Phylogenetic and Epigenetic Footprinting of the Putative Enhancers of the Peg3 Domain

PLoS One. 2016 Apr 22;11(4):e0154216. doi: 10.1371/journal.pone.0154216. eCollection 2016.


The Peg3 (Paternally Expressed Gene 3) imprinted domain is predicted to be regulated through a large number of evolutionarily conserved regions (ECRs) that are localized within its middle 200-kb region. In the current study, we characterized these potential cis-regulatory regions using phylogenetic and epigenetic approaches. According to the results, the majority of these ECRs are potential enhancers for the transcription of the Peg3 domain. Also, these potential enhancers can be divided into two groups based on their histone modification and DNA methylation patterns: ubiquitous and tissue-specific enhancers. Phylogenetic and bioinformatic analyses further revealed that several cis-regulatory motifs are frequently associated with the ECRs, such as the E box, PITX2, NF-κB and RFX1 motifs. A series of subsequent ChIP experiments demonstrated that the trans factor MYOD indeed binds to the E box of several ECRs, further suggesting that MYOD may play significant roles in the transcriptional control of the Peg3 domain. Overall, the current study identifies, for the first time, a set of cis-regulatory motifs and corresponding trans factors that may be critical for the transcriptional regulation of the Peg3 domain.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Binding Sites / genetics
  • Chromatin Immunoprecipitation
  • DNA Methylation
  • E-Box Elements / genetics
  • Enhancer Elements, Genetic / genetics*
  • Epigenomics / methods*
  • Female
  • Gene Expression Regulation
  • Humans
  • Kruppel-Like Transcription Factors / classification
  • Kruppel-Like Transcription Factors / genetics*
  • Mice, Inbred C57BL
  • MyoD Protein / metabolism
  • Nucleotide Motifs / genetics
  • Phylogeny*
  • Protein Binding
  • Regulatory Sequences, Nucleic Acid / genetics
  • Sequence Homology, Amino Acid
  • Transcription, Genetic*


  • Kruppel-Like Transcription Factors
  • MyoD Protein