TRIM71 binds to IMP1 and is capable of positive and negative regulation of target RNAs

Abstract

TRIM71 is an important RNA-binding protein in development and disease, yet its direct targets have not been investigated globally. Here we describe a number of disease and developmentallyrelevant TRIM71 RNA targets such as the MBNL family, LIN28B, MDM2, and TCF7L2. We describe a new role for TRIM71 as capable of positive or negative RNA regulation depending on the RNA target. We found that TRIM71 co-precipitated with IMP1 which could explain its multiple mechanisms of RNA regulation, as IMP1 is typically thought to stabilize RNAs. Deletion of the NHL domain of TRIM71 impacted its ability to bind to RNA and RNAs bound by congenital hydrocephalusassociated point mutations in the RNA-binding NHL domain of TRIM71 clustered closely with RNAs bound by the NHL deletion mutant. Our work expands the possible mechanisms by which TRIM71 may regulate RNAs and elucidates further potential RNA targets.

The stem cell-specific protein TRIM71 inhibits maturation and activity of the pro-differentiation miRNA let-7 via two independent molecular mechanisms

“…A very recent study has shown that TRIM71 is able to bind and stabilize specific mRNAs in the HCC cell line HepG2 47 . Beyond the fact that we found some of these mRNAs to be let-7 targets, our work also confirms that TRIM71 is capable of positively regulating mRNA expression post-transcriptionally in ESCs.…”

“…TRIM71 is upregulated in patients with hepatocellular carcinoma (HCC) and its expression is correlated with advanced tumor stages and poor prognosis 24,44 . Several studies have shown that TRIM71 promotes proliferation in several HCC cell lines, including HepG2, Hep3B and Huh7 24,44,47 . In one of these studies, an increase of let-7 activity was observed in TRIM71 knockdown cells 44 .…”

“…To evaluate whether TRIM71 was also able to interact with some of these let-7 targets in hepatocellular carcinoma cells, we used another available TRIM71 RNA-IP dataset from HepG2 cells 47 , and overlapped it with genes found to be downregulated in TRIM71 KO Huh7 cells ( Fig. 9A-C).…”

“…B) Co-expression network analysis for WT and TRIM71 KO Huh7 cells using an available dataset (GSE134125) 23 revealed genes downregulated in TRIM71 KO Huh7 cells (modules A-E marked with a yellow asterisk). C) Overlap of TRIM71 RNA-IP data in HepG2 cells 47 with gene expression data, showing the number of TRIM71-bound mRNAs in HCC cells within each module from B. D) miRNA network showing targets for the different let-7 family members found among commonly downregulated genes in in TRIM71 KO Huh7 cells (modules A-E), with let-7 targets directly bound by TRIM71 in HCC cells marked in orange.…”

“…We additionally used genes commonly downregulated in Trim71 KO ESCs, Trim71 RING mutant (C12LC15A) ESCs and Trim71 NHL mutant (R738A) ESCs, derived from a previous study which also included mRNAs enriched in TRIM71 RNA-IPs of ESCs (GSE134125) 23 . Last, we used two published datasets derived from previous studies in HCC cells 23,47 , and focused on genes significantly downregulated in TRIM71 KO Huh7 cells (GSE134125) 23 and genes significantly enriched in TRIM71 RNA-IPs of HepG2 cells 47 . In general, miRNA enrichment analysis was first conducted on negative modules to identify let-7 targets among the mRNAs found stabilized in the presence of TRIM71.…”