TY - JOUR
T1 - Time-course transcriptome profiling of a poxvirus using long-read full-length assay
AU - Tombácz, D. ra
AU - Prazsák, István
AU - Torma, G. bor
AU - Csabai, Zsolt
AU - Balázs, Zsolt
AU - Moldován, Norbert
AU - Dénes, B. la
AU - Snyder, Michael
AU - Boldogkői, Zsolt
N1 - Funding Information:
Funding: This study was supported by the National Research, Development and Innovation Office (NRDIO) grants FK 128252 to DT and K 128247 to ZBo. IP was supported by the ÚNKP-20-4 -SZTE-140 New National Excellence Program of the Ministry of Human Capacities.
Publisher Copyright:
© 2021 by the authors.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2021/8/1
Y1 - 2021/8/1
N2 - Viral transcriptomes that are determined using first- and second-generation sequencing techniques are incomplete. Due to the short read length, these methods are inefficient or fail to distinguish between transcript isoforms, polycistronic RNAs, and transcriptional overlaps and readthroughs. Additionally, these approaches are insensitive for the identification of splice and transcriptional start sites (TSSs) and, in most cases, transcriptional end sites (TESs), especially in transcript isoforms with varying transcript ends, and in multi-spliced transcripts. Long-read sequencing is able to read full-length nucleic acids and can therefore be used to assemble complete transcriptome atlases. Although vaccinia virus (VACV) does not produce spliced RNAs, its transcriptome has a high diversity of TSSs and TESs, and a high degree of polycistronism that leads to enormous complexity. We applied single-molecule, real-time, and nanopore-based sequencing methods to investigate the time-lapse transcriptome patterns of VACV gene expression.
AB - Viral transcriptomes that are determined using first- and second-generation sequencing techniques are incomplete. Due to the short read length, these methods are inefficient or fail to distinguish between transcript isoforms, polycistronic RNAs, and transcriptional overlaps and readthroughs. Additionally, these approaches are insensitive for the identification of splice and transcriptional start sites (TSSs) and, in most cases, transcriptional end sites (TESs), especially in transcript isoforms with varying transcript ends, and in multi-spliced transcripts. Long-read sequencing is able to read full-length nucleic acids and can therefore be used to assemble complete transcriptome atlases. Although vaccinia virus (VACV) does not produce spliced RNAs, its transcriptome has a high diversity of TSSs and TESs, and a high degree of polycistronism that leads to enormous complexity. We applied single-molecule, real-time, and nanopore-based sequencing methods to investigate the time-lapse transcriptome patterns of VACV gene expression.
KW - Gene expression
KW - Long-read sequencing
KW - Nanopore sequencing
KW - Transcriptome profiling
KW - Vaccinia virus
UR - http://www.scopus.com/inward/record.url?scp=85111704949&partnerID=8YFLogxK
U2 - 10.3390/pathogens10080919
DO - 10.3390/pathogens10080919
M3 - Article
C2 - 34451383
VL - 10
JO - Pathogens
JF - Pathogens
SN - 2076-0817
IS - 8
M1 - 919
ER -