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Cytosine base modifications regulate DNA duplex stability and metabolism.

ABSTRACT: DNA base modifications diversify the genome and are essential players in development. Yet, their influence on DNA physical properties and the ensuing effects on genome metabolism are poorly understood. Here, we focus on the interplay of cytosine modifications and DNA processes. We show by a combination of in vitro reactions with well-defined protein compositions and conditions, and in vivo experiments within the complex networks of the cell that cytosine methylation stabilizes the DNA helix, increasing its melting temperature and reducing DNA helicase and RNA/DNA polymerase speed. Oxidation of methylated cytosine, however, reverts the duplex stabilizing and genome metabolic effects to the level of unmodified cytosine. We detect this effect with DNA replication and transcription proteins originating from different species, ranging from prokaryotic and viral to the eukaryotic yeast and mammalian proteins. Accordingly, lack of cytosine methylation increases replication fork speed by enhancing DNA helicase unwinding speed in cells. We further validate that this cannot simply be explained by altered global DNA decondensation, changes in histone marks or chromatin structure and accessibility. We propose that the variegated deposition of cytosine modifications along the genome regulates DNA helix stability, thereby providing an elementary mechanism for local fine-tuning of DNA metabolism.

SUBMITTER: Rausch C

PROVIDER: S-EPMC8682791 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Cytosine base modifications regulate DNA duplex stability and metabolism.

Rausch Cathia C Zhang Peng P Casas-Delucchi Corella S CS Daiß Julia L JL Engel Christoph C Coster Gideon G Hastert Florian D FD Weber Patrick P Cardoso M Cristina MC

Nucleic acids research 20211201 22

DNA base modifications diversify the genome and are essential players in development. Yet, their influence on DNA physical properties and the ensuing effects on genome metabolism are poorly understood. Here, we focus on the interplay of cytosine modifications and DNA processes. We show by a combination of in vitro reactions with well-defined protein compositions and conditions, and in vivo experiments within the complex networks of the cell that cytosine methylation stabilizes the DNA helix, inc ...[more]

PMID: 34133727

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Project description:The exocyclic 1, N(2)-ethenodeoxyguanosine (1,N(2)-is an element of dG) adduct, arising from the reaction of vinyl halides and other vinyl monomers, including chloroacetaldehyde, and lipid peroxidation products with dG, was examined at pH 5.2 in the oligodeoxynucleotide duplex 5'-d(CGCATXGAATCC)-3'.5'-d(GGATTCCATGCG)-3' (X = 1,N(2)-is an element of dG). Previously, X(anti).C(anti) pairing was established in this duplex, containing the 5'-TXG-3' sequence context, at pH 8.6 [Shanmugam, G., Goodenough, A. K., Kozekov, I. D., Harris, T. M., Guengerich, F. P., Rizzo, C. J., and Stone, M. P. (2007) Chem. Res. Toxicol. 20, 1601- 1611]. At pH 5.2, the 1,N(2)-is an element of dG adduct decreased the thermal stability of the duplex by approximately 13 degrees C. The 1,N(2)-is an element of dG adduct rotated about the glycosyl bond from the anti to the syn conformation. This resulted in the observation of a strong nuclear Overhauser effect (NOE) between the imidazole proton of 1,N(2)-is an element of dG and the anomeric proton of the attached deoxyribose, accompanied by an NOE to the minor groove A(20) H2 proton from the complementary strand. The syn conformation of the glycosyl bond at 1,N(2)-is an element of dG placed the exocyclic etheno moiety into the major groove. This resulted in the observation of NOEs between the etheno protons and the major groove protons of the 5'-neighboring thymine. The 1,N(2)-is an element of dG adduct formed a Hoogsteen pair with the complementary cytosine, characterized by downfield shifts of the amino protons of the cytosine complementary to the exocyclic adduct. The pattern of chemical shift perturbations indicated that the lesion introduced a localized structural perturbation involving the modified base pair and its 3'- and 5'-neighbor base pairs. A second conformational equilibrium was observed, in which both the modified base pair and its 3'-neighboring G.C base pair formed tandem Hoogsteen pairs. The results support the conclusion that at neutral pH, in the 5'-TXG-3' sequence, the 1,N(2)-is an element of dG adduct exists as a blend of conformations in duplex DNA. These involve the interconversion of the glycosyl torsion angle between the anti and the syn conformations, occurring at an intermediate rate on the NMR time scale.

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Cytosine base modifications regulate DNA duplex stability and metabolism.

Publications

Cytosine base modifications regulate DNA duplex stability and metabolism.

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