EBER-associated promoter contacts mark accessible but transcriptionally constrained RNAPII promoter hubs in EBV-positive B cells.

Shaik Ismail Mohammed Thangameeran, Hemalatha Mani, Chih-Wen Peng

Abstract read

In one paragraph

Article in Epigenetics & chromatin, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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5 · Who and what money

Authors and funding

3 authors.

Shaik Ismail Mohammed ThangameeranDepartment of Biochemistry and Molecular Medicine, National Dong Hwa University, Shoufeng, Hualien, 974301, Taiwan (R.O.C.).

Hemalatha ManiDepartment of Biochemistry and Molecular Medicine, National Dong Hwa University, Shoufeng, Hualien, 974301, Taiwan (R.O.C.).

Chih-Wen PengDepartment of Biochemistry and Molecular Medicine, National Dong Hwa University, Shoufeng, Hualien, 974301, Taiwan (R.O.C.). pengcw@gms.ndhu.edu.tw.ORCID https://orcid.org/0000-0003-1985-018X

Funding

National Dong Hwa University 114T2560-09National Science and Technology Council NSTC 112-2314-B-259-002-MY3

6 · The paper itself

Abstract

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% vs 2.00%; OR ~ 0.21; Fisher's exact p ~ 6.3 × 10

Indexed as

B-LymphocytesHerpesvirus 4, HumanPromoter Regions, GeneticRNA Polymerase IIRNA, ViralChromatinHumansTranscription, GeneticChromatinRNA Polymerase IIRNA, ViralATAC-seqChromatin accessibilityComputational genomicsEBEREpstein–Barr virus (EBV)Promoter loopingRNA-chromatin interactionsRNAPII ChIA-PETTNFA/NFκB

Identifiers

PMID42477823

DOI10.1186/s13072-026-00688-9

PMCPMC13663097

What Socratic holds

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Read underepoch 390

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.