During Meiosis, Gene Expression Is Silenced in Aberrantly Unsynapsed Chromatin and in Heterogametic Sex Chromosomes.

During meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we utilized a novel approach of CRISPR-cas9 engineering in Caenorhabditis elegans to create non-translocated, bisected X chromosomes. We analyzed the sequence of the entire X chromosome, identified highly homologous regions within it, and directed four gRNAs to both regions. Using Nanopore long read technology, we screened several lines with small deletions, and identified two strain in which the cuts within the chromosome led to genomic cleavage and aberrant repair that bisected the chromosome. One of the strains contained a linear and circular mini-chromosome was created using DNA vectors, and the other which had only linear segments was created by a RNP approach. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase ii staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed. Moreover, our work highlight that CRISPR can be used to create new genomic setups that can highlight hidden molecular processes.