Transcriptome Profiling Identifies a Natural Antisense Transcript of IRF4 Associated with EBV Latency

Abstract

Epstein-Barr virus (EBV) establishes distinct latency programs that drive B-cell transformation through coordinated viral and host gene regulation. However, the contribution of host long noncoding RNAs (lncRNAs) to EBV-mediated pathogenesis remains poorly understood. Here, we performed transcriptome-wide lncRNA profiling comparing Type I and Type III EBV latency and identified differentially expressed host lncRNAs, among which we characterized a previously unannotated natural antisense transcript (NAT) of IRF4, designated IRF4-AS1. IRF4-AS1 is markedly upregulated in Type III latency and positively correlates with IRF4 expression across EBV-transformed lymphoblastoid cell lines (LCLs) established from diverse clinical backgrounds. Functional studies indicate a context-dependent positive regulatory relationship between IRF4-AS1 and IRF4. While overexpression of IRF4-AS1 increased IRF4 expression and IRF4 overexpression increased IRF4-AS1 levels, loss-of-function analyses suggest that this relationship is modulated by additional regulatory inputs in established transformed cells. In contrast to IRF4, IRF4-AS1 transcription is not regulated by the LMP1- NF{kappa}B signaling, indicating that the two transcripts are regulated through partially distinct mechanisms. In addition, we identified MIR3142HG as a highly induced latency-associated lncRNA and found that its embedded miRNAs, miR-146a and miR-3142, exhibited divergent expression patterns, suggesting differential post-transcriptional regulation. Together, these findings identify IRF4-AS1 as a NAT lncRNA for IRF4 and reveal extensive remodeling of host lncRNA networks during EBV latency, providing a foundation for future studies of lncRNA- mediated host-virus interactions in EBV pathogenesis. ImportanceEBV drives B-cell transformation through extensive reprogramming of host transcriptional networks, yet the contribution of host long noncoding RNAs (lncRNAs) to this process remains poorly defined. Transcriptome-wide lncRNA profiling, together with functional analysis, identified IRF4-AS1 as a previously unannotated natural antisense transcript of IRF4. IRF4- AS1 is upregulated in Type III latency and positively correlates with IRF4 expression across EBV-transformed cells. Together, this study provides a foundation for future mechanistic studies of lncRNA-mediated host-virus interactions in EBV pathogenesis.