Reassessment of Piwi Binding to the Genome and Piwi Impact on RNA Polymerase II Distribution

• Published in: Developmental cell Vol. 32; no. 6; pp. 772 - 774
• Main Authors: Lin, Haifan, Chen, Mengjie, Kundaje, Anshul, Valouev, Anton, Yin, Hang, Liu, Na, Neuenkirchen, Nils, Zhong, Mei, Snyder, Michael
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 23.03.2015
• Subjects: Animals; Argonaute Proteins - genetics; Base Sequence; Binding Sites - genetics; Chromatin Immunoprecipitation; Chromosomal Proteins, Non-Histone - genetics; DNA-Binding Proteins - genetics; Drosophila melanogaster; Drosophila Proteins - genetics; Genome; High-Throughput Nucleotide Sequencing; Histone-Lysine N-Methyltransferase - genetics; Methyltransferases - genetics; RNA Interference; RNA Polymerase II - genetics; RNA, Small Interfering - genetics; Sequence Analysis, DNA
• ISSN: 1534-5807; 1878-1551; 1878-1551
• DOI: 10.1016/j.devcel.2015.03.004

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. •A direct response to the Marinov et al. (2015) Matters Arising is presented•New analysis indicates that Piwi genomic targets still remain to be identified•Three independent analyses support the notion that Piwi influences Pol II distribution Lin et al. address the Marinov et al. (2015) Matters Arising. The authors reanalyzed Drosophila Piwi and RNA polymerase II ChIP-seq data reported by Huang et al. (2013), confirming that Piwi influences RNA polymerase II distribution in the genome but also suggesting that Piwi’s genomic targets remain to be identified.