The human genome encodes for over 1,500 RNA-binding proteins (RBPs), which coordinate regulatory events on RNA transcripts. Most studies of RBPs have concentrated on their action on host protein-encoding mRNAs, which constitute a minority of the transcriptome. A widely neglected subset of our transcriptome derives from integrated retroviral elements, termed endogenous retroviruses (ERVs), that comprise ∼8% of the human genome. Some ERVs have been shown to be transcribed under physiological and pathological conditions, suggesting that sophisticated regulatory mechanisms to coordinate and prevent their ectopic expression exist. However, it is unknown how broadly RBPs and ERV transcripts directly interact to provide a posttranscriptional layer of regulation. Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA-sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-binding motif protein 4 (RBM4). We used photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation to demonstrate that RBM4 indeed bound ERV transcripts at CGG consensus elements. Loss of RBM4 resulted in an elevated transcript level of bound ERVs of the HERV-K and -H families, as well as increased expression of HERV-K envelope protein. We pinpointed RBM4 regulation of HERV-K to a CGG-containing element that is conserved in the LTRs of HERV-K-10, -K-11, and -K-20, and validated the functionality of this site using reporter assays. In summary, we systematically identified RBPs that may regulate ERV function and demonstrate a role for RBM4 in controlling ERV expression.

人类基因组编码超过1,500种RNA结合蛋白（RBP），可协调RNA转录本上的调控事件。RBP的大多数研究都集中在它们对宿主蛋白编码mRNA的作用上，后者构成转录组的一小部分。转录组的一个被广泛忽略的子集来自称为内源性逆转录病毒（ERV）的整合逆转录病毒元件，占人类基因组的8％。已显示一些ERV在生理和病理条件下转录，表明存在协调和防止其异位表达的复杂调节机制。但是，尚不清楚RBP和ERV转录本如何直接广泛相互作用以提供转录后的调控层。这里，我们实施了一条计算管道，以从单细胞或大量RNA测序数据确定各个RBP和ERV之间的表达相关性。RNA结合基序蛋白4（RBM4）是RBP负调控ERV表达的最佳候选药物之一。我们使用了可光活化的核糖核苷增强的交联和免疫沉淀来证明RBM4确实在CGG共有元件上结合了ERV转录本。RBM4的丧失导致HERV-K和-H家族的结合ERV的转录水平升高，以及HERV-K包膜蛋白的表达增加。我们将HERV-K的RBM4调控精确定位为HERV-K-10，-K-11和-K-20的LTR中保守的含CGG元素，并使用报告基因分析验证了该位点的功能。综上所述，