Integrative RNA-seq and CLIP-seq analysis reveals hnRNP-F regulation of the TNFα/NFκB signaling in high glucose conditions

Lan Wang^1,2,3Huimeng Li¹Xinyuan Guo¹Xiaoqin Wang^2,3*

• ¹Hubei University of Chinese Medicine, Wuhan, China
• ²Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei Province, China
• ³Hubei Shizhen Laboratory, Hubei University of Chinese Medicine, Wuhan, Hebei Province, China

Background: Diabetic kidney disease (DKD), with its complex pathogenesis, is the most important cause of end-stage renal disease and has become an urgent public health problem worldwide. Heterogeneous Nuclear Ribonucleoprotein F (hnRNP-F) is a member of a subfamily of widely expressed nuclear heterogeneous ribonucleoproteins with biological roles in regulating gene expression and variable splicing. Studies related to hnRNP-F in DKD have been partially reported. However, its potential mechanism in renal intrinsic cells have rarely been reported. Therefore, it is necessary to further investigate its potential mechanism in DKD, which will provide a novel idea to find new therapeutic targets for DKD. Results: In this study, RNA sequencing (RNA-seq) was utilized to demonstrate that the upregulation of hnRNP-F in HK-2 cells cultured under high glucose conditions resulted in a substantial decrease in the expression of genes associated with the inflammatory response and suppression of the TNFα-NFκB signaling pathway. This was also verified in MPC5 cells.By analyzing CLIP-seq and RNA-seq data, we found that hnRNP-F may inhibit gene expression by binding to lncRNA SNHG1. Conversely, this upregulation led to a significant increase in alternative splicing events of genes implicated in diabetic kidney disease (DKD), such as hnRNPA2B1, OSML, UGT2B7, TRIP6, and IRF3. Combining CLIP-seq data, we found that hnRNPF binds to and regulates variable splicing of the hnRNP protein family and splicing factors. This result suggests that hnRNPF may regulate alternative splicing through the coordinated action of multiple splicing factors. Conclusions: hnRNP-F have dual functions in mRNA transcriptional and post-transcriptional levels and may bind with lncRNA SNHG1 to negatively regulate the transcription of genes involved in TNFα/NFκB signaling pathway. Meanwhile, hnRNP-F may function in the co-regulation of alternative splicing events in cells by interacting with ZFP36 to form a complex.