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Genome-wide transcript structure resolution reveals novel features of gammaherpesvirus transcription and yields an extensively revised murine gammaherpesvirus 68 genome annotation

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE117651 | GEO | 2019/06/25

REPOSITORIES: GEO

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Genome-wide transcript structure resolution reveals novel features of gammaherpesvirus transcription and yields an extensively revised murine gammaherpesvirus 68 genome annotation

Project description:Genome-wide transcript structure resolution reveals novel features of gammaherpesvirus transcription and yields an extensively revised murine gammaherpesvirus 68 genome annotation

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Genome-wide transcript structure resolution in murine gammaherpesvirus 68: Iso-Seq

Project description:Pacific Biosciences Iso-Seq was used in conjunction with Illumina RNA-Seq and deepCAGE to globally resolve transcript structures in lytic murine gammaherpesvirus 68.

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Genome-wide transcript structure resolution in murine gammaherpesvirus 68: 3T12 deepCAGE

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Genome-wide Transcript Structure Resolution Reveals Abundant Alternate Isoform Usage from Murine Gammaherpesvirus 68.

Project description:The gammaherpesviruses, including Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and murine gammaherpesvirus 68 (MHV68, MuHV-4, γHV68), are etiologic agents of a wide range of lymphomas and non-hematological malignancies. These viruses possess large and highly dense dsDNA genomes that feature >80 bidirectionally positioned open reading frames (ORFs). The abundance of overlapping transcripts and extensive splicing throughout these genomes have until now prohibited high throughput-based resolution of transcript structures. Here, we integrate the capabilities of long-read sequencing with the accuracy of short-read platforms to globally resolve MHV68 transcript structures using the transcript resolution through integration of multi-platform data (TRIMD) pipeline. This approach reveals highly complex features, including: (1) pervasive overlapping transcript structures; (2) transcripts containing intra-gene or trans-gene splices that yield chimeric ORFs; (3) antisense and intergenic transcripts containing ORFs; and (4) noncoding transcripts. This work sheds light on the underappreciated complexity of gammaherpesvirus transcription and provides an extensively revised annotation of the MHV68 transcriptome.

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Genome-wide transcript structure resolution in murine gammaherpesvirus 68: Illumina RNA-Seq

Project description:Strand-specific Illumina RNA-Seq was used in conjunction with Pacific Biosciences Iso-Seq and deepCAGE to globally resolve transcript structures in lytic murine gammaherpesvirus 68.

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Genome-wide transcript structure resolution in murine gammaherpesvirus 68: HE 2.1 deepCAGE

Project description:deepCAGE was used in conjunction with Pacific Biosciences Iso-Seq and Illumina RNA-Seq to globally resolve transcript structures in lytic murine gammaherpesvirus 68.

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Project description:Viral genetic studies typically focus on large open reading frames (ORFs) identified during genome annotation (ORF-based annotation). Here we describe tools for examining viral gene expression nucleotide by nucleotide across the genome. Using these tools on the 119,450 base pair (bp) genome of murine gammaherpesvirus 68 (gammaHV68) allowed us to establish that gammaHV68 RNA expression was significantly more complex than predicted from ORF-based annotation, including over 73,000 nucleotides of unexpected transcription within 30 expressed genomic regions (EGRs). Approximately 90% of this RNA expression was antisense to genomic regions containing known large ORFs. We verified the existence of previously undefined transcripts in three EGRs and determined which parts of the transcriptome depend on protein or viral DNA synthesis. This study redefines the genetic map of gammaHV68, indicating that herpesviruses contain significantly more genetic complexity than predicted from ORF-based genome annotations, and provides alternative tools and approaches for viral genetic studies.

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