title: Influenza A virus preferentially snatches noncoding RNA caps.
abstract: Influenza A virus (IAV) lacks the enzyme for adding 5' caps to its RNAs and snatches the 5' ends of host capped RNAs to prime transcription. Neither the preference of the host RNA sequences snatched nor the effect of cap-snatching on host processes is completely defined. Previous studies of influenza cap-snatching used poly(A)-selected RNAs from infected cells or relied on annotated host genes to define the snatched host RNAs, and thus lack details on many noncoding host RNAs including snRNAs, snoRNAs, and promoter-associated capped small (cs)RNAs, which are made by "paused" Pol II during transcription initiation. In this study, we used a nonbiased technique, CapSeq, to identify host and viral-capped RNAs including nonpolyadenylated RNAs in the same samples, and investigated the substrate-product correlation between the host RNAs and the viral RNAs. We demonstrated that noncoding host RNAs, particularly U1 and U2, are the preferred cap-snatching source over mRNAs or pre-mRNAs. We also found that csRNAs are highly snatched by IAV. Because the functions of csRNAs remain mostly unknown, especially in somatic cells, our finding reveals that csRNAs at least play roles in the process of IAV infection. Our findings support a model where nascent RNAs including csRNAs are the preferred targets for cap-snatching by IAV and raise questions about how IAV might use snatching preferences to modulate host-mRNA splicing and transcription.
authors.affiliation: Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA.
authors.forename: Weifeng
authors.initials: W
authors.lastname: Gu
authors.affiliation: Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Glen R
authors.initials: GR
authors.lastname: Gallagher
authors.affiliation: Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Dai
authors.affiliation: Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Ping
authors.initials: P
authors.lastname: Liu
authors.affiliation: Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA.
authors.forename: Ruidong
authors.initials: R
authors.lastname: Li
authors.affiliation: Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Melanie I
authors.initials: MI
authors.lastname: Trombly
authors.affiliation: RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Don B
authors.initials: DB
authors.lastname: Gammon
authors.affiliation: RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.
authors.forename: Craig C
authors.initials: CC
authors.lastname: Mello
authors.affiliation: Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Jennifer P
authors.initials: JP
authors.lastname: Wang
authors.affiliation: Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Finberg
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D015967:Gene Expression Regulation, Viral; D005814:Genes, Viral; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics* / Q000378:metabolism; D012315:RNA Caps / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000235:genetics / Q000378:metabolism
chemical_list: D012315:RNA Caps; D012333:RNA, Messenger; D012367:RNA, Viral
keywords: cap-snatching; influenza; noncoding RNA