Super-silencers are crucial for development and carcinogenesis in B cells.
The strength of the repressive histone H3 lysine 27 trimethylation modification signal varies drastically at individual silencers. Focusing on cases of an unusually strong repressive signal in regions that we refer to as super-silencers, we demonstrate that the regions that become B-cell super-silencers are originally associated with gene upregulation during development, and their target genes are highly expressed in stem cells, especially during early developmental stages. About 13% of B-cell super-silencers transmute to super-enhancers in B-cell lymphoma and 22% of these conversions recur across more than half of patients. Notably, genes associated with these conversions, like BCL6 and BACH2, are downregulated more swiftly than others when subjected to JQ1, a super-enhancer-disrupting bromodomain and extra-terminal domain inhibitor utilized in cancer chemotherapy. Furthermore, super-silencers are characterized by an over-representation of B-cell-cancer-associated mutations, both somatic and germline, and B-cell-cancer translocation breakpoints. This surpasses the prevalence found in other regulatory elements, such as CTCF binding sites, underlining the crucial role of super-silencers in forming and stabilizing regulatory topologies in standard B cells. For example, over 80% of cases involving the B-cell-lymphoma translocation t(3;14)(q27;q32) fuse super-silencers in the BCL6 locus with enhancer-rich domains. Finally, we demonstrate that the repressive mechanisms of super-silencers are partially governed by the CpG content in their sequences. While CpG-rich super-silencers often prevent promoters from interacting with enhancers, CpG-depleted super-silencers typically suppress the chromatin looping of nearby enhancers. In summary, our findings accentuate the critical role super-silencers play in the normal function of B-cells, suggesting that sequence mutations and activity modifications in these elements could be primary factors in B-cell carcinogenesis.