The TREX complex (TREX) plays key roles in nuclear export of mRNAs. However, little is known about its transcriptome-wide binding targets. We used individual cross-linking and immunoprecipitation (iCLIP) to identify the binding sites of ALYREF, an mRNA export adaptor in TREX, in human cells. Consistent with previous in vitro studies, ALYREF binds to a region near the 5′ end of the mRNA in a CBP80-dependent manner. Unexpectedly, we identified PABPN1-dependent ALYREF binding near the 3′ end of the mRNA. Furthermore, the 3′ processing factor CstF64 directly interacts with ALYREF and is required for the overall binding of ALYREF on the mRNA. In addition, we found that numerous middle exons harbor ALYREF binding sites and identified ALYREF-binding motifs that promote nuclear export of intronless mRNAs. Together, our study defines enrichment of ALYREF binding sites at the 5′ and the 3′ regions of the mRNA in vivo, identifies export-promoting ALYREF-binding motifs, and reveals CstF64- and PABPN1-mediated coupling of mRNA nuclear export to 3′ processing.

中文翻译：

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ALYREF在体内主要结合mRNA的5'和3'区域

TREX复合物（TREX）在mRNA的核输出中起关键作用。然而，对其转录组范围的结合靶标知之甚少。我们使用单独的交联和免疫沉淀（iCLIP）来识别人细胞中TREX中的mRNA输出衔接子ALYREF的结合位点。与以前的体外试验一致研究表明，ALYREF以CBP80依赖的方式与mRNA 5'端附近的区域结合。出乎意料的是，我们发现了mRNA的3'端附近的PABPN1依赖性ALYREF结合。此外，3'加工因子CstF64直接与ALYREF相互作用，并且是ALYREF在mRNA上的整体结合所必需的。此外，我们发现许多中间外显子都具有ALYREF结合位点，并鉴定了促进无内含子mRNA核输出的ALYREF结合基序。总之，我们的研究定义了体内mRNA的5'和3'区域中ALYREF结合位点的富集，鉴定了促进出口的ALYREF结合基序，并揭示了CstF64和PABPN1介导的mRNA核输出与3'的偶联。加工。