Interaction networks between chromatin complexes and long noncoding RNAs have become a recurrent theme in epigenetic regulation. However, technical limitations have precluded identification of RNA binding motifs for chromatin-associated proteins. Here, we add a denaturation step to UV-crosslink RNA immunoprecipitation (dCLIP) and apply dCLIP to mouse and human chromobox homolog 7 (CBX7), an RNA binding subunit of Polycomb repressive complex 1 (PRC1). In both species, CBX7 predominantly binds 3′ UTRs of messenger RNAs. CBX7 binds with a median RNA “footprint” of 171–183 nucleotides, the small size of which facilitates motif identification by bioinformatics. We find four families of consensus RNA motifs in mouse, and independent analysis of human CBX7 dCLIP data identifies similar motifs. Their mutation abolishes CBX7 binding in vitro. Pharmacological intervention with antisense oligonucleotides paradoxically increases CBX7 binding and enhances gene expression. These data support the utility of dCLIP and reveal an unexpected functional interaction between CBX7 and the 3′ UTRs of mRNA.

染色质复合物和长链非编码 RNA 之间的相互作用网络已成为表观遗传调控中反复出现的主题。然而，技术限制排除了染色质相关蛋白的 RNA 结合基序的鉴定。在这里，我们在 UV 交联 RNA 免疫沉淀 (dCLIP) 中添加了一个变性步骤，并将 dCLIP 应用于小鼠和人类 chromobox 同源物 7 (CBX7)，它是 Polycomb 抑制复合物 1 (PRC1) 的 RNA 结合亚基。在这两个物种中，CBX7 主要结合信使 RNA 的 3' UTR。CBX7 与 171-183 个核苷酸的中值 RNA “足迹”结合，其小尺寸便于生物信息学识别基序。我们在小鼠中发现了四个共有 RNA 基序家族，并且对人类 CBX7 dCLIP 数据的独立分析确定了相似的基序。它们的突变消除了 CBX7 结合体外。反义寡核苷酸的药理干预自相矛盾地增加了 CBX7 的结合并增强了基因表达。这些数据支持 dCLIP 的效用，并揭示了 CBX7 与 mRNA 的 3' UTR 之间意想不到的功能相互作用。