Multi-platform analysis reveals a complex transcriptome architecture of a circovirus

Norbert Moldován, Zsolt Balázs, Dóra Tombácz, Zsolt Csabai, Attila Szűcs, Michael Snyder, Z. Boldogkői

Research output: Article

8 Citations (Scopus)

Abstract

In this study, we used Pacific Biosciences RS II long-read and Illumina HiScanSQ short-read sequencing technologies for the characterization of porcine circovirus type 1 (PCV-1) transcripts. Our aim was to identify novel RNA molecules and transcript isoforms, as well as to determine the exact 5′- and 3′-end sequences of previously described transcripts with single base-pair accuracy. We discovered a novel 3′-UTR length isoform of the Cap transcript, and a non-spliced Cap transcript variant. Additionally, our analysis has revealed a 3′-UTR isoform of Rep and two 5′-UTR isoforms of Rep’ transcripts, and a novel splice variant of the longer Rep’ transcript. We also explored two novel long transcripts, one with a previously identified splice site, and a formerly undetected mRNA of ORF3. Altogether, our methods have identified nine novel RNA molecules, doubling the size of PCV-1 transcriptome that had been known before. Additionally, our investigations revealed an intricate pattern of transcript overlapping, which might produce transcriptional interference between the transcriptional machineries of adjacent genes, and thereby may potentially play a role in the regulation of gene expression in circoviruses.

Original languageEnglish
Pages (from-to)37-46
Number of pages10
JournalVirus Research
Volume237
DOIs
Publication statusPublished - jún. 2 2017

Fingerprint

Circovirus
Transcriptome
Protein Isoforms
3' Untranslated Regions
RNA
5' Untranslated Regions
Gene Expression Regulation
Base Pairing
Technology
Messenger RNA
Genes

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases
  • Cancer Research

Cite this

Multi-platform analysis reveals a complex transcriptome architecture of a circovirus. / Moldován, Norbert; Balázs, Zsolt; Tombácz, Dóra; Csabai, Zsolt; Szűcs, Attila; Snyder, Michael; Boldogkői, Z.

In: Virus Research, Vol. 237, 02.06.2017, p. 37-46.

Research output: Article

Moldován N, Balázs Z, Tombácz D, Csabai Z, Szűcs A, Snyder M et al. Multi-platform analysis reveals a complex transcriptome architecture of a circovirus. Virus Research. 2017 jún. 2;237:37-46. https://doi.org/10.1016/j.virusres.2017.05.010
Moldován, Norbert ; Balázs, Zsolt ; Tombácz, Dóra ; Csabai, Zsolt ; Szűcs, Attila ; Snyder, Michael ; Boldogkői, Z. / Multi-platform analysis reveals a complex transcriptome architecture of a circovirus. In: Virus Research. 2017 ; Vol. 237. pp. 37-46.
@article{221d30d7b224469ca22c9f03e85a991c,
title = "Multi-platform analysis reveals a complex transcriptome architecture of a circovirus",
abstract = "In this study, we used Pacific Biosciences RS II long-read and Illumina HiScanSQ short-read sequencing technologies for the characterization of porcine circovirus type 1 (PCV-1) transcripts. Our aim was to identify novel RNA molecules and transcript isoforms, as well as to determine the exact 5′- and 3′-end sequences of previously described transcripts with single base-pair accuracy. We discovered a novel 3′-UTR length isoform of the Cap transcript, and a non-spliced Cap transcript variant. Additionally, our analysis has revealed a 3′-UTR isoform of Rep and two 5′-UTR isoforms of Rep’ transcripts, and a novel splice variant of the longer Rep’ transcript. We also explored two novel long transcripts, one with a previously identified splice site, and a formerly undetected mRNA of ORF3. Altogether, our methods have identified nine novel RNA molecules, doubling the size of PCV-1 transcriptome that had been known before. Additionally, our investigations revealed an intricate pattern of transcript overlapping, which might produce transcriptional interference between the transcriptional machineries of adjacent genes, and thereby may potentially play a role in the regulation of gene expression in circoviruses.",
keywords = "Isoform sequencing, Long-read sequencing, PacBio sequencing, Porcine circovirus, Short-read sequencing, Transcriptional interference, Transcriptome",
author = "Norbert Moldov{\'a}n and Zsolt Bal{\'a}zs and D{\'o}ra Tomb{\'a}cz and Zsolt Csabai and Attila Szűcs and Michael Snyder and Z. Boldogkői",
year = "2017",
month = "6",
day = "2",
doi = "10.1016/j.virusres.2017.05.010",
language = "English",
volume = "237",
pages = "37--46",
journal = "Virus Research",
issn = "0168-1702",
publisher = "Elsevier",

