Both UV-cross-linking and immunoprecipitation (CLIP) and RNA editing (TRIBE) can identify the targets of RNA-binding proteins. To evaluate false-positives of CLIP and TRIBE, endogenous β-actin mRNA was tagged with MS2 stem loops, making it the only bona fide target mRNA for the MS2 capsid protein (MCP). CLIP and TRIBE detected β-actin, albeit with false-positives. False-positive CLIP signals were attributed to nonspecific antibody interactions. In contrast, putative false-positive TRIBE targets were genes spatially proximal to the β-actin gene. MCP-ADAR edited nearby nascent transcripts consistent with interchromosomal contacts observed in Hi-C. The identification of nascent contacts implies RNA regulatory proteins (e.g., splicing factors) associated with multiple nascent transcripts, forming domains of post-transcriptional activity. Repeating these results with an integrated inducible MS2 reporter indicated that MS2-TRIBE can be applied to a broad array of cells and transcripts to study spatial organization and nuclear RNA regulation.

紫外线交联和免疫沉淀（CLIP）和RNA编辑（TRIBE）均可识别RNA结合蛋白的靶标。为了评估CLIP和TRIBE的假阳性，将内源性β-肌动蛋白mRNA标记为MS2茎环，使其成为MS2衣壳蛋白（MCP）的唯一真正靶标mRNA。CLIP和TRIBE检测到β-肌动蛋白，尽管有假阳性。假阳性CLIP信号归因于非特异性抗体相互作用。相反，假定的假阳性TRIBE靶标是在空间上邻近β-actin基因的基因。MCP-ADAR编辑了与Hi-C中观察到的染色体间接触一致的附近新生转录本。新生接触的鉴定暗示与多个新生转录物相关联的RNA调节蛋白（例如剪接因子），其形成转录后活性的结构域。