title: Alternative Computational Analysis Shows No Evidence for Nucleosome Enrichment at Repetitive Sequences in Mammalian Spermatozoa.
abstract: Samans et al. (2014) reported the enrichment of nucleosomes in human and bovine spermatozoa at centromere repeats and retrotransposon sequences such as LINE-1 and SINE. We demonstrate here that nucleosomal enrichments at repetitive sequences as reported result from bioinformatic analyses that make redundant use of sequencing reads that map to multiple locations in the genome. To illustrate that this computational approach is flawed, we observed comparable artificial enrichments at repetitive sequences when aligning control genomic DNA or simulated reads of uniform genome coverage. These results imply that the main conclusions of the article by Samans et al. (2014) are confounded by an inappropriate computational methodology used to analyze the primary data.
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland.
authors.forename: Hélène
authors.initials: H
authors.lastname: Royo
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland. Electronic address: michael.stadler@fmi.ch.
authors.forename: Michael Beda
authors.initials: MB
authors.lastname: Stadler
authors.affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland. Electronic address: antoine.peters@fmi.ch.
authors.forename: Antoine Hendrik Felix Marie
authors.initials: AHFM
authors.lastname: Peters
mesh_terms: D000818:Animals; D042002:Chromatin Assembly and Disassembly / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D005786:Gene Expression Regulation; D006801:Humans; D008297:Male; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D013094:Spermatozoa / Q000378:metabolism*
chemical_list: D009707:Nucleosomes; D004247:DNA
keywords: bowtie; nucleosome; sequence alignment; spermatozoa