Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses

Long-read sequencing (LRS) techniques are very recent advancements, but they have already been used for transcriptome research in all of the three subfamilies of herpesviruses. These techniques have multiplied the number of known transcripts in each of the examined viruses. Meanwhile, they have revealed a so far hidden complexity of the herpesvirus transcriptome with the discovery of a large number of novel RNA molecules, including coding and non-coding RNAs, as well as transcript isoforms, and polycistronic RNAs. Additionally, LRS techniques have uncovered an intricate meshwork of transcriptional overlaps between adjacent and distally located genes. Here, we review the contribution of LRS to herpesvirus transcriptomics and present the complexity revealed by this technology, while also discussing the functional significance of this phenomenon.

• Publication year

  2018

• Venue

  Frontiers in Genetics

• Publication date

  2018-07-17

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.3389/fgene.2018.00259PMID 30065753PMCID 6056645
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Herpes simplex virus ICP27 protein provides viral mRNAs with access to the cellular mRNA export pathway

  2023cited by this paper
• SMRT-Cappable-seq reveals complex operon variants in bacteria

  2018influential reference
• Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus

  2018influential reference
• Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing

  2017cited by this paper
• Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials

  2017influential reference
• Nanopore sequencing and assembly of a human genome with ultra-long reads

  2017cited by this paper
• Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis

  2017cited by this paper
• SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

  2017cited by this paper
• Transcriptome-wide characterization of human cytomegalovirus in natural infection and experimental latency

  2017cited by this paper
• Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1

  2017cited by this paper
• Role of N Terminus-Truncated NS1 Proteins of Influenza A Virus in Inhibiting IRF3 Activation

  2016cited by this paper
• Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses

  2016cited by this paper
• Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus

  2016cited by this paper
• Highly parallel direct RNA sequencing on an array of nanopores

  2016cited by this paper
• The Splicing History of an mRNA Affects Its Level of Translation and Sensitivity to Cleavage by the Virion Host Shutoff Endonuclease during Herpes Simplex Virus Infections

  2016cited by this paper
• Global transcript structure resolution of high gene density genomes through multi-platform data integration

  2016cited by this paper
• PacBio Sequencing and Its Applications

  2015cited by this paper
• Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches

  2015cited by this paper
• Characterization of pseudorabies virus transcriptome by Illumina sequencing

  2015cited by this paper
• KSHV 2.0: A Comprehensive Annotation of the Kaposi's Sarcoma-Associated Herpesvirus Genome Using Next-Generation Sequencing Reveals Novel Genomic and Functional Features

  2014influential reference
• Sources of PCR-induced distortions in high-throughput sequencing data sets

  2014cited by this paper
• Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

  2013cited by this paper
• Dual Short Upstream Open Reading Frames Control Translation of a Herpesviral Polycistronic mRNA

  2013cited by this paper
• Modulation of the UGT2B7 Enzyme Activity by C-Terminally Truncated Proteins Derived from Alternative Splicing

  2013influential reference
• Assessment of transcript reconstruction methods for RNA-seq

  2013cited by this paper
• Epstein–Barr virus protein EB2 stimulates cytoplasmic mRNA accumulation by counteracting the deleterious effects of SRp20 on viral mRNAs

  2012cited by this paper
• Non-canonical translation in RNA viruses

  2012cited by this paper
• An Integrated Encyclopedia of DNA Elements in the Human Genome

  2012cited by this paper
• Decoding Human Cytomegalovirus

  2012cited by this paper
• Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci

  2012cited by this paper
• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

  2012cited by this paper
• Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci

  2012cited by this paper
• High-resolution human cytomegalovirus transcriptome

  2011cited by this paper
• Herpesviruses: General Properties

  2010cited by this paper
• Virology: Principles and Applications

  2008cited by this paper
• Recruitment of the Complete hTREX Complex Is Required for Kaposi's Sarcoma–Associated Herpesvirus Intronless mRNA Nuclear Export and Virus Replication

  2008cited by this paper
• HUMAN CYTOMEGALOVIRUS: INFECTIONS AND DIAGNOSIS

  2008cited by this paper
• Noncanonical TATA Sequence in the UL44 Late Promoter of Human Cytomegalovirus Is Required for the Accumulation of Late Viral Transcripts

  2007cited by this paper
• Simian Varicella Virus Expresses a Latency-Associated Transcript That Is Antisense to Open Reading Frame 61 (ICP0) mRNA in Neural Ganglia of Latently Infected Monkeys

  2007cited by this paper
• Comparative analysis of the genomes

  2007cited by this paper
• Reverse transcriptase template switching and false alternative transcripts.

