Targeting of >1.5 Mb of human DNA into the mouse X chromosome reveals presence of cis-acting regulators of epigenetic silencing

Genetics. 2012 Dec;192(4):1281-93. doi: 10.1534/genetics.112.143743. Epub 2012 Sep 28.

Abstract

Regulatory sequences can influence the expression of flanking genes over long distances, and X chromosome inactivation is a classic example of cis-acting epigenetic gene regulation. Knock-ins directed to the Mus musculus Hprt locus offer a unique opportunity to analyze the spread of silencing into different human DNA sequences in the identical genomic environment. X chromosome inactivation of four knock-in constructs, including bacterial artificial chromosome (BAC) integrations of over 195 kb, was demonstrated by both the lack of expression from the inactive X chromosome in females with nonrandom X chromosome inactivation and promoter DNA methylation of the human transgene in females. We further utilized promoter DNA methylation to assess the inactivation status of 74 human reporter constructs comprising >1.5 Mb of DNA. Of the 47 genes examined, only the PHB gene showed female DNA hypomethylation approaching the level seen in males, and escape from X chromosome inactivation was verified by demonstration of expression from the inactive X chromosome. Integration of PHB resulted in lower DNA methylation of the flanking HPRT promoter in females, suggesting the action of a dominant cis-acting escape element. Female-specific DNA hypermethylation of CpG islands not associated with promoters implies a widespread imposition of DNA methylation during X chromosome inactivation; yet transgenes demonstrated differential capacities to accumulate DNA methylation when integrated into the identical location on the inactive X chromosome, suggesting additional cis-acting sequence effects. As only one of the human transgenes analyzed escaped X chromosome inactivation, we conclude that elements permitting ongoing expression from the inactive X are rare in the human genome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromosomes, Artificial, Bacterial
  • CpG Islands
  • DNA Methylation
  • DNA, Intergenic
  • Epigenesis, Genetic*
  • Female
  • Gene Expression Regulation*
  • Homeobox Protein PITX2
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism
  • Humans
  • Hypoxanthine Phosphoribosyltransferase / genetics
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Nerve Tissue Proteins / genetics
  • Prohibitins
  • Promoter Regions, Genetic
  • Receptors, Nerve Growth Factor / genetics
  • Regulatory Sequences, Nucleic Acid
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription Initiation Site
  • Transgenes
  • X Chromosome Inactivation
  • X Chromosome*

Substances

  • DNA, Intergenic
  • Homeodomain Proteins
  • NGFR protein, human
  • Nerve Tissue Proteins
  • PHB protein, human
  • Prohibitins
  • Receptors, Nerve Growth Factor
  • Transcription Factors
  • Hypoxanthine Phosphoribosyltransferase