The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [RIP-seq]

Eukaryotic chromosomes fold into topologically associating domains (TADs), which further gather in active (A) or inactive (B) genomic compartments. Here we show that Scaffold Attachment Factor B (SAFB), a nuclear matrix-associated protein with RNA binding functions, modulates global chromatin condensation in a dosage-dependent manner. Upon the depletion of SAFB, the genome coverage of Lamina-associated-domains (LADs) decreases from 53.33% to 45.93%, and both inter- and intra-TAD chromatin-chromatin interactions in compartment B decrease significantly. In the nucleus, SAFB favorably co-localizes with H3K9me3, a marker of heterochromatin, and the disruption of SAFB leads to a collapse of H3K9me3 foci. Furthermore, we show that SAFB proteins can form liquid-liquid phase separation in the cell and in vitro. Intriguingly, SAFB interacts with RNAs from repetitive elements enriched in heterochromatin (e.g., Major Satellites and LINE1), which can promote SAFB-mediated phase separation, depending on the density of SAFB recognizing motifs in the RNAs. Identification and characterization of RNAs associated with SAFB in AML12 cells