@ARTICLE{10.3389/fmicb.2017.02519, AUTHOR={Lin, Wenzhong and Qiu, Ping and Jin, Jing and Liu, Shunmin and Ul Islam, Saif and Yang, Jinguang and Zhang, Jie and Kormelink, Richard and Du, Zhenguo and Wu, Zujian}, TITLE={The Cap Snatching of Segmented Negative Sense RNA Viruses as a Tool to Map the Transcription Start Sites of Heterologous Co-infecting Viruses}, JOURNAL={Frontiers in Microbiology}, VOLUME={8}, YEAR={2017}, URL={https://www.frontiersin.org/articles/10.3389/fmicb.2017.02519}, DOI={10.3389/fmicb.2017.02519}, ISSN={1664-302X}, ABSTRACT={Identification of the transcription start sites (TSSs) of a virus is of great importance to understand and dissect the mechanism of viral genome transcription but this often requires costly and laborious experiments. Many segmented negative-sense RNA viruses (sNSVs) cleave capped leader sequences from a large variety of mRNAs and use these cleaved leaders as primers for transcription in a conserved process called cap snatching. The recent developments in high-throughput sequencing have made it possible to determine most, if not all, of the capped RNAs snatched by a sNSV. Here, we show that rice stripe tenuivirus (RSV), a plant-infecting sNSV, co-infects Nicotiana benthamiana with two different begomoviruses and snatches capped leader sequences from their mRNAs. By determining the 5′ termini of a single RSV mRNA with high-throughput sequencing, the 5′ ends of almost all the mRNAs of the co-infecting begomoviruses could be identified and mapped on their genomes. The findings in this study provide support for the using of the cap snatching of sNSVs as a tool to map viral TSSs.} }