  2006cited by this paper
• Identification of a Novel Bovine Herpesvirus 1 Transcript Containing a Small Open Reading Frame That Is Expressed in Trigeminal Ganglia of Latently Infected Cattle

  2004cited by this paper
• Viral Regulation of mRNA Export

  2004cited by this paper
• Expression

  2003cited by this paper
• Regulation of herpes simplex virus gene expression.

  2001cited by this paper
• Identification of a novel 0.7-kb polyadenylated transcript in the LAT promoter region of HSV-1 that is strain specific and may contribute to virulence.

  1999cited by this paper
• Latency-associated transcripts of equine herpesvirus type 4 in trigeminal ganglia of naturally infected horses.

  1999cited by this paper
• Human cytomegalovirus latent gene expression in granulocyte-macrophage progenitors in culture and in seropositive individuals.

  1996cited by this paper
• The detection of latency-associated transcripts of equine herpesvirus 1 in ganglionic neurons.

  1995cited by this paper
• G and C accumulation at silent positions of codons produces additional ORFs.

  1995cited by this paper
• In vitro promoter activity associated with the latency-associated transcript gene of herpes simplex virus type 1.

  1989cited by this paper
• The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1.

  1988cited by this paper
• Determinant of cistron specificity in bacterial ribosomes

  1975cited by this paper
• IDENTIFICATION OF NOVEL

  1964cited by this paper

• Cross-Species Analysis of Transcriptomic Response to Alpha-Herpesvirus Infection in Human, Bovine and Equine Cells

  2026cites this paper
• Cross‐Species Insights Into Gamma Herpesvirus Transcriptomes: Long‐Read and Multi‐Omics Perspectives

  2026cites this paper
• Development of an mRNA-specific real-time PCR for the detection of replicating cyprinid herpesvirus-3 (CyHV-3) in carp and non-target species.

  2025cites this paper
• Virally-Encoded Long and Short Non-Coding RNAs

  2023cites this paper
• EST–SSR Marker Development and Full-Length Transcriptome Sequence Analysis of Tiger Lily (Lilium lancifolium Thunb)

  2022cites this paper
• Full-Length Transcriptome Sequencing and EST-SSR marker development of tiger lily (Lilium lancifolium Thunb.)

  2021cites this paper
• New approach of genetic characterization of group A rotaviruses by the nanopore sequencing method.

  2021cites this paper
• MinION nanopore sequencing and assembly of a complete human papillomavirus genome

  2021cites this paper
• PacBio Long-Read Sequencing Transcriptome Dataset of Adult Harmonia axyridis Under Diapause Inducing and Reproductive Inducing Photoperiod

  2020cites this paper
• The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

  2020cites this paper
• Long-read assays shed new light on the transcriptome complexity of a viral pathogen

  2020cites this paper
• Meta-analytic approach for transcriptome profiling of herpes simplex virus type 1

  2020cites this paper
• Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus

  2020cites this paper
• Meta-analytic approach for transcriptome profiling of herpes simplex virus type 1

  2020cites this paper
• Demand for Multiplatform and Meta-analytic Approaches in Transcriptome Profiling

  2019cites this paper
• RNA splicing analysis in genomic medicine.

  2019cites this paper
• LONG-READ RNA SEQUENCING ANALYSIS OF THE LYTIC HUMAN CYTOMEGALOVIRUS TRANSCRIPTOME

  2019cites this paper
• Multiple Long-read Sequencing Survey of Herpes Simplex Virus Lytic Transcriptome

  2019cites this paper
• Physiological roles of antisense RNAs in prokaryotes.

  2019cites this paper
• MinION sequencing to genotype US strains of infectious laryngotracheitis virus

  2019cites this paper
• Futuristic Methods in Virus Genome Evolution Using the Third-Generation DNA Sequencing and Artificial Neural Networks

  2019cites this paper
• Proteogenomic Identification of a Novel Protein-Encoding Gene in Bovine Herpesvirus 1 That Is Expressed during Productive Infection

  2018cites this paper