title: Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified.
abstract: Huang et al. (2013) recently reported that chromatin immunoprecipitation sequencing (ChIP-seq) reveals the genome-wide sites of occupancy by Piwi, a piRNA-guided Argonaute protein central to transposon silencing in Drosophila. Their study also reported that loss of Piwi causes widespread rewiring of transcriptional patterns, as evidenced by changes in RNA polymerase II occupancy across the genome. Here we reanalyze their data and report that the underlying deep-sequencing dataset does not support the authors' genome-wide conclusions.
authors: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors: Georgi K
authors: GK
authors: Marinov
authors: Department of Biochemistry, University at Buffalo, Buffalo, NY 14214, USA.
authors: Jie
authors: J
authors: Wang
authors: Institute of Molecular Biotechnology of the Austrian Academy of Sciences IMBA, Vienna Biocenter (VBC), 1030 Vienna, Austria.
authors: Dominik
authors: D
authors: Handler
authors: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors: Barbara J
authors: BJ
authors: Wold
authors: Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors: Zhiping
authors: Z
authors: Weng
authors: Watson School of Biological Sciences, Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
authors: Gregory J
authors: GJ
authors: Hannon
authors: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
authors: Alexei A
authors: AA
authors: Aravin
authors: Howard Hughes Medical Institute, RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
authors: Phillip D
authors: PD
authors: Zamore
authors: Institute of Molecular Biotechnology of the Austrian Academy of Sciences IMBA, Vienna Biocenter (VBC), 1030 Vienna, Austria. Electronic address: julius.brennecke@imba.oeaw.ac.at.
authors: Julius
authors: J
authors: Brennecke
authors: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address: kft@caltech.edu.
authors: Katalin Fejes
authors: KF
authors: Toth
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics*; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D008780:Methyltransferases; D034622:RNA Interference; D012319:RNA Polymerase II / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D060565:Argonaute Proteins; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D034741:RNA, Small Interfering; C116498:piwi protein, Drosophila; D008780:Methyltransferases; C445404:SU(VAR)3-9; D012319:RNA Polymerase II