title: Vespucci: a system for building annotated databases of nascent transcripts.
abstract: Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the unique problem of identifying transcriptional units de novo from short reads located all across the genome. Here, we present a novel algorithm for de novo transcript identification from GRO-sequencing data, along with a system that determines transcript regions, stores them in a relational database and associates them with known reference annotations. We use this method to analyze GRO-sequencing data from primary mouse macrophages and derive novel quantitative insights into the extent and characteristics of non-coding transcription in mammalian cells. In doing so, we demonstrate that Vespucci expands existing annotations for mRNAs and lincRNAs by defining the primary transcript beyond the polyadenylation site. In addition, Vespucci generates assemblies for un-annotated non-coding RNAs such as those transcribed from enhancer-like elements. Vespucci thereby provides a robust system for defining, storing and analyzing diverse classes of primary RNA transcripts that are of increasing biological interest.
authors.affiliation: Department of Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA, Department of Bioinformatics and Systems Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA, San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA, A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine, University of Eastern Finland, P.O. Box 1627, 70120 Kuopio, Finland, Institute for Genomic Medicine and Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA and Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
authors.forename: Karmel A
authors.initials: KA
authors.lastname: Allison
authors.forename: Minna U
authors.initials: MU
authors.lastname: Kaikkonen
authors.forename: Terry
authors.initials: T
authors.lastname: Gaasterland
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Glass
mesh_terms: D000465:Algorithms; D000818:Animals; D002478:Cells, Cultured; D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D061986:MCF-7 Cells; D008264:Macrophages / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D058977:Molecular Sequence Annotation; D012313:RNA / Q000032:analysis / Q000737:chemistry* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D017423:Sequence Analysis, RNA / Q000379:methods*; D061806:Transcription Termination, Genetic; D014158:Transcription, Genetic
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012313:RNA