Mechanisms of OCT4-SOX2 motif readout on nucleosomes

Abstract

Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo–electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.

Interaction of the pioneer transcription factor GATA3 with nucleosomes

“…Likewise, our proposal that transcription factor binding events may differ in productivity based on location on the nucleosome surface parallels a recent study by Thoma and colleagues 41 . In this work, nucleosome binding by Oct4 and Sox2 was explored by biochemical selection followed by sequencing.…”

Nucleosome binding by the pioneer transcription factor OCT4

“…This may happen because the POU S domain mainly binds to the nucleosomal DNA at the entry/exit site of the nucleosome. This is consistent with the cryo-EM structure, in which the POU S domain, but not the POU HD domain, of OCT4 binds to the nucleosomal target site 33 . The POU S domain may be a primary recognition module for the nucleosomal target site, and the POU HD domain may have a distinct function in later stages of gene regulation.…”

“…These findings are consistent with the previous study showing that POU-family TFs prefer the ends of nucleosomal DNA 32 . Recently, the cryo-EM structures of the OCT4-SOX2-nucleosome complexes with designed DNA sequences were reported 33 . In the structures, SOX2 peels the DNA end from the histone surface, and facilitates OCT4 binding to its target site (Fig.…”

“…In the structures, SOX2 peels the DNA end from the histone surface, and facilitates OCT4 binding to its target site (Fig. S9) 33 . These results, along with our previous findings, suggest that OCT4 prefers to bind the DNA loosely associated with or detached from the histone surface in the nucleosome.…”

“…In cells, when the OCT4 target DNA sequence is entirely wrapped in the nucleosome, it may not be targeted by OCT4 without repositioning via a nucleosome remodeling mechanism, which may be induced by the other pioneer TFs and nucleosome remodelers. Intriguingly, the cryo-EM OCT4-SOX2-nucleosome structures revealed that OCT4 binds to the nucleosomal target site with assistance from SOX2, which may induce the DNA peeling from the histone surface of the nucleosome 33 . Similar to SOX2, SOX11 also induces the DNA peeling of the nucleosomal DNA ends 35 .…”