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SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

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SOX2 binds distinct enhancer regions in ESCs and NPCs.

(A) SOX2 peaks mapping to annotated transcriptional start sites, intragenic regions, and intergenic regions. Numbers on pie chart indicate fraction of bound regions that fall into each category. (B) Fraction of total start sites or total marked enhancers associated with SOX2 enriched regions. Numbers above bars reflect absolute numbers of bound regions and genomic features. (C) Box and Violin plots representing expression data from Affymetrix arrays of genes linked to SOX2-bound poised and active enhancers. y-axis corresponds to percentile expression rank, * denotes p-value<0.01, Student's T-test, two tailed. (D, E) Analysis of GO biological processes enriched in SOX2 bound poised and active enhancer datasets in ESCs and NPCs. x-axis reflects negative log base 10 of binomial raw p-value for enrichment versus a whole genome background. (F) Gene plots showing SOX2, H3K4me1, and H3K27Ac density at Nanog in ESCs and Notch1 in NPCs. y-axis corresponds to reads per million. Genomic positions reflect NCBI Mouse Genome Build 36 (mm8). Gray boxes indicate putative enhancers occupied by SOX2. * denotes known enhancer region.

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doi: https://doi.org/10.1371/journal.pgen.1003288.g002