Technical CommentsGenetics

Response to Comment on “Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing”

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Science  16 Jun 2017:
Vol. 356, Issue 6343, eaam5439
DOI: 10.1126/science.aam5439

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  • RE: Genotypes
    • John Edward Froberg, Graduate Research Assistant, Harvard Medical School/Mass. General Hospital
    • Other Contributors:
      • Chen-Yu Wang, Graduate Research Assistant, Harvard Medical School/Mass. General Hospital
      • Roy Blum, Bioinformatician, HHMI/Mass. General Hospital
      • Yesu Jeon, Research Associate, Mass. General Hospital
      • Jeannie T Lee, Principal Investigator, HHMI/Harvard Medical School/Mass. General Hospital

    We appreciate the response of Chen et al. to our Technical Comment. However, we do not believe the response satisfies our concerns regarding the genotypes of the cells used in Chen et al. We outline our critique below and invite commentary from the community:

    1. Chen et al. continued to maintain that ∆LBS is a true deletion and stated that they confirmed ∆LBS by Sanger sequencing. They should provide FASTA files containing the Sanger sequence data from the same clone used in the study.

    2. Chen et al. erroneously stated that our idea of an LBS inversion was based on the presence of discordant reads within the Xist locus. The “inversion reads” are a specific subset of discordant reads with one end mapped within the LBS region and the other just outside and where both reads align to the same strand. Whereas discordant reads can indeed be found outside of the LBS region in both WT and ∆LBS cells, such inversion reads can only be detected in ∆LBS and ∆LBS rescue, but not in WT, LBR knockdown, and SHARP knockdown samples. Thus, “inversion reads” are specific to ∆LBS and ∆LBS rescue and not simply an artifact of the discordant RAP reads.

    3. In Figure 2, Chen et al. proposed that the discordant reads that suggest an inversion are simply an artifact of sequencing the RAP capture probes. This cannot be the case. The inversion reads were also found in input samples for both ∆LBS and ∆LBS rescue. The input was set aside before addition of capture probes, ther...

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    Competing Interests: None declared.