - Angewandte Chemie - International Edition

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ER -

Site-Specific 5-Formyl Cytosine Mediated DNA-Histone Cross-Links: Synthesis and Polymerase Bypass by Human DNA Polymerase η

Abstract

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