SRA

Genomic regions preferentially associate with regions of similar transcriptional activity, partitioning genomes into active and inactive compartments within the nucleus. Here we explored mechanisms controlling genome compartment organization in C. elegans and investigated roles for compartments in regulating gene expression. The distal arms of C. elegans chromosomes, which are enriched for heterochromatic histone modifications including H3K9me, interact with each other both in cis and in trans, while interacting less frequently with central regions of chromosomes, leading to genome compartmentalization. Arms are anchored to the nuclear periphery via the nuclear envelope protein CEC-4, which binds to H3K9me. By performing genome-wide chromosome conformation capture experiments (Hi-C), we showed that eliminating H3K9me1/me2/me3 through mutations in the methyltransferase genes met-2 and set-25 significantly impaired formation of genome compartments. cec-4 mutations also impaired compartmentalization, but to a lesser extent. We found that H3K9me promotes compartmentalization through two distinct mechanisms: perinuclear anchoring of chromosome arms via CEC-4 to promote their cis association, and an anchoring-independent mechanism that compacts individual chromosome arms. In both met-2 set-25 and cec-4 mutants, no dramatic changes in gene expression were found for genes that switched compartments or for genes that remained in their original compartment, suggesting that compartment strength does not dictate gene expression levels. Furthermore, H3K9me, but not perinuclear anchoring, also contributes to formation of another prominent feature of chromosome organization, megabase-scale topologically associating domains on X that are established by the dosage-compensation condensin complex. Our results demonstrate that H3K9me plays crucial roles in regulating genome organization at multiple levels. Overall design: We performed in situ Hi-C on nuclei isolated from mixed stage embryos and processed data as in (Brejc et al., 2017). We performed Hi-C for three biological replicates of GW0638 met-2 set-25 and two biological replicates of RB2301 cec-4 mutant embryos.