title: A human haploid gene trap collection to study lncRNAs with unusual RNA biology.
abstract: Many thousand long non-coding (lnc) RNAs are mapped in the human genome. Time consuming studies using reverse genetic approaches by post-transcriptional knock-down or genetic modification of the locus demonstrated diverse biological functions for a few of these transcripts. The Human Gene Trap Mutant Collection in haploid KBM7 cells is a ready-to-use tool for studying protein-coding gene function. As lncRNAs show remarkable differences in RNA biology compared to protein-coding genes, it is unclear if this gene trap collection is useful for functional analysis of lncRNAs. Here we use the uncharacterized LOC100288798 lncRNA as a model to answer this question. Using public RNA-seq data we show that LOC100288798 is ubiquitously expressed, but inefficiently spliced. The minor spliced LOC100288798 isoforms are exported to the cytoplasm, whereas the major unspliced isoform is nuclear localized. This shows that LOC100288798 RNA biology differs markedly from typical mRNAs. De novo assembly from RNA-seq data suggests that LOC100288798 extends 289kb beyond its annotated 3' end and overlaps the downstream SLC38A4 gene. Three cell lines with independent gene trap insertions in LOC100288798 were available from the KBM7 gene trap collection. RT-qPCR and RNA-seq confirmed successful lncRNA truncation and its extended length. Expression analysis from RNA-seq data shows significant deregulation of 41 protein-coding genes upon LOC100288798 truncation. Our data shows that gene trap collections in human haploid cell lines are useful tools to study lncRNAs, and identifies the previously uncharacterized LOC100288798 as a potential gene regulator.
authors.affiliation: a CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3 , 1090 Vienna , Austria.
authors.forename: Aleksandra E
authors.initials: AE
authors.lastname: Kornienko
authors.affiliation: a CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3 , 1090 Vienna , Austria.|b Institute of Medical Genetics, Medical University of Vienna, Währingerstrasse 10 , 1090 Vienna , Austria.
authors.forename: Irena
authors.initials: I
authors.lastname: Vlatkovic
authors.affiliation: b Institute of Medical Genetics, Medical University of Vienna, Währingerstrasse 10 , 1090 Vienna , Austria.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Neesen
authors.affiliation: a CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3 , 1090 Vienna , Austria.
authors.forename: Denise P
authors.initials: DP
authors.lastname: Barlow
authors.affiliation: a CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3 , 1090 Vienna , Austria.
authors.forename: Florian M
authors.initials: FM
authors.lastname: Pauler
mesh_terms: D002460:Cell Line; D019295:Computational Biology; D005786:Gene Expression Regulation / Q000235:genetics*; D015894:Genome, Human; D006238:Haploidy; D006801:Humans; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger
keywords: Gene trap insertion; KBM7; LOC100288798; RNA biology; RNA-seq; SLC38A4-AS; genetic truncation; human haploid cell line; lncRNA splicing