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Native RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen

Identifiers: SRA: ERP109994
BioProject: PRJEB27861
NEW YORK UNIVERSITY SCHOOL OF MEDICINE: ena-STUDY-NEW YORK UNIVERSITY SCHOOL OF MEDICINE-20-07-2018-14:47:29:488-672
Study Type: 
Other
Abstract: Viral genomes exhibit a higher gene density and more diversified transcriptome than the host cell. Coding potential is maximized through the use of multiple reading frames, placement of genes on opposing strands, inefficient or modified use of termination signals, and the deployment of complex alternative splicing patterns. As a consequence, detailed characterization of viral transcriptomes by conventional methods can be challenging. Full length native RNA sequencing (nRNA-seq) using nanopore arrays offers an exciting alternative. Individual transcripts are sequenced directly, without potential biases inherent to the recoding or amplification steps included in other sequencing methodologies. nRNA-seq simplifies the detection of variation brought about by RNA splicing, use of alternative transcription initiation and termination sites, and other RNA modifications. Here we use nRNA-seq to profile the herpes simplex virus 1 transcriptome during early and late stages of productive infection of primary cells. We demonstrate the effectiveness of the approach and identify new intergenic transcripts, including a mRNA that accumulates late in infection that codes for a novel fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L.
Description: Viral genomes exhibit a higher gene density and more diversified transcriptome than the host cell. Coding potential is maximized through the use of multiple reading frames, placement of genes on opposing strands, inefficient or modified use of termination signals, and the deployment of complex alternative splicing patterns. As a consequence, detailed characterization of viral transcriptomes by conventional methods can be challenging. Full length native RNA sequencing (nRNA-seq) using nanopore arrays offers an exciting alternative. Individual transcripts are sequenced directly, without potential biases inherent to the recoding or amplification steps included in other sequencing methodologies. nRNA-seq simplifies the detection of variation brought about by RNA splicing, use of alternative transcription initiation and termination sites, and other RNA modifications. Here we use nRNA-seq to profile the herpes simplex virus 1 transcriptome during early and late stages of productive infection of primary cells. We demonstrate the effectiveness of the approach and identify new intergenic transcripts, including a mRNA that accumulates late in infection that codes for a novel fusion of the viral E3 ubiquitin ligase ICP0 and viral membrane glycoprotein L.

Related SRA data

Experiments:
16 ( 16 samples )
Runs:
16 (9.3Gbp; 6.4Gb)
Additional objects:
File type count
fastq 12
nanopore 5