TRIM71 directly binds and stabilizes let-7 targets in HCC cells. (A) Schematic representation for the analysis conducted in B–D. Genes down-regulated in TRIM71 KO Huh7 cells (yellow)—obtained from B—are enriched for let-7 targets (blue) (Supplemental Table 4). Genes found enriched (greater than twofold) in TRIM71 RNA-IPs in HepG2 cells (green) were overlapped with genes down-regulated in TRIM71 KO Huh7 cells (yellow)—overlap depicted in C—to identify genes bound and stabilized by TRIM71. For those genes, miRNA enrichment analysis was conducted (Supplemental Table 5) to identify let-7 targets bound and stabilized by TRIM71 in HCC cells (orange). (B) Coexpression network analysis for WT and TRIM71 KO Huh7 cells using an available data set (GSE134125) revealed genes down-regulated in TRIM71 KO Huh7 cells (modules A–E marked with a yellow asterisk). (C) Overlap of TRIM71 RNA-IP data in HepG2 cells 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 the down-regulated genes in TRIM71 KO Huh7 cells (modules A–E), with let-7 targets directly bound by TRIM71 in HepG2 cells marked in orange. See also Supplemental Tables 4, 5.
