ИСТИНА

Mammalian ribosomes have a complex molecular architecture with an additional outer layer of flexible RNA. The rRNA expansion segments, protruding far beyond the conserved ribosome core, likely bind some translational machinery components and have important regulatory functions. Here, using publicly available data of the enhanced crosslinking and immunoprecipitation (eCLIP) experiments for 233 proteins provided by the ENCODE project [1], we found a number of mRNA-binding proteins that bind ribosomal RNA in human cells. To identify the binding sites, we used a newly developed computational protocol for mapping the eCLIP data on selected repetitive sequences and following statistical evaluation. For three proteins with known ribosomal localization, RPS3, RPS11, and SBDS, the sites identified by our model were in good agreement with structural data. Next, we determined ribosomal localization of general mRNA-binding proteins and components of stress granules (PABPC4, G3BP1, LIN28B), specific mRNA regulators and virus IRES trans-acting factors (La/SSB, PCBP2/HNRNPE2, HNRNPA1, HNRNPM), translation factor (DDX3X), ribosome biogenesis factors (UTP18, WDR3) and a component of the RNA-induced silencing complex RISC (SND1). In many cases, the identified contacts were mapped to the rRNA expansion segments, pointing to their role in mRNA-specific translational control and other ribosome-associated events.