Gene expression of Rif1-depleted ES cells

Rif1 depletion in mouse ES cells increases the populations derepressing 2-cell zygote-specific genes including Zscan4. We investigated the chromatin structural change in the Zscan4 gene loci, and found that this region was deprived of major histone modifications except for moderately coded by H3 lysine9 trimethylation. Rif1 depletion caused no significant alteration in DNA methylation and histone modifications including common active marks, but only a notable increase in H3K27Ac active mark in gene bodies and neighboring regions, indicating that atypical broad enhancer-like chromatin with semi-silent property has been emerged in Zscan4 gene loci.
In this study, we used microarrays to present the global changes in gene expression caused by transient depletion of Rif1. Total RNA was purified from untreated or Rif1-depleted E14tg2a cells using RNeasy micro kit (QIAGEN) for two times. Cy3-labeled samples were hybridized to Mouse Gene Expression slides (G4846A, Agilent Technologies). Normalized data was obtained using the Feature Extraction software (Agilent Technologies).