Genes in SARS-CoV-2 and other viruses in the order of Nidovirales are expressed by a process of discontinuous transcription which is distinct from alternative splicing in eukaryotes and is mediated by the viral RNA-dependent RNA polymerase. Here, we introduce the DISCONTINUOUS TRANSCRIPT ASSEMBLYproblem of finding transcripts and their abundances given an alignment of paired-end short reads under a maximum likelihood model that accounts for varying transcript lengths. We show, using simulations, that our method, JUMPER, outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1, SARS-CoV-2 and MERS-CoV samples, we find that JUMPER not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are supported by subsequent orthogonal analyses. Moreover, application of JUMPER on samples with and without treatment reveals viral drug response at the transcript level. As such, JUMPER enables detailed analyses of Nidovirales transcriptomes under varying conditions. @melkebir @psashittal et al. develop a graph-based method for the assembly of discontinuous transcripts produced in Coronaviruses and other Nidovirales, enabling the discovery of transcriptional changes missed by existing methods.
【저자키워드】 Gene Expression, Software, Genome informatics, RNA splicing, 【초록키워드】 Treatment, viruses, Transcriptome, SARS-CoV-2, virus, SARS-CoV-1, MERS-CoV, Viral, RNA-dependent RNA polymerase, Viral RNA, RNA polymerase, discontinuous transcription, expression, predict, assembly, Analysis, transcriptomes, viral RNA-dependent RNA polymerase, transcripts, drug response, alignment, eukaryotes, Nidovirales, Transcriptional changes, JUMPER, transcript, likelihood, produced, classical, identify, develop, subsequent, supported, expressed, reveal, analyses, conditions, Nidovirale, canonical, eukaryote, transcriptional change, outperform, 【제목키워드】 coronavirus, transcript,