Nucleolar migration regulates meiotic sex chromosome inactivation via phase separation during mammalian spermatogenesis

During spermatogenesis, the unsynapsed XY chromosomes undergo meiotic sex chromosome inactivation (MSCI) and form a heterochromatic XY body. Defects in MSCI lead to meiotic arrest and male infertility. Although DNA damage response (DDR) factors are established as key initiators of MSCI, how transcriptional silencing is subsequently achieved remains elusive. Here, we identify the nucleolar components NPM1, SENP3, and rRNA as essential downstream effectors of DDR signaling in MSCI. During pachytene, these components migrate to and transiently cover the XY body during MSCI establishment, before becoming restricted to a corner of the XY body. Genetic deletion of Npm1 or Senp3, or inhibition of rRNA transcription severely impairs MSCI. Mechanistically, SENP3-mediated deSUMOylation of NPM1 promotes its interaction with rRNA, enabling liquid-liquid phase separation, via which they exclude Pol II from the XY body. Together, these data reveal a previously unrecognized role of nucleolar components in the transcriptional regulation of MSCI in mammalian spermatogenesis. Overall design: Small scale in situ high throughput chromatin conformation capture (sisHi-C) or RNA-seq for WT and mutant zygotene, pachytene, or diplotene spermatocytes