ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth

PLoS Biol. 2009 Dec;7(12):e1000256. doi: 10.1371/journal.pbio.1000256. Epub 2009 Dec 15.


A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat deposition. Here, we have identified the repressor and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (ChIP) sequencing using C2C12 cells identified about 2,500 ZBED6 binding sites in the genome, and the deduced consensus motif gave a perfect match with the established binding site in Igf2. Genes associated with ZBED6 binding sites showed a highly significant enrichment for certain Gene Ontology classifications, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6 is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Carrier Proteins / metabolism
  • Cell Line
  • Cell Nucleolus / metabolism
  • Cell Proliferation
  • Chromatin Immunoprecipitation
  • DNA Transposable Elements
  • Gene Expression Regulation, Developmental
  • Genetic Diseases, Inborn
  • Humans
  • Insulin-Like Growth Factor II / metabolism*
  • Mass Spectrometry
  • Mice
  • Muscle Development*
  • Nuclear Proteins
  • Quantitative Trait Loci
  • RNA Interference
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • Repressor Proteins / metabolism*
  • Swine
  • Wound Healing


  • Carrier Proteins
  • DNA Transposable Elements
  • IGF2 protein, mouse
  • Nuclear Proteins
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • Repressor Proteins
  • ZBED6 protein, human
  • ZBED6 protein, mouse
  • Zc3h11a protein, mouse
  • Insulin-Like Growth Factor II