The long noncoding RNA SPRIGHTLY acts as an intranuclear organizing hub for pre-mRNA molecules

Molecular mechanisms by which long noncoding RNA (lncRNA) molecules may influence cancerous condition are poorly understood. The aberrant expression of SPRIGHTLY lncRNA, encoded within the drosophila gene homolog Sprouty-4 intron, is correlated with a variety of cancers, including human melanomas. A team led by researchers at the Sanford Burnham Prebys Medical Discovery Institute demonstrate by SHAPE-seq and dChIRP that SPRIGHTLY RNA secondary structure has a core pseudoknotted domain. This lncRNA interacts with the intronic regions of six pre-mRNAs: SOX5, SMYD3, SND1, MEOX2, DCTN6, and RASAL2, all of which have cancer-related functions. Hemizygous knockout of SPRIGHTLY by CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 in melanoma cells significantly decreases SPRIGHTLY lncRNA levels, simultaneously decreases the levels of its interacting pre-mRNA molecules, and decreases anchorage-independent growth rate of cells and the rate of in vivo tumor