EBER-associated Promoter Contacts Mark Accessible but Transcriptionally Constrained RNAPII Promoter Hubs in EBV-positive B Cells

Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) are abundant viral noncoding RNAs that associate with host chromatin, but the promoter-scale consequences of those contacts remain unclear. We re-analyzed GSE281522 in EBV-positive GM12878 cells integrating RNA–DNA contacts, RNAPII ChIA-PET, RNA-seq and internal ATAC-seq after EBER depletion. Promoters were classified according to increased RNAPII-associated promoter-looping signal after EBER depletion relative to the matched control conditions, defined as LoopRecovery; increased transcriptional output, defined as ExprUp; or the coordinated occurrence of both responses, defined as Recovery + Up. EBER-contacted promoters were markedly depleted for Recovery + Up relative to non-contacted promoters (0.42