Serine and arginine-rich splicing factor 3 (SRSF3), the smallest member of the Ser/Arg-rich (SR) RNA-binding protein family, regulates multiple aspects of post-transcriptional gene expression program. Although SRSF3 is essential for early embryo development, reprogramming, and pluripotency maintenance, the RNA targets and specificity of RNA recognition of SRSF3 are not well understood in human pluripotent stem cells. In this study, we used inducible TRIBE (targets of RNA binding sites by editing) to identify RNA targets and binding motifs of SRSF3 in human embryonic stem cells (hESCs). We identified 3888 confident binding sites of SRSF3, corresponding to 1222 gene targets. Our results showed that nearly half of the binding sites were distributed in exons, reflecting the alternative splicing function of SRSF3. Motif analysis demonstrated that two of the SRSF3 recognition sequences were the same as the motifs identified in mouse embryonic stem cells, suggesting the recognition sequences of SRSF3 may be conserved in mammals. Overall, our analyses revealed the RNA targets of SRSF3 and uncovered its RNA recognition specificity, providing a valuable resource for understanding the function of SRSF3 in human embryonic stem cells.

富含丝氨酸和精氨酸的剪接因子 3 (SRSF3) 是富含 Ser/Arg (SR) RNA 结合蛋白家族的最小成员，它调节转录后基因表达程序的多个方面。尽管 SRSF3 对早期胚胎发育、重编程和多能性维持至关重要，但人类多能干细胞中对 SRSF3 的 RNA 靶标和 RNA 识别的特异性尚不清楚。在这项研究中，我们使用诱导型 TRIBE（通过编辑的 RNA 结合位点的靶标）来识别人类胚胎干细胞 (hESCs) 中 SRSF3 的 RNA 靶标和结合基序。我们确定了 3888 个 SRSF3 的可靠结合位点，对应于 1222 个基因靶点。我们的结果表明，近一半的结合位点分布在外显子中，反映了 SRSF3 的可变剪接功能。基序分析表明，两个SRSF3识别序列与小鼠胚胎干细胞中鉴定的基序相同，表明SRSF3的识别序列在哺乳动物中可能是保守的。总体而言，我们的分析揭示了 SRSF3 的 RNA 靶标并揭示了其 RNA 识别特异性，为了解 SRSF3 在人类胚胎干细胞中的功能提供了宝贵的资源。