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 223 proteins provided by the ENCODE project, 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 two proteins with known ribosomal localization, RPS3 and RPS11, the sites identified by our model were in good agreement with structural data. Next, the results obtained for SBDS and NIP7 known as large subunit maturation factors in eukaryotic cells suggest conservative functions for these proteins in humans. Among general mRNA-binding proteins we have determined ribosomal localization of stress granule components (G3BP1, SND1), specific mRNA regulators and virus IRES trans-acting factors (PCBP1/hnRNP E1, AATF, NIPBL), aminoacyl tRNA synthetase (AARS), pseudouridine synthases (PUS1, DKC1) and ribosome biogenesis factors (UTP18, UTP3, DDX51, DDX52, WDR3, WDR43). In a number of 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. The study was supported by the Russian Science Foundation (RSF 18-14-00291).