Evolutional heterochromatin condensation delineates chromocenter formation and retrotransposon constraint in plants

Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. However, it is a riddle why the presence of chromocenters is variable across species. Here, we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimera of ADCP1 and HMGA, which enables formation of chromocenters remarkably. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and constraining retrotransposons. 1. Arabidopsis ChIP: ADCP1 ChIP were performed with GFP antibody using ADCP1-GFP tagged transgenic plants, HMGA ChIP were performed with mCherry antibody using mCherry-HMGA tagged transgenic plants, and Col-0 with no tag as control. H3K9me2 ChIP performed in Col-0 and H3 ChIP as control. 2. Tobacco ChIP: AtADCP1/NbADCP1/NbADCP1+Atlinkers ChIP were performed with GFP antibody using corresponding GFP tagged transgenic tobacco plants, and tobacco with no tag as control. H3K9me2 ChIP performed in tobacco with no tag. 3. Tomato ChIP: AtADCP1 ChIP were performed with GFP antibody using corresponding GFP tagged transgenic tomato plants, and tomato with no tag as control. H3K9me2 ChIP performed in tomato with no tag. Arabidopsis ADCP1 ChIP were performed with GFP antibody using ADCP1-GFP tagged transgenic plants, and Col-0 with no tag as control. H3K9me2 ChIP performed in suvh456, and H3 ChIP as control.