An ultraconserved snoRNA-like element in long noncoding RNACRNDEpromotes ribosome biogenesis and cell proliferation

Abstract

ABSTRACTCancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here we performed CRISPRi screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively-spliced isoform of lncRNAColorectal Neoplasia Differentially Expressedcontaining an ultraconserved element (UCE), referred to asCRNDEUCE, is required for RCC cell proliferation.CRNDEUCElocalizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE ofCRNDEfunctions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eIF6, a key 60S biogenesis factor, which binds toCRNDEUCEthrough a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.