ArticleNucleic acids research2016
Global transcript structure resolution of high gene density genomes through multi-platform data integration.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
69 citing papers in PubMed.
- Omics-Level Approaches to Studying Gammaherpesvirus Infection.Pathogens (Basel, Switzerland) · 2026Review
- Herpesvirus-encoded lncRNA targets host splicing by interacting with splicing factors.PLoS pathogens · 2026Article
- Veterinary Herpesviruses: Experimental Tools for Transcriptomics and Neuroscience.Veterinary sciences · 2026Review
- Cross-Species Insights Into Gamma Herpesvirus Transcriptomes: Long-Read and Multi-Omics Perspectives.Journal of medical virology · 2026Review
- A direct RNA-seq-based EBV latency transcriptome offers insights into the biogenesis of EBV gene products.The Journal of general virology · 2025Article
- Comprehensive resolution and classification of the Epstein Barr virus transcriptome.Nature communications · 2025Article
- Long-read transcriptomics of caviid gammaherpesvirus 1: compiling a comprehensive RNA atlas.mSystems · 2025Article
- Mapping the temporal transcriptomic signature of a viral pathogen through CAGE and nanopore sequencing.PloS one · 2025Article
- Long-read Transcriptomics of Caviid Gammaherpesvirus 1: Compiling a Comprehensive RNA Atlas.bioRxiv : the preprint server for biology · 2024Article
- Unveiling axolotl transcriptome for tissue regeneration with high-resolution annotation via long-read sequencing.Computational and structural biotechnology journal · 2024Article
- Exploring the transcriptomic profile of human monkeypox virus via CAGE and native RNA sequencing approaches.mSphere · 2024Article
- High-density resolution of the Kaposi's sarcoma associated herpesvirus transcriptome identifies novel transcript isoforms generated by long-range transcription and alternative splicing.Nucleic acids research · 2024Article
- Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection.EMBO reports · 2024Article
- KSHV 3.0: a state-of-the-art annotation of the Kaposi's sarcoma-associated herpesvirus transcriptome using cross-platform sequencing.mSystems · 2024Article
- Evaluation of immune sensor responses to a viral small noncoding RNA.Frontiers in cellular and infection microbiology · 2024Article
- Identification of herpesvirus transcripts from genomic regions around the replication origins.Scientific reports · 2023Article
- KSHV 3.0: A State-of-the-Art Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Transcriptome Using Cross-Platform Sequencing.bioRxiv : the preprint server for biology · 2023Article
- Better late than never: A unique strategy for late gene transcription in the beta- and gammaherpesviruses.Seminars in cell & developmental biology · 2023Review
- Hybrid sequencing discloses unique aspects of the transcriptomic architecture in equid alphaherpesvirus 1.Heliyon · 2023Article
- Reactivation of Epstein-Barr Virus from Latency Involves Increased RNA Polymerase Activity at CTCF Binding Sites on the Viral Genome.Journal of virology · 2023Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity than is captured by existing annotation. The pervasive nature of overlapping transcription throughout herpesvirus genomes, however, poses substantial problems in resolving transcript structures using these methods alone. We present an approach that combines the unique attributes of Pacific Biosciences Iso-Seq long-read, Illumina short-read and deepCAGE (Cap Analysis of Gene Expression) sequencing to globally resolve polyadenylated isoform structures in replicating Epstein-Barr virus (EBV). Our method, Transcriptome Resolution through Integration of Multi-platform Data (TRIMD), identifies nearly 300 novel EBV transcripts, quadrupling the size of the annotated viral transcriptome. These findings illustrate an array of mechanisms through which EBV achieves functional diversity in its relatively small, compact genome including programmed alternative splicing (e.g. across the IR1 repeats), alternative promoter usage by LMP2 and other latency-associated transcripts, intergenic splicing at the BZLF2 locus, and antisense transcription and pervasive readthrough transcription throughout the genome.
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Registered trials
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 OpenQuestion graph.