ChIP-seq analysis of genomic binding regions of five major transcription factors in mouse epiblast stem cells that highlights a central role for ZIC2 [TECHNIQUES AND RESOURCES ARTICLE]

Kazunari Matsuda, Tomoyuki Mikami, Shinya Oki, Hideaki Iida, Munazah Andrabi, Jeremy M. Boss, Katsushi Yamaguchi, Shuji Shigenobu, and Hisato Kondoh

To obtain an insight into the transcription factor (TF)-dependent regulation of epiblast stem cells (EpiSCs), we performed ChIP-seq analysis of the genomic binding regions in EpiSCs of five major TFs, ZIC2, OTX2, SOX2, POU5F1, and POU3F1, using biotinylated TFs, identifying the following new features: (1) The genomic domains of megabase scale rich in ZIC2 peaks and genes, and those rich in POU3F1 but sparse in genes alternate in EpiSCs, reflecting the clustering of regulatory regions that act in short- and long-ranges, which involve binding of ZIC2 and POU3F1, respectively. (2) The enhancers bound by ZIC2 and OTX2 prominently regulate TF genes in EpiSCs. (3) The binding sites for SOX2 and POU5F1 in mouse embryonic stem cells (ESCs) and EpiSCs are divergent, reflecting the shift of major-acting TFs from SOX2/POU5F1 in ESCs to OTX2/ZIC2 in EpiSCs. (4) This shift in the major-acting TFs appears to be primed by binding of ZIC2 in ESCs at relevant genomic positions that later function as enhancers following the disengagement of SOX2/POU5F1from the major regulatory functions and subsequent binding by OTX2.

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