DNA-binding and dimerization of the SOG1 NAC domain are functionally linked with its ability to undergo liquid-liquid phase separation

Abstract

Liquid-liquid phase separation is a key phenomenon in the regulation of transcription in eukaryotes leading to the formation of so-called membraneless organelles. While transcription factors take part in several types of membrane-less organelles, it remains unclear how specific DNA binding, multivalent interactions with DNA/RNA and condensation are interlinked. Here we show that the NAC domain of SOG1 (SOG1NAC), a transcription factor that is central to the DNA damage response in plants, can undergo liquid-liquid phase separation in vitro in the presence of both RNA or double stranded DNA. This behaviour, as well as the ability of SOG1NAC to bind DNA in a sequence-specific manner are dependent on its potential to form homodimers and the presence of a cluster of positive charges in its DNA binding site. Short double-stranded DNA fragments containing the sequence motif that is specifically recognized by SOG1NAC inhibit RNA-mediated phase separation, suggesting overlapping binding sites for DNA and RNA. This may reflect a complex interplay between DNA and RNA binding that could control the formation of condensates at transcription sites.