Highlights d HP1, SUV39H1, and TRIM28 constitute heterochromatic H3K9me3 recognition complexes d These complexes contain multiple H3K9me3 reader chromodomains d Multivalent H3K9me3-chromodomain engagement triggers liquid-liquid phase separation d Histone modifications regulate chromatin compartmentalization via phase separation

An important component of cellular biochemistry is the concentration of proteins and nucleic acids in non-membranous compartments1,2. These biomolecular condensates are formed from processes including liquid-liquid phase separation (LLPS). The multivalent interactions necessary for LLPS have been studied extensively in vitro1,3. However, what regulates LLPS in vivo is still poorly understood. Here, we identify an in vivo regulator of LLPS through a genetic suppressor screen for loss of function of the Arabidopsis RNA-binding protein FCA. FCA contains prion-like domains that phase-separate in vitro, and exhibits behavior in vivo consistent with phase separation. The mutant screen identified a functional requirement for a coiled coil protein, FLL2, in FCA nuclear body formation. FCA reduces transcriptional read-through by promoting proximal polyadenylation at many sites in the Arabidopsis genome3,4. FLL2 was required to promote this proximal polyadenylation, but not binding of FCA to target RNA. Ectopic expression of FLL2 increased the size and number of FCA nuclear bodies. Crosslinking with formaldehyde captured in vivo interactions between FLL2, FCA and the polymerase and nuclease modules of the RNA 3’ end processing machinery. These 3’ RNA processing components were found to colocalize with FCA in the nuclear bodies in vivo. We conclude that FLL2 promotes liquid-liquid phase separation, important for dynamics of polyadenylation complexes at specific poly A sites. Our findings show that coiled coil proteins can promote LLPS, expanding our understanding of the principles governing the in vivo dynamics of liquid-like bodies.