Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1

In this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize the poly(A)+ fraction of the lytic transcriptome of the herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, 10 non-coding RNAs, as well as...

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Main Authors: Dóra Tombácz, Zsolt Csabai, Attila Szűcs, Zsolt Balázs, Norbert Moldován, Donald Sharon, Michael Snyder, Zsolt Boldogkői
Format: Article
Language:English
Published: Frontiers Media S.A. 2017-06-01
Series:Frontiers in Microbiology
Subjects:
Online Access:http://journal.frontiersin.org/article/10.3389/fmicb.2017.01079/full
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author Dóra Tombácz
Zsolt Csabai
Attila Szűcs
Zsolt Balázs
Norbert Moldován
Donald Sharon
Michael Snyder
Zsolt Boldogkői
author_facet Dóra Tombácz
Zsolt Csabai
Attila Szűcs
Zsolt Balázs
Norbert Moldován
Donald Sharon
Michael Snyder
Zsolt Boldogkői
author_sort Dóra Tombácz
collection DOAJ
description In this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize the poly(A)+ fraction of the lytic transcriptome of the herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, 10 non-coding RNAs, as well as 17 polycistronic and complex transcripts. This work also led us to identify many transcript isoforms, including 13 splice and 68 transcript end variants, as well as several transcript overlaps. Additionally, we determined previously unascertained transcriptional start and polyadenylation sites. We analyzed the transcriptional activity from the complementary DNA strand in five convergent HSV gene pairs with quantitative RT-PCR and detected antisense RNAs in each gene. This part of the study revealed an inverse correlation between the expressions of convergent partners. Our work adds new insights for understanding the complexity of the pervasive transcriptional overlaps by suggesting that there is a crosstalk between adjacent and distal genes through interaction between their transcription apparatuses. We also identified transcripts overlapping the HSV replication origins, which may indicate an interplay between the transcription and replication machineries. The relative abundance of HSV-1 transcripts has also been established by using a novel method based on the calculation of sequencing reads for the analysis.
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spelling doaj.art-69899a488fe84f208eda6484d0109cfe2022-12-21T19:54:26ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2017-06-01810.3389/fmicb.2017.01079275160Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1Dóra Tombácz0Zsolt Csabai1Attila Szűcs2Zsolt Balázs3Norbert Moldován4Donald Sharon5Michael Snyder6Zsolt Boldogkői7Department of Medical Biology, Faculty of Medicine, University of SzegedSzeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of SzegedSzeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of SzegedSzeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of SzegedSzeged, HungaryDepartment of Medical Biology, Faculty of Medicine, University of SzegedSzeged, HungaryDepartment of Genetics, School of Medicine, Stanford UniversityStanford, CA, United StatesDepartment of Genetics, School of Medicine, Stanford UniversityStanford, CA, United StatesDepartment of Medical Biology, Faculty of Medicine, University of SzegedSzeged, HungaryIn this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize the poly(A)+ fraction of the lytic transcriptome of the herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, 10 non-coding RNAs, as well as 17 polycistronic and complex transcripts. This work also led us to identify many transcript isoforms, including 13 splice and 68 transcript end variants, as well as several transcript overlaps. Additionally, we determined previously unascertained transcriptional start and polyadenylation sites. We analyzed the transcriptional activity from the complementary DNA strand in five convergent HSV gene pairs with quantitative RT-PCR and detected antisense RNAs in each gene. This part of the study revealed an inverse correlation between the expressions of convergent partners. Our work adds new insights for understanding the complexity of the pervasive transcriptional overlaps by suggesting that there is a crosstalk between adjacent and distal genes through interaction between their transcription apparatuses. We also identified transcripts overlapping the HSV replication origins, which may indicate an interplay between the transcription and replication machineries. The relative abundance of HSV-1 transcripts has also been established by using a novel method based on the calculation of sequencing reads for the analysis.http://journal.frontiersin.org/article/10.3389/fmicb.2017.01079/fullhuman herpesvirus 1herpes simplex virus type 1transcriptometranscriptional interferencefull-length sequencinglong-read sequencing
spellingShingle Dóra Tombácz
Zsolt Csabai
Attila Szűcs
Zsolt Balázs
Norbert Moldován
Donald Sharon
Michael Snyder
Zsolt Boldogkői
Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
Frontiers in Microbiology
human herpesvirus 1
herpes simplex virus type 1
transcriptome
transcriptional interference
full-length sequencing
long-read sequencing
title Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
title_full Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
title_fullStr Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
title_full_unstemmed Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
title_short Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1
title_sort long read isoform sequencing reveals a hidden complexity of the transcriptional landscape of herpes simplex virus type 1
topic human herpesvirus 1
herpes simplex virus type 1
transcriptome
transcriptional interference
full-length sequencing
long-read sequencing
url http://journal.frontiersin.org/article/10.3389/fmicb.2017.01079/full
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