Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1

Scientific Reports · 7 authors, 4 centres

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TL;DR

This preclinical study used LIG1 null mouse and lig1 mutant human cell lines to investigate replication protein dynamics in DNA ligase I (LigI) deficiency. The central result is that PCNA and DNMT1 association and turnover on newly synthesized DNA are unchanged, but cells show a stable increase in the non-replicative linker histone variant H1.0.

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This laboratory study used proteomic approaches to analyze replication protein dynamics in LIG1 null mouse cells and LigI-deficient human fibroblasts. The researchers found that the absence of LigI did not alter the recruitment or turnover kinetics of the replication clamp PCNA or the maintenance methyltransferase DNMT1 on newly synthesized DNA. Core histone deposition was also unaffected. However, LigI-deficient cells exhibited elevated levels of the replication-independent linker histone H1.0 on chromatin, a change that persisted even after genetic complementation with wild-type LigI. The study suggests the LigIIIα/XRCC1 complex effectively substitutes for LigI in Okazaki fragment ligation to maintain PCNA dynamics, but cannot fully prevent increased DNA strand breaks. The stable alteration in H1.0 composition represents a potential epigenetic change.

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other

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preclinical research

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ORIGINAL PAPER

PMC10020546

Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1

Scientific Reports

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ABSTRACT

Abstract DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol δ. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIα (LigIIIα)-dependent backup pathway. Here we examined the effect of LigI-deficiency on proteins at the replication fork. Notably, LigI-deficiency did not alter the kinetics of association of the PCNA clamp, the leading strand polymerase Pol ε, DNA maintenance methylation proteins and core histones with newly synthesized DNA. While the absence of major changes in replication and methylation proteins is consistent with the similar proliferation rate and DNA methylation levels of the LIG1 null cells compared with the parental cells, the increased levels of LigIIIα/XRCC1 and Pol δ at the replication fork and in bulk chromatin indicate that there are subtle replication defects in the absence of LigI. Interestingly, the non-replicative histone H1 variant, H1.0, is enriched in the chromatin of LigI-deficient mouse CH12F3 and human 46BR.1G1 cells. This alteration was not corrected by expression of wild type LigI, suggesting that it is a relatively stable epigenetic change that may contribute to the immunodeficiencies linked with inherited LigI-deficiency syndrome. Subject terms: Biochemistry, Biological techniques

CITATION EXPORT

Seema Khattri Bhandari, Nathaniel Wiest, Annahita Sallmyr et al.. Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1. Scientific Reports. (2023). https://doi.org/10.1038/s41598-023-31367-4

AUTHORS

7 · 4 CENTRES

Seema Khattri Bhandari, Nathaniel Wiest, Annahita Sallmyr, Ruofei Du, Laure Ferry, Pierre-Antoine Defossez, Alan E Tomkinson

1Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM 87131 USA
2Epigenetics and Cell Fate, CNRS, Université Paris Cité, 750013 Paris, France
3Present Address: Division of Hematology and Medical Oncology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL 32224 USA
4Present Address: Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA