Abstract
Genome structure or nuclear organization has fascinated researchers investigating genome function. Recently, much effort has gone into defining relationships between specific genome structures and gene expression in pluripotent cells. We previously analyzed chromosomal interactions of the endogenous Oct4 distal enhancer in pluripotent cells. Here, we derive ES and iPS cells from a transgenic Oct4 distal enhancer reporter mouse. Using sonication-based Circularized Chromosome Conformation Capture (4C) coupled with next generation sequencing, we determined and compared the genome-wide interactome of the endogenous and transgenic Oct4 distal enhancers. Integrative genomic analysis indicated that the transgenic enhancer binds to a similar set of loci and shares similar key enrichment profiles with its endogenous counterpart. Both the endogenous and transgenic Oct4 enhancer interacting loci were enriched in the open nucleus compartment, which is associated with active histone marks (H3K4me1, H3K27ac, H3K4me3 and H3K9ac), active cis-regulatory sequences (DNA hypersensitivity sites (DHS)), 5-hydroxymethylcytosine (5-hmc), and early DNA replication domains. In addition, binding of some pluripotency-related transcription factors was consistently enriched in our 4C sites, and genes in those sites were generally more highly expressed. Overall, our work reveals critical features that may function in gene expression regulation in mouse pluripotent cells.
Highlights
Genome structure or nuclear organization has fascinated researchers investigating genome function
We identified some regions that interact with both the endogenous and transgenic Oct[4] distal enhancer (13 for MES and 24 for MIPS, Supplementary Table 2), suggesting that both bind a similar set of genomic loci and that these regions could be relevant to stem cell fate
Chromatin compartments are defined by DNA replication domains[22], and some studies show that DNA replication timing shapes the genomic landscape in specific cell types[23,24,25]. These findings suggest that early and late DNA replication might occur in different chromatin compartments
Summary
Genome structure or nuclear organization has fascinated researchers investigating genome function. Using sonication-based Circularized Chromosome Conformation Capture (4C) coupled with generation sequencing, we determined and compared the genome-wide interactome of the endogenous and transgenic Oct[4] distal enhancers. In addition to the linear arrangement of information encoded on DNA fibers, the 3-D architecture of the genome is increasingly thought to be a defining factor in gene regulation[6] Both critical stem cell activities, self-renewal and pluripotency, require a distinct www.nature.com/scientificreports/. Since 2002, when chromosome conformation capture (3C) was first used to investigate interactions between two genomic segments[8], a repertoire of high-throughput assays (4C9, 4C-seq10,11, 5C12, Hi-C13, and ChIA-PET14) has been developed to create chromatin interaction maps These methods have greatly advanced our understanding of genome organization. This modified approach was found as effective as enzyme-based methods but minimized bias due to enzyme digestion[17]
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