9 research outputs found
In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing
The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level
Identification of herpesvirus transcripts from genomic regions around the replication origins
Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a ‘super regulatory center’ in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries
Short and Long-Read Sequencing Survey of the Dynamic Transcriptomes of African Swine Fever Virus and the Host Cells
To provide a detailed transcription map about the
transcription dynamics of the African Swine Fever Virus, we performed multiplatform
sequencing using both next-generation short-read sequencing (SRS) and third-generation long-read sequencing (LRS) techniques. The presented
dataset represent a key resource for studying the ASFV
transcriptome at different time points after infection, and of the
effect of infection on the host gene expression.
Regarding the SRS approach, the MiSeq instrument
(Illumina) was used , whereas we applied the MinION portable
sequencer from Oxford Nanopore Technologies (ONT) for
full-length sequencing. The random-primed SRS library was
run on a single MiSeq v3 flow cell, whereas three different ONT
libraries [direct RNA sequencing (dRNA-Seq), direct cDNA
sequencing (dcDNA-Seq) and amplified cDNA sequencing)
were sequenced on three individual flow cells. Altogether the
three LRS experiments resulted in 20,021,413 sequencing reads, of which 139,711 aligned to the viral
genome (MN715134.1). The longest average read length was
obtained using the dcDNA technique (1,299 bp). The average
length for the amplified approach ranged between 598 and
1,017 bp, whereas the dRNA-Seq resulted in an average read
length of 953 bp
Identification of herpesvirus transcripts from genomic regions around the replication origins
Abstract Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a ‘super regulatory center’ in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries
In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing
Abstract The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level