Re-analysis of CLAP data affirms PRC2 as an RNA binding protein.

YongWoo Lee, Priyojit Das, Barry Kesner, Michael Rosenberg, Roy Blum, Jeannie T Lee
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Abstract

Using CLAP methodology, Guo et al. recently concluded that PRC2 is not an RNA binding protein (RBP). They suggest that prior findings were CLIP artifacts and argue against RNA's direct role in PRC2 regulation. Here, we re-analyze their raw datasets and reach contrary conclusions. Through an independent computational pipeline, we observe significant PRC2 enrichment throughout the transcriptome, including XIST. Applying the authors' published computational pipeline also reaffirms PRC2 as an RBP. Detailed investigation of the authors' pipeline reveals several unconventional practices. First, Guo et al. retained reads from foreign species and other unmappable reads to obtain a normalization factor. Second, they selectively removed read duplicates from the mappable fraction, while retaining them in the unmappable fraction. Finally, the authors applied an arbitrary cutoff for enrichment values in XIST. Their pipeline thereby inflated PRC2's background reads and suppressed mappable signals, creating the impression that PRC2 is not a robust RBP.

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对 CLAP 数据的重新分析证实 PRC2 是一种 RNA 结合蛋白。
最近,Guo 等人利用 Halo 标记的 PRC2 和 "CLAP "方法得出了 PRC2 不是 RNA 结合蛋白(RBP)的结论。他们认为之前的发现是 CLIP 的伪影,并认为 RNA 不能在 PRC2 的调控中发挥直接作用。在这里,我们对作者的原始数据集进行了重新分析,得出了相反的结论。首先,CLAP 在整个转录组中显示出明显的 PRC2 富集,包括在 XIST 的 Repeat A(RepA)基序中。其次,我们对作者的 CLAP 和 CLIP 数据集的重新分析表明,这两种方法产生的结果相似,都显示了 PRC2 在转录组中的富集。此外,PRC2 比 SAF-A 和 PTBP1 显示出更多的 RNA 结合峰。此外,对 CLAP 的重新分析与作者关于 CTCF 和 YY1 不是 RBP 的结论相矛盾。出现这些差异的原因可能是作者采用了非常规的数据归一化方法、确定显著性的方法,以及某些实验缺乏负标签和输入对照。
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