engleski

Analysis of the MCMV spliceome

Recent advances in high-throughput sequencing technologies have enabled us to gain a deeper understanding of the mechanisms that cytomegaloviruses employ to invade the host, manipulate its immune system and cause disease. Previously we and others have demonstrated that the transcriptome of the murine cytomegalovirus (MCMV), a model virus used in the study of HCMV, is far more complex and has the potential to encode greater number of proteins than has previously been anticipated. In addition, our analysis revealed multiple novel host responses to MCMV infection at the molecular level and identified several CMV genes with completely unknown functions, such as MAT, M116 and m119, which dominate the MCMV transcriptome. Encouraged by these results, we have decided to expand the study of MCMV transcriptome by performing deeper temporal analysis of the MCMV and host transcriptomes during infection using strand-specific RNASeq with 72-bp read length and six different splice-aware short read mappers (STAR, Tophat2, Subjunc, MapSplice2, Olego and HISAT). All six mappers identified several hundreds of potentially novel splice-sites in the MCMV transcriptome, of which 74 with highest splice-junction coverage have so far been confirmed by PCR. In addition to splice junction analysis, molecular characterization revealed multiple transcripts originating in the M116 and m119 regions, further demonstrating that the coding capacity and the extent of splicing in the MCMV transcriptome might have been severely underestimated.

Cytomegalovirus; transcriptome; splicing; M116; m119

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