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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
O'Grady T,Wang X,Höner Zu Bentrup K,Baddoo M,Concha M,Flemington EKdoi
10.1093/nar/gkw629subject
Has Abstractpub_date
2016-10-14 00:00:00pages
e145issue
18eissn
0305-1048issn
1362-4962pii
gkw629journal_volume
44pub_type
杂志文章abstract：:A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexibl...
journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2014-06-01 00:00:00
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journal_title：Nucleic acids research
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journal_title：Nucleic acids research
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journal_title：Nucleic acids research
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doi：10.1093/nar/gkv912
更新日期：2016-02-18 00:00:00
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journal_title：Nucleic acids research
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更新日期：2018-09-06 00:00:00
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更新日期：2003-07-01 00:00:00
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journal_title：Nucleic acids research
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2014-01-01 00:00:00
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更新日期：2007-01-01 00:00:00
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更新日期：2011-01-01 00:00:00
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更新日期：1995-06-25 00:00:00
