title: Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.
abstract: Drosophila Piwi was reported by Huang et al. (2013) to be guided by piRNAs to piRNA-complementary sites in the genome, which then recruits heterochromatin protein 1a and histone methyltransferase Su(Var)3-9 to the sites. Among additional findings, Huang et al. (2013) also reported Piwi binding sites in the genome and the reduction of RNA polymerase II in euchromatin but its increase in pericentric regions in piwi mutants. Marinov et al. (2015) disputed the validity of the Huang et al. bioinformatic pipeline that led to the last two claims. Here we report our independent reanalysis of the data using current bioinformatic methods. Our reanalysis agrees with Marinov et al. (2015) that Piwi's genomic targets still remain to be identified but confirms the Huang et al. claim that Piwi influences RNA polymerase II distribution in the genome. This Matters Arising Response addresses the Marinov et al. (2015) Matters Arising, published concurrently in this issue of Developmental Cell.
authors: Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA. Electronic address: haifan.lin@yale.edu.
authors: Haifan
authors: H
authors: Lin
authors: Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.
authors: Mengjie
authors: M
authors: Chen
authors: Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
authors: Anshul
authors: A
authors: Kundaje
authors: Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
authors: Anton
authors: A
authors: Valouev
authors: Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
authors: Hang
authors: H
authors: Yin
authors: Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA.
authors: Na
authors: N
authors: Liu
authors: Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA.
authors: Nils
authors: N
authors: Neuenkirchen
authors: Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA.
authors: Mei
authors: M
authors: Zhong
authors: Department of Genetics, Stanford University, Stanford, CA 94305, USA.
authors: Michael
authors: M
authors: Snyder
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics*; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D000090266:Chromobox Protein Homolog 5; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D000076983:Histone Methyltransferases; D011495:Histone-Lysine N-Methyltransferase / Q000235:genetics; D008780:Methyltransferases / Q000235:genetics*; D034622:RNA Interference; D012319:RNA Polymerase II / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D060565:Argonaute Proteins; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D034741:RNA, Small Interfering; C116498:piwi protein, Drosophila; D000090266:Chromobox Protein Homolog 5; D000076983:Histone Methyltransferases; D008780:Methyltransferases; C445404:SU(VAR)3-9; D011495:Histone-Lysine N-Methyltransferase; D012319:RNA Polymerase II