EBV-BACs

EBV-BACs provides scripts, analyzed data, and an improved annotation for characterizing Epstein-Barr virus transcriptomes using direct RNA-seq.

Key Features:

• Direct RNA-seq pipeline: Ensures appropriate mapping of the W promoter (Wp) 5' exon and corrects W1-W2 exon counts that misalign to internal repeat 1 (IR1).
• Improved EBV annotation: Provides an updated B95-8-BAC and prototype EBV transcriptome annotation in gff3 format based on direct RNA-seq findings.
• Analyzed datasets: Includes processed and analyzed data from LCLs generated with B95-8 EBV-BACs, including one engineered with barcodes in the first and last repeat of IR1.
• Transcript characterization: Identifies a short variant of exon W2, a novel polyA site before EBNA2, and transcripts extending across established gene boundaries from EBNA to BART to LMP2 gene regions.

Scientific Applications:

• EBV latency transcriptome analysis: Characterizes EBV transcripts in lymphoblastoid cell lines (LCLs) in Latency III, including EBNAs, LMPs, microRNAs, and BART long non-coding RNAs.
• Alternative splicing analysis: Investigates extensive alternative splicing in BART and EBNA transcription units, including splicing across IR1 and Wp-derived versus Cp-derived transcript patterns.
• miRNA processing studies: Provides insights into BHRF1 miRNA processing and coordination between polyA and splice site usage.
• BAC transcriptome integrity assessment: Identifies disruptions to BART transcript integrity caused by premature polyadenylation and cryptic splice sites in the hygromycin expression cassette of the BAC region.

Methodology:

Long-read nanopore direct RNA-seq was used to analyze EBV transcriptomes from LCLs generated with B95-8 EBV-BACs. The pipeline ensures appropriate mapping of the W promoter (Wp) 5' exon and corrects W1-W2 exon counts that misalign to IR1.