The epigenetic control of E-box and Myc-dependent chromatin modifications regulate the licensing of lamin B2 origin during cell cycle

Nucleic Acids Res. 2012 Oct;40(18):9021-35. doi: 10.1093/nar/gks617. Epub 2012 Jul 5.

Abstract

Recent genome-wide mapping of the mammalian replication origins has suggested the role of transcriptional regulatory elements in origin activation. However, the nature of chromatin modifications associated with such trans-factors or epigenetic marks imprinted on cis-elements during the spatio-temporal regulation of replication initiation remains enigmatic. To unveil the molecular underpinnings, we studied the human lamin B2 origin that spatially overlaps with TIMM 13 promoter. We observed an early G(1)-specific occupancy of c-Myc that facilitated the loading of mini chromosome maintenance protein (MCM) complex during subsequent mid-G(1) phase rather stimulating TIMM 13 gene expression. Investigations on the Myc-induced downstream events suggested a direct interaction between c-Myc and histone methyltransferase mixed-lineage leukemia 1 that imparted histone H3K4me3 mark essential for both recruitment of acetylase complex HBO1 and hyperacetylation of histone H4. Contemporaneously, the nucleosome remodeling promoted the loading of MCM proteins at the origin. These chromatin modifications were under the tight control of active demethylation of E-box as evident from methylation profiling. The active demethylation was mediated by the Ten-eleven translocation (TET)-thymine DNA glycosylase-base excision repair (BER) pathway, which facilitated spatio-temporal occupancy of Myc. Intriguingly, the genome-wide 43% occurrence of E-box among the human origins could support our hypothesis that epigenetic control of E-box could be a molecular switch for the licensing of early replicating origins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Chromatin Assembly and Disassembly*
  • DNA-Binding Proteins / metabolism
  • E-Box Elements*
  • Epigenesis, Genetic*
  • G1 Phase / genetics*
  • HEK293 Cells
  • HL-60 Cells
  • HeLa Cells
  • Histone Methyltransferases
  • Histone-Lysine N-Methyltransferase / metabolism
  • Histones / metabolism
  • Humans
  • Lamin Type B / genetics*
  • Mitochondrial Membrane Transport Proteins / biosynthesis
  • Mitochondrial Membrane Transport Proteins / genetics
  • Myeloid-Lymphoid Leukemia Protein / metabolism
  • Nucleosomes / metabolism
  • Promoter Regions, Genetic
  • Proto-Oncogene Proteins c-myc / metabolism*
  • Replication Origin*

Substances

  • DNA-Binding Proteins
  • Histones
  • KMT2A protein, human
  • Lamin Type B
  • Mitochondrial Membrane Transport Proteins
  • Nucleosomes
  • Proto-Oncogene Proteins c-myc
  • TIMM13 protein, human
  • lamin B2
  • Myeloid-Lymphoid Leukemia Protein
  • Histone Methyltransferases
  • Histone-Lysine N-Methyltransferase