Falese James P, McFadden Emily J, D'Inzeo Christopher A, Hargrove Amanda E
Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA.
Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
RNA. 2025 Aug 18;31(9):1260-1286. doi: 10.1261/rna.080488.125.
The lncRNA second chromosome locus associated with prostate 1 (SChLAP1) was previously identified as a predictive biomarker and potential driver of aggressive prostate cancer. Recent work suggested that SChLAP1 may bind the SWI/SNF chromatin remodeling complex to promote prostate cancer metastasis, though the exact role of SWI/SNF recognition is debated. To date, there are no detailed biochemical studies of SChLAP1 or SChLAP1:protein complexes. Herein, we report the first secondary structure model of SChLAP1 using SHAPE-MaP in vitro, in cellulo, and ex cellulo (protein-free). Comparison of the ex cellulo and in cellulo data via ΔSHAPE identified putative protein binding regions within SChLAP1. In addition, phylogenetic analysis revealed that SChLAP1 is a primate-conserved lncRNA, with two exons significantly derived from primate-specific retroviral insertions. In particular, we characterized a complex structural landscape in a protein binding region at the 3'-end of SChLAP1 derived from a THE1B-type retroviral insertion, suggesting a role for an exapted RNA structure in SChLAP1:protein recognition and prostate cancer progression. Lastly, pulldowns of SChLAP1 substructures enabled identification of previously unestablished SChLAP1-interacting proteins. This work lays the foundation for future efforts to selectively target and disrupt SChLAP1 structures and/or protein interfaces and to develop new therapeutic avenues in prostate cancer treatment.
长链非编码RNA 2号染色体前列腺相关位点1（SChLAP1）先前被鉴定为侵袭性前列腺癌的预测生物标志物和潜在驱动因子。最近的研究表明，SChLAP1可能与SWI/SNF染色质重塑复合物结合以促进前列腺癌转移，尽管SWI/SNF识别的确切作用仍存在争议。迄今为止，尚未对SChLAP1或SChLAP1：蛋白质复合物进行详细的生化研究。在此，我们报告了首个使用体外、细胞内和无细胞（无蛋白质）SHAPE-MaP技术构建的SChLAP1二级结构模型。通过ΔSHAPE比较无细胞和细胞内数据，确定了SChLAP1内的假定蛋白质结合区域。此外，系统发育分析表明，SChLAP1是一种灵长类保守的长链非编码RNA，有两个外显子显著来源于灵长类特异性逆转录病毒插入。特别是，我们对源自THE1B型逆转录病毒插入的SChLAP1 3'端蛋白质结合区域的复杂结构景观进行了表征，表明适应性RNA结构在SChLAP1：蛋白质识别和前列腺癌进展中发挥作用。最后，对SChLAP1亚结构的下拉实验能够鉴定出先前未确定的与SChLAP1相互作用的蛋白质。这项工作为未来选择性靶向和破坏SChLAP1结构和/或蛋白质界面以及开发前列腺癌治疗新途径的努力奠定了基础。
