Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites
Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites
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DOI：
10.1016/j.molcel.2019.02.002
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发表时间：
2019-06-20
期刊：
影响因子：
16
通讯作者：
Zhang, Chaolin
中科院分区：
文献类型：
--
作者：
Feng, Huijuan;Bao, Suying;Zhang, Chaolin
RNA结合蛋白（RBP）通过识别其靶转录物中的短和简并序列基序来调节转录后基因表达，但精确定义其结合特异性仍然具有挑战性。交联和免疫沉淀（CLIP）允许精确的蛋白质-RNA交联位点的映射，其通常以单核苷酸分辨率驻留在RBP基序中的特定位置。在这里，我们已经开发了一种计算方法，命名为mCross，共同建模RBP结合特异性，同时精确地注册基序位点的交联位置。我们使用ENCODE eCLIP数据将mCross应用于112个RBP，并通过等位基因结合位点的全基因组分析来验证所发现的基序的可靠性。我们的分析表明，原型SR蛋白SRSF 1除了其典型的GGAGGA基序外，还识别GGA半位点簇。因此，SRSF 1调节剪接的转录物的更大的剧目比以前认识到，包括HNRNPD和HNRNPDL，这是参与多价蛋白质组装和相分离。
RNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence motifs in their target transcripts, but precisely defining their binding specificity remains challenging. Crosslinking and immuno-precipitation (CLIP) allows for mapping of the exact protein-RNA crosslink sites, which frequently reside at specific positions in RBP motifs at single-nucleotide resolution. Here, we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the discovered motifs by genome-wide analysis of allelic binding sites. Our analyses revealed that the prototypical SR protein SRSF1 recognizes clusters of GGA half-sites in addition to its canonical GGAGGA motif. Therefore, SRSF1 regulates splicing of a much larger repertoire of transcripts than previously appreciated, including HNRNPD and HNRNPDL, which are involved in multivalent protein assemblies and phase separation.