RNA-binding proteins (RNA-BPs) play critical roles in development and disease to regulate gene expression. However, genome-wide identification of their targets in primary human cells has been challenging. Here, we applied a modified CLIP-seq strategy to identify genome-wide targets of the FMRP translational regulator 1 (FMR1), a brain-enriched RNA-BP, whose deficiency leads to Fragile X Syndrome (FXS), the most prevalent inherited intellectual disability. We identified FMR1 targets in human dorsal and ventral forebrain neural progenitors and excitatory and inhibitory neurons differentiated from human pluripotent stem cells. In parallel, we measured the transcriptomes of the same four cell types upon FMR1 gene deletion. We discovered that FMR1 preferentially binds long transcripts in human neural cells. FMR1 targets include genes unique to human neural cells and associated with clinical phenotypes of FXS and autism. Integrative network analysis using graph diffusion and multitask clustering of FMR1 CLIP-seq and transcriptional targets reveals critical pathways regulated by FMR1 in human neural development. Our results demonstrate that FMR1 regulates a common set of targets among different neural cell types but also operates in a cell type-specific manner targeting distinct sets of genes in human excitatory and inhibitory neural progenitors and neurons. By defining molecular subnetworks and validating specific high-priority genes, we identify novel components of the FMR1 regulation program. Our results provide new insights into gene regulation by a critical neuronal RNA-BP in human neurodevelopment.

中文翻译：

---

人类神经发育中 FMR1 调节分子网络的鉴定。

RNA 结合蛋白 (RNA-BPs) 在发育和疾病中发挥关键作用以调节基因表达。然而，在原代人类细胞中对它们的靶标进行全基因组鉴定一直具有挑战性。在这里，我们应用修改后的 CLIP-seq 策略来识别 FMRP 翻译调节因子 1 (FMR1) 的全基因组目标，这是一种富含大脑的 RNA-BP，其缺陷会导致脆性 X 综合征 (FXS)，这是最普遍的遗传性知识分子失能。我们确定了人类背侧和腹侧前脑神经祖细胞以及从人类多能干细胞分化而来的兴奋性和抑制性神经元中的 FMR1 靶标。同时，我们测量了 FMR1 基因缺失后相同四种细胞类型的转录组。我们发现 FMR1 优先结合人类神经细胞中的长转录物。FMR1 靶点包括人类神经细胞特有的基因以及与 FXS 和自闭症临床表型相关的基因。使用 FMR1 CLIP-seq 和转录目标的图扩散和多任务聚类的综合网络分析揭示了 FMR1 在人类神经发育中调节的关键通路。我们的结果表明，FMR1 调节不同神经细胞类型之间的一组共同目标，但也以细胞类型特定的方式运作，针对人类兴奋性和抑制性神经祖细胞和神经元中的不同基因组。通过定义分子子网络和验证特定的高优先级基因，我们确定了 FMR1 调控程序的新组件。我们的研究结果为人类神经发育中关键神经元 RNA-BP 的基因调控提供了新的见解。