}

TY - JOUR

T1 - Multi-platform analysis reveals a complex transcriptome architecture of a circovirus

AU - Moldován, Norbert

AU - Balázs, Zsolt

AU - Tombácz, Dóra

AU - Csabai, Zsolt

AU - Szűcs, Attila

AU - Snyder, Michael

AU - Boldogkői, Z.

PY - 2017/6/2

Y1 - 2017/6/2

N2 - In this study, we used Pacific Biosciences RS II long-read and Illumina HiScanSQ short-read sequencing technologies for the characterization of porcine circovirus type 1 (PCV-1) transcripts. Our aim was to identify novel RNA molecules and transcript isoforms, as well as to determine the exact 5′- and 3′-end sequences of previously described transcripts with single base-pair accuracy. We discovered a novel 3′-UTR length isoform of the Cap transcript, and a non-spliced Cap transcript variant. Additionally, our analysis has revealed a 3′-UTR isoform of Rep and two 5′-UTR isoforms of Rep’ transcripts, and a novel splice variant of the longer Rep’ transcript. We also explored two novel long transcripts, one with a previously identified splice site, and a formerly undetected mRNA of ORF3. Altogether, our methods have identified nine novel RNA molecules, doubling the size of PCV-1 transcriptome that had been known before. Additionally, our investigations revealed an intricate pattern of transcript overlapping, which might produce transcriptional interference between the transcriptional machineries of adjacent genes, and thereby may potentially play a role in the regulation of gene expression in circoviruses.

AB - In this study, we used Pacific Biosciences RS II long-read and Illumina HiScanSQ short-read sequencing technologies for the characterization of porcine circovirus type 1 (PCV-1) transcripts. Our aim was to identify novel RNA molecules and transcript isoforms, as well as to determine the exact 5′- and 3′-end sequences of previously described transcripts with single base-pair accuracy. We discovered a novel 3′-UTR length isoform of the Cap transcript, and a non-spliced Cap transcript variant. Additionally, our analysis has revealed a 3′-UTR isoform of Rep and two 5′-UTR isoforms of Rep’ transcripts, and a novel splice variant of the longer Rep’ transcript. We also explored two novel long transcripts, one with a previously identified splice site, and a formerly undetected mRNA of ORF3. Altogether, our methods have identified nine novel RNA molecules, doubling the size of PCV-1 transcriptome that had been known before. Additionally, our investigations revealed an intricate pattern of transcript overlapping, which might produce transcriptional interference between the transcriptional machineries of adjacent genes, and thereby may potentially play a role in the regulation of gene expression in circoviruses.

KW - Isoform sequencing

KW - Long-read sequencing

KW - PacBio sequencing

KW - Porcine circovirus

KW - Short-read sequencing

KW - Transcriptional interference

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=85019742704&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85019742704&partnerID=8YFLogxK

U2 - 10.1016/j.virusres.2017.05.010

DO - 10.1016/j.virusres.2017.05.010

M3 - Article

C2 - 28549855

AN - SCOPUS:85019742704

VL - 237

SP - 37

EP - 46

JO - Virus Research

JF - Virus Research

SN - 0168-1702

ER -