NDLI: Integrative profiling of Epstein–Barr virus transcriptome using a multiplatform approach

Content Provider	Springer Nature : BioMed Central
Author	Fülöp, Ádám Torma, Gábor Moldován, Norbert Szenthe, Kálmán Bánáti, Ferenc Almsarrhad, Islam A. A. Csabai, Zsolt Tombácz, Dóra Minárovits, János Boldogkői, Zsolt
Abstract	Background Epstein–Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various sequencing methods have distinct strengths and limitations, the use of multiplatform approaches have proven to be valuable. The aim of this study is to provide a more complete picture on the transcriptomic architecture of EBV. Methods In this work, we apply the Oxford Nanopore Technologies MinION (long-read sequencing) platform for the generation of novel transcriptomic data, and integrate these with other’s data generated by another LRS approach, Pacific BioSciences RSII sequencing and Illumina CAGE-Seq and Poly(A)-Seq approaches. Both amplified and non-amplified cDNA sequencings were applied for the generation of sequencing reads, including both oligo-d(T) and random oligonucleotide-primed reverse transcription. EBV transcripts are identified and annotated using the LoRTIA software suite developed in our laboratory. Results This study detected novel genes embedded into longer host genes containing 5′-truncated in-frame open reading frames, which potentially encode N-terminally truncated proteins. We also detected a number of novel non-coding RNAs and transcript length isoforms encoded by the same genes but differing in their start and/or end sites. This study also reports the discovery of novel splice isoforms, many of which may represent altered coding potential, and of novel replication-origin-associated transcripts. Additionally, novel mono- and multigenic transcripts were identified. An intricate meshwork of transcriptional overlaps was revealed. Conclusions An integrative approach applying multi-technique sequencing technologies is suitable for reliable identification of complex transcriptomes because each techniques has different advantages and limitations, and the they can be used for the validation of the results obtained by a particular approach.
Related Links	https://virologyj.biomedcentral.com/counter/pdf/10.1186/s12985-021-01734-6.pdf
Ending Page	17
Page Count	17
Starting Page	1
File Format	HTM / HTML
DOI	10.1186/s12985-021-01734-6
Journal	Virology Journal
Issue Number	1
Volume Number	19
Language	English
Publisher	BioMed Central
Publisher Date	2022-01-06
Access Restriction	Open
Subject Keyword	Virology Epstein–Barr virus Herpesvirus Transcriptome Transcript isoform Splice variant Transcription start site Transcription end site Long-read sequencing Nanopore sequencing PacBio sequencing
Content Type	Text
Resource Type	Article
Subject	Virology Infectious Diseases
Journal Impact Factor	4/2023
5-Year Journal Impact Factor	3.8/2023

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