About: Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome
Creator	Snyder, Michael Boldogkői, Zsolt Balázs, Zsolt Boldogkő, Miklós Boldogkő, Zsolt Csabai, Zsolt Gulyás, Gábor Moldován, Norbert Ratnaparkhe, Milind Tombácz, Dóra
source	PMC
abstract	Long-read sequencing (LRS) has become increasingly important in RNA research due to its strength in resolving complex transcriptomic architectures. In this regard, currently two LRS platforms have demonstrated adequate performance: the Single Molecule Real-Time Sequencing by Pacific Biosciences (PacBio) and the nanopore sequencing by Oxford Nanopore Technologies (ONT). Even though these techniques produce lower coverage and are more error prone than short-read sequencing, they continue to be more successful in identifying polycistronic RNAs, transcript isoforms including splice and transcript end variants, as well as transcript overlaps. Recent reports have successfully applied LRS for the investigation of the transcriptome of viruses belonging to various families. These studies have substantially increased the number of previously known viral RNA molecules. In this work, we used the Sequel and MinION technique from PacBio and ONT, respectively, to characterize the lytic transcriptome of the herpes simplex virus type 1 (HSV-1). In most samples, we analyzed the poly(A) fraction of the transcriptome, but we also performed random oligonucleotide-based sequencing. Besides cDNA sequencing, we also carried out native RNA sequencing. Our investigations identified more than 2,300 previously undetected transcripts, including coding, and non-coding RNAs, multi-splice transcripts, as well as polycistronic and complex transcripts. Furthermore, we found previously unsubstantiated transcriptional start sites, polyadenylation sites, and splice sites. A large number of novel transcriptional overlaps were also detected. Random-primed sequencing revealed that each convergent gene pair produces non-polyadenylated read-through RNAs overlapping the partner genes. Furthermore, we identified novel replication-associated transcripts overlapping the HSV-1 replication origins, and novel LAT variants with very long 5’ regions, which are co-terminal with the LAT-0.7kb transcript. Overall, our results demonstrated that the HSV-1 transcripts form an extremely complex pattern of overlaps, and that entire viral genome is transcriptionally active. In most viral genes, if not in all, both DNA strands are expressed.
has issue date	2019-09-24(xsd:dateTime)
bibo:doi	10.3389/fgene.2019.00834
bibo:pmid	31608102
has license	cc-by
sha1sum (hex)	70854e087e3757f5f8edadee91fcf9de1609b0bd
schema:url	https://doi.org/10.3389/fgene.2019.00834
resource representing a document's title	Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome
has PubMed Central identifier	PMC6769088
has PubMed identifier	31608102
schema:publication	Front Genet
resource representing a document's body	covid:70854e087e3757f5f8edadee91fcf9de1609b0bd#body_text
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