title: Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data.
abstract: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the 'allelome' by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3,1090 Vienna, Austria.
authors.forename: Daniel
authors.initials: D
authors.lastname: Andergassen
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3,1090 Vienna, Austria.
authors.forename: Christoph P
authors.initials: CP
authors.lastname: Dotter
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3,1090 Vienna, Austria.
authors.forename: Tomasz M
authors.initials: TM
authors.lastname: Kulinski
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3,1090 Vienna, Austria.
authors.forename: Philipp M
authors.initials: PM
authors.lastname: Guenzl
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3,1090 Vienna, Austria.
authors.forename: Philipp C
authors.initials: PC
authors.lastname: Bammer
authors.affiliation: 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: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3,1090 Vienna, Austria FPauler@cemm.oeaw.ac.at.
authors.forename: Florian M
authors.initials: FM
authors.lastname: Pauler
authors.affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3,1090 Vienna, Austria QHudson@cemm.oeaw.ac.at.
authors.forename: Quanah J
authors.initials: QJ
authors.lastname: Hudson
mesh_terms: D000483:Alleles; D000818:Animals; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D042421:Histone Code; D051379:Mice; D008815:Mice, Inbred Strains; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software