LENG8 Functions as a Quality Control Checkpoint for Nuclear Retention and Degradation of Misprocessed RNAs

Quality control is essential for maintaining proper gene expression. For example, aberrantly processed RNAs are retained and degraded in the nucleus, and defects in this process have been linked to various diseases, including cancer and neurodegeneration. However, the underlying mechanisms of RNA nuclear retention and degradation remain poorly understood. Through a genome wide CRISPR screen, we identified not only known factors involved in nuclear RNA degradation but also candidate proteins mediating RNA nuclear retention, including the poorly characterized protein LENG8. Our findings reveal that LENG8 is recruited to pre-mRNAs by splicing factors, including components of the U1 snRNP. Once RNA-bound, LENG8 is both necessary and sufficient to sequester RNA in the nucleus. Depletion of LENG8 leads to the leakage of intron containing RNAs and numerous nuclear noncoding RNAs into the cytoplasm, demonstrating its crucial role in RNA retention. Mechanistically, we further discovered that LENG8 lacks a specific region required for forming an intact TREX2 complex, unlike its paralog GANP. As a result, LENG8 retains misprocessed RNAs in the nucleus through a dominant-negative mechanism of TREX2/GANP, despite its ability to recruit TREX and the PCID2-SEM1 complex. Additionally, LENG8 interacts with the ZFC3H1-MTR4-exosome complex to degrade nuclear-retained RNAs, linking it to both RNA retention and degradation pathways. In conclusion, our study uncovers a novel mechanism of gene expression quality control, highlighting LENG8 as a key regulator of RNA nuclear retention and degradation, with potential implications for human disease. Fraction mRNA-seq to study if misprocessed RNAs are exported into cytoplasm after depletion of LENG8; PAS-seq to study if IPAs are degraded by LENG8 and if IPAs are exported into cytoplasm after depletion of LENG8