Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified

Dev Cell. 2015 Mar 23;32(6):765-71. doi: 10.1016/j.devcel.2015.01.013.


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.

MeSH terms

  • Animals
  • Argonaute Proteins / genetics*
  • Base Sequence
  • Binding Sites / genetics
  • Chromatin Immunoprecipitation
  • DNA-Binding Proteins / genetics*
  • Drosophila Proteins / genetics*
  • Drosophila melanogaster
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Methyltransferases
  • RNA Interference
  • RNA Polymerase II / genetics*
  • RNA, Small Interfering / genetics
  • Sequence Analysis, DNA


  • Argonaute Proteins
  • DNA-Binding Proteins
  • Drosophila Proteins
  • RNA, Small Interfering
  • piwi protein, Drosophila
  • Methyltransferases
  • SU(VAR)3-9
  • RNA Polymerase II