ICAM1 mRNA entraps ILF2/ILF3 to inhibit transcription of EIF4E and global protein synthesis.

The view of mRNA function as a translational template is being challenged beyond translation. However, how these non-canonical mRNAs function independently of their coding protein remains largely unexplored. Here, we found that intercellular adhesion molecule 1 (ICAM1) depletion via CRISPR-Cas9 protein knockout and shRNA-mediated RNA knockdown produces opposite effects on cell proliferation in human cells, which is validated by overexpression of mutated coding ICAM1 mRNA and ICAM1 coding sequence (CDS). Mechanistically, cis-antisense transcripts of ICAM1/ICAM1-AS form a double-stranded RNA (dsRNA), which entraps the interleukin enhancer binding factor 2 (ILF2)/ILF3 complex to inhibit DNA binding in a length-dependent manner, thus suppressing EIF4E transcription and global protein synthesis. Clinical analysis highlights the coordinated downregulation of ICAM1/ICAM1-AS, independent of highly expressed ICAM1 protein in lung cancer. In conclusion, this study reveals a role for ICAM1 mRNA in regulating cellular transcription via the dsRNA-ILF2/3 axis. Our findings challenge the phenotype explanation of gene silencing between RNA knockdown and protein knockout and underscore independent mRNA functions.