Genome-wide identification of protein binding sites on RNAs in mammalian cells

PARP1-RNA interaction analysis: PARP1 regulates the expression of extracellular matrix-related genes in HK-2 renal proximal tubular epithelial cells

Recent studies suggest that Poly(ADP-ribose) polymerase 1 (PARP1) acts as an RNA-binding protein in a majority of renal diseases with tubular cell injury. However, detailed knowledge of RNA targets and the RNA-binding regions for PARP1 is unknown. Herein, mapping of iRIP-seq reads in HK-2 renal tubular epithelial cells showed a biased distribution at coding sequence (CDS) and intron regions that is specific to these cells. A total of 1708 differentially expressed genes were identified after PARP1 knockdown using RNA-seq. Furthermore, transcriptome analysis also showed that selective variable splicing was globally regulated by PARP1 in HK-2 cells. By comparison of PARP1 RNA-seq and iRIP-seq data, we found 68 overlapping genes that are enriched in 'extracellular matrix' pathway. Follow-up identification of their interactions may contribute vital insights into the regulatory role of PARP1 as an RNA-binding protein in HK-2 cells.

Eukaryotic initiation Factor 4AIII facilitates hepatocellular carcinoma cell proliferation, migration, and epithelial-mesenchymal transition process via antagonistically binding to WD repeat domain 66 with miRNA-2113

Hepatocellular carcinoma (HCC) is one of the malignant cancers with high incidence and mortality rates worldwide. RNA-binding protein eukaryotic initiation Factor 4A-III (eIF4AIII) is a carcinogene in the biological process of tumors and microRNA (miRNA)-2113 has rarely been studied in cancers, not to mention in HCC. The regulation mechanism between eIF4AIII and miR-2113 involved in HCC is yet to be explored. The purpose of this research is to probe the function role and associated underlying mechanism of eIF4AIII participated in HCC. The results revealed that eIF4AIII was overexpressed in HCC. Lost-of-function assays found that eIF4AIII knockdown, WD (Trp-Asp [tryptophan and asparaginic acid]) repeat domain 66 (WDR66) silence or miR-2113 promotion repressed cell proliferation, migration, and epithelial-mesenchymal transition (EMT) process in HCC. Furthermore, eIF4AIII could interact with WDR66 and further stabilize WDR66 messenger RNA. In addition, WDR66 was a target gene of miR-2113. Besides, WDR66 was antagonistically regulated by eIF4AIII and miR-2113. Rescue assays verified that eIF4AIII promoted HCC cell proliferation, migration, and EMT process via antagonistically binding to WDR66 with miR-2113. Taken together, these findings indicated an important role and a novel mechanism of eIF4AIII in HCC, providing an optional therapy for HCC patients.

Beyond CLIP: advances and opportunities to measure RBP-RNA and RNA-RNA interactions

RNA is an essential player in almost all biological processes, and has an ever-growing number of roles in regulating cellular growth and organization. RNA functions extend far beyond just coding for proteins and RNA has been shown to function in signaling events, chromatin organization and transcriptional regulation. Dissecting how the complex network of RNA-binding proteins (RBPs) and regulatory RNAs interact with their substrates within the cell is a real, but exciting, challenge for the RNA community. Investigating these biological questions has fueled the development of new quantitative technologies to measure how RNA and RBPs interact both locally and on a global scale. In this review, we provide an assessment of available approaches to enable researchers to select the protocol most applicable for their experimental question.