Transient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation

The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differentiation and during embryonic development. We describe homologous pairing of the Oct4 alleles during ESC differentiation and embryogenesis, and we present evidence that pairing is correlated with the kinetics of ESC differentiation. Importantly, we identify critical DNA elements within the Oct4 promoter/enhancer region that mediate pairing of Oct4 alleles. Finally, we show that mutation of OCT4/SOX2 binding sites within this region abolishes inter-chromosomal interactions and affects accumulation of the repressive H3K9me2 modification at the Oct4 enhancer. Our findings demonstrate that chromatin organization and transcriptional programs are intimately connected in ESCs and that the dynamic positioning of the Oct4 alleles is associated with the transition from pluripotency to lineage specification. [Display omitted] •Homologous alleles of the Oct4 gene transiently associate as ESCs exit pluripotency•Onset of Oct4 allelic pairing is determined by the kinetics of ESC differentiation•The 5′ regulatory region of Oct4 is necessary and sufficient for allelic pairing•OCT4/SOX2 binding motifs are critical mediators of homologous allele pairing Hogan et al. describe association of the Oct4 alleles at the onset of ESC differentiation. These inter-chromosomal interactions are mediated by OCT4/SOX2 binding motifs within the promoter/enhancer region of the Oct4 gene, suggesting a transvection-like mechanism that influences gene regulation at the Oct4 locus.