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

Abstract

Gene expression during natural and induced reprogramming is controlled by pioneer transcription factors that initiate transcription from closed chromatin. Nr5a2 is a key pioneer factor that regulates zygotic genome activation in totipotent embryos, pluripotency in embryonic stem cells and metabolism in adult tissues, but the mechanism of its pioneer activity remains poorly understood. Here, we present a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome. The structure shows that the conserved carboxy-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. Mutational analysis showed that NR5A2 D159 of the CTE is dispensable for DNA binding but required for stable nucleosome association and persistent DNA ‘unwrapping’. These findings suggest that NR5A2 belongs to an emerging class of pioneer factors that can use DNA minor groove anchor competition to destabilize nucleosomes and facilitate gene expression during reprogramming.

Pioneer Transcription Factors: The First Domino in Zygotic Genome Activation

“…Collectively, the combination of genome-wide binding profiles, chromatin accessibility assays and in vitro nucleosome binding has proven that Nr5a2 exhibits properties consistent with pioneer transcription factors [ 21 ]. Recently, Kobayashi et al further demonstrated the mechanism underlying how Nr5a2 engages with nucleosomes to exert its pioneer activity [ 58 ]. The crystallographic analysis of the human NR5A2-DNA complex revealed that the α-helix of the zinc finger domain binds to the major groove, while the CTE (carboxy-terminal extension) binds to the minor groove [ 59 ].…”

“…Nr5a2, acting as a monomer, specifically binds to the DNA motif on both naked DNA and nucleosomes [ 21 , 60 ]. Through presenting a cryo-electron microscopy structure of human NR5A2 bound to a nucleosome, Kobayashi et al observed the CTE loop of the NR5A2 DNA-binding domain interacts competitively with a DNA minor groove anchor of the nucleosome, facilitating the release of entry–exit site DNA, corresponding to the model in which histone–DNA interactions are compensated with pioneer transcription factor–DNA interactions [ 58 , 61 ]. Additionally, while the D159 residue of the CTE is not essential for DNA binding, it is crucial for maintaining stable nucleosome association and continuous DNA “unwrapping” [ 61 ].…”