Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication

Nucleic Acids Res. 2013 Mar 1;41(5):2846-56. doi: 10.1093/nar/gks1336. Epub 2013 Jan 15.


Genome-wide gene expression analyses of the human somatic cell cycle have indicated that the set of cycling genes differ between primary and cancer cells. By identifying genes that have cell cycle dependent expression in HaCaT human keratinocytes and comparing these with previously identified cell cycle genes, we have identified three distinct groups of cell cycle genes. First, housekeeping genes enriched for known cell cycle functions; second, cell type-specific genes enriched for HaCaT-specific functions; and third, Polycomb-regulated genes. These Polycomb-regulated genes are specifically upregulated during DNA replication, and consistent with being epigenetically silenced in other cell cycle phases, these genes have lower expression than other cell cycle genes. We also find similar patterns in foreskin fibroblasts, indicating that replication-dependent expression of Polycomb-silenced genes is a prevalent but unrecognized regulatory mechanism.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Cycle / genetics*
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism
  • Cell Line
  • CpG Islands
  • DNA Replication*
  • Fibroblasts / metabolism
  • Gene Expression Profiling
  • Genes, Essential
  • Histones / physiology
  • Humans
  • Keratinocytes / metabolism
  • Keratinocytes / physiology
  • Least-Squares Analysis
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Polycomb-Group Proteins / physiology*
  • Promoter Regions, Genetic
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Transcription, Genetic
  • Transcriptome
  • Up-Regulation*


  • Cell Cycle Proteins
  • Histones
  • Polycomb-Group Proteins
  • RNA, Messenger