H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication

Nucleic Acids Res. 2017 Jan 9;45(1):169-180. doi: 10.1093/nar/gkw848. Epub 2016 Sep 26.

Abstract

DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase δ, but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex.

MeSH terms

  • Animals
  • Cell Cycle / genetics
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Cell Line, Tumor
  • Cell Nucleus / genetics
  • Cell Nucleus / metabolism
  • Chromatin / chemistry
  • Chromatin / metabolism*
  • DNA Polymerase III / genetics
  • DNA Polymerase III / metabolism
  • DNA Replication*
  • HCT116 Cells
  • HeLa Cells
  • Histones / genetics*
  • Histones / metabolism
  • Humans
  • Jumonji Domain-Containing Histone Demethylases / antagonists & inhibitors
  • Jumonji Domain-Containing Histone Demethylases / genetics*
  • Jumonji Domain-Containing Histone Demethylases / metabolism
  • Lamin Type B / genetics
  • Lamin Type B / metabolism
  • Methylation
  • Mice
  • Minichromosome Maintenance Complex Component 4 / genetics
  • Minichromosome Maintenance Complex Component 4 / metabolism
  • NIH 3T3 Cells
  • Osteoblasts / cytology
  • Osteoblasts / metabolism
  • Proliferating Cell Nuclear Antigen / genetics
  • Proliferating Cell Nuclear Antigen / metabolism
  • Proto-Oncogene Proteins c-myc / genetics
  • Proto-Oncogene Proteins c-myc / metabolism
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism

Substances

  • CDC45 protein, human
  • Cell Cycle Proteins
  • Chromatin
  • Histones
  • Lamin Type B
  • MYC protein, human
  • Proliferating Cell Nuclear Antigen
  • Proto-Oncogene Proteins c-myc
  • RNA, Small Interfering
  • Jumonji Domain-Containing Histone Demethylases
  • KDM4D protein, human
  • DNA Polymerase III
  • MCM4 protein, human
  • Minichromosome Maintenance Complex Component 4