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. 2025 Apr 17;85(8):1543-1560.e10.
doi: 10.1016/j.molcel.2025.03.006. Epub 2025 Apr 3.

An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation

Jong-Sun Lee  1 , Tu Dan  2 , He Zhang  3 , Yujing Cheng  1 , Frederick Rehfeld  1 , James Brugarolas  4 , Joshua T Mendell  5
Affiliations

An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation

Jong-Sun Lee et al. Mol Cell. .

Abstract

Cancer 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 CRISPR interference (CRISPRi) screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively spliced isoform of lncRNA colorectal neoplasia differentially expressed (CRNDE) containing an ultraconserved element (UCE), referred to as CRNDEUCE, is required for RCC cell proliferation. CRNDEUCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eukaryotic initiation factor 6 (eIF6), a key 60S biogenesis factor, which binds to CRNDEUCE through 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.

Keywords: 60S ribosomal subunit; CRNDE; eIF6; lncRNA; long noncoding RNA; ribosome biogenesis; small nucleolar RNA; snoRNA.

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Conflict of interest statement

Declaration of interests J.T.M. is a scientific advisor for Ribometrix, Inc. and Nuago Therapeutics, Inc. and owns equity in Orbital Therapeutics, Inc.

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