Figure 4.

SOX4 Promotes Open Chromatin Patterns during Reprogramming

(A) Immunoblot validation of shRNA-mediated SOX4 knockdown.

(B) SOX4 knockdown significantly reduces neuronal conversion (mean ± SD; n = 10 random image fields from biological triplicates). Reprogramming efficiency represents (GFP⁺ and MAP2⁺ cells)/(total GFP⁺ cells).

(C) Area-proportional Venn diagram depicting the total number of SOX4 binding events and the proportion shared with NEUROG2. The adjacent pie diagram represents the relative fold increase in normalized transcript number for co-bound genes in NEUROG2-transduced fibroblasts in the presence versus absence of FD from RNA-seq datasets.

(D) NEUROG2 ChIP-seq track (2 DPT) and ATAC-seq tracks generated from fibroblasts (MRC-5), NEUROG2-transduced fibroblasts (N), NFD-treated fibroblasts (NFD), and NFD-treated fibroblasts co-expressing SOX4 shRNA (NFD + SOX4 shRNA) around the NEUROD1 and NEUROD4 loci. Gray shading highlights representative regions of FD-enhanced chromatin accessibility lost upon SOX4 knockdown.

(E) Area-proportional Venn diagram depicting the total number of ATAC-seq events in NFD-treated fibroblasts relative to the number of events detected at the same locations upon SOX4 knockdown. The adjacent pie diagram represents the relative peak score change for shared sites (NFD peak score)/(NFD + SOX4 shRNA peak score).

(F) NEUROD1 and NEUROD4 ChIP-qPCR at sites of newly open chromatin or NFD-induced genes (mean ± SD; biological triplicates).