Identification of a silencer-like non-coding RNA transcribed from a region on the super-enhancer conferring B-cell lymphomagenesis

However, the functional complexity of SE-derived non-coding RNAs in B-cell lymphoma remains poorly understood. Here, we identify a lymphoma-specific SE located between the RGS1 and RGS13 loci (RGS-SE) through integrative in silico analysis of diffuse large B-cell lymphoma (DLBCL) enhancer landscapes.

CRISPR/Cas9-mediated deletion of RGS-SE markedly impaired proliferation of Burkitt lymphoma cells and suppressed xenograft tumor growth, establishing its oncogenic relevance. Capture Hi-C revealed physical interactions between RGS-SE and the promoters of both RGS1 and RGS13, indicating a cis-regulatory architecture. Unexpectedly, transcriptomic analyses demonstrated that RGS-SE deletion increased RGS1 expression while modestly affecting RGS13, suggesting non-canonical regulatory activity.