Nuclear fractionation reveals chromatin-enriched RNA binding proteins and transcriptional regulatory activity of QKI5 during monocytic differentiation

Background: Cellular RNA binding proteins (RBPs) have multiple roles in post-transcriptional control, and some are shown to bind DNA. However, the global localization and the general chromatin-binding ability of RBPs are not well-characterized and remain undefined in hematopoietic cells. Results: We first provide a full view of RBPs' distribution pattern in the nucleus and screen for chromatin-enriched RBPs (Che-RBPs) in different human cells. Subsequently, by generating ChIP-seq, CLIP-seq and RNA-seq datasets and conducting combined analysis, the transcriptional regulatory potential of certain hematopoietic Che-RBPs are predicted. From this analysis, quaking (QKI5) emerges as a potential transcriptional activator during monocytic differentiation. QKI5 is over-represented in gene promoter regions, independent of RNA or transcription factors. Furthermore, DNA-bound QKI5 activates the transcription of several critical monocytic differentiation-associated genes, including CXCL2, IL16 and PTPN6. Finally, we show that the differentiation promoting activity of QKI5 is largely dependent on CXCL2, irrespective of its RNA binding capacity. Conclusions: Our study indicates that Che-RBPs are versatile factors that orchestrate gene expression in different cellular contexts, and identifies QKI5, a classic RBP regulating RNA processing, as a novel transcriptional activator during monocytic differentiation. ChIP-seq, RIP-seq, and RNA-seq

本研究背景：细胞内RNA结合蛋白（RNA binding proteins, RBPs）在转录后基因表达调控中发挥多重功能，部分RBPs还被证实可结合DNA。然而，目前RBPs的全局定位及普遍染色质结合特性尚未得到充分表征，且在造血细胞中相关研究仍属空白。
研究结果：本研究首先系统阐明了RBPs在细胞核内的分布全貌，并在不同人类细胞中筛选得到染色质富集型RNA结合蛋白（chromatin-enriched RBPs, Che-RBPs）。随后，通过构建ChIP-seq、CLIP-seq及RNA-seq数据集并开展联合分析，我们预测了部分造血来源Che-RBPs的转录调控潜能。经此分析，QKI5（quaking）被鉴定为单核细胞分化过程中的潜在转录激活因子。QKI5在基因启动子区域显著富集，且该富集过程不依赖于RNA或转录因子。进一步研究发现，与DNA结合的QKI5可激活若干关键单核细胞分化相关基因的转录，包括CXCL2、IL16及PTPN6。最后，本研究证实QKI5的促分化活性在很大程度上依赖于CXCL2，且与其RNA结合能力无关。
研究结论：本研究表明，Che-RBPs是一类在不同细胞环境中统筹基因表达的多功能因子，并证实了经典RNA加工调控蛋白QKI5是单核细胞分化过程中的新型转录激活因子。ChIP-seq、RIP-seq及RNA-seq