Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by minor groove anchor competition

Abstract

AbstractGene expression during natural and induced reprogramming is controlled by pioneer transcription factors, which bind nucleosomal DNA and initiate gene expression from closed chromatin. How pioneer factors perform this function is poorly understood. Nr5a2 is a pioneer factor that is critical for zygotic genome activation (ZGA) in totipotent embryos, pluripotency in embryonic stem cells and metabolic regulation in adult tissues. To study how Nr5a2 functions as a pioneer factor, we used cryo-electron microscopy to determine a structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved C-terminal extension (CTE) loop of the NR5A2 DNA-binding domain competes with a DNA minor groove anchor of the nucleosome and releases entry-exit site DNA at a ∼50° angle. Residue aspartic acid 159 of the CTE loop induces the rearrangement by shifting a histone H2A α2 helix towards the nucleosome center. Mutational analysis showed that NR5A2 D159 is largely dispensable for DNA binding but required for stable nucleosome association and persistent DNA unwrapping. These findings suggest that NR5A2 belongs to a previously unknown class of pioneer factors that can use minor groove anchor competition to destabilize nucleosomes and facilitate gene expression changes during reprogramming.