Anu Thomas1, Frederick Rehfeld1, He Zhang2,3, Tsung-Cheng Chang1, Mohammad Goodarzi4, Frank Gillet1,8 and Joshua T. Mendell1,5,6,7 1Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 2Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 3Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 4Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 5Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 6Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 7Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA Corresponding author: joshua.mendellutsouthwestern.edu

↵8 Present address: Vaccine Research and Development, Pfizer, Inc., Pearl River, NY 10965, USA.

Abstract

Although splicing is a major driver of RNA nuclear export, many intronless RNAs are efficiently exported to the cytoplasm through poorly characterized mechanisms. For example, GC-rich sequences promote nuclear export in a splicing-independent manner, but how GC content is recognized and coupled to nuclear export is unknown. Here, we developed a genome-wide screening strategy to investigate the mechanism of export of NORAD, an intronless cytoplasmic long noncoding RNA (lncRNA). This screen revealed an RNA binding protein, RBM33, that directs the nuclear export of NORAD and numerous other transcripts. RBM33 directly binds substrate transcripts and recruits components of the TREX–NXF1/NXT1 RNA export pathway. Interestingly, high GC content emerged as the feature that specifies RBM33-dependent nuclear export. Accordingly, RBM33 directly binds GC-rich elements in target transcripts. These results provide a broadly applicable strategy for the genetic dissection of nuclear export mechanisms and reveal a long-sought nuclear export pathway for transcripts with GC-rich sequences.

Received February 3, 2022. Accepted May 3, 2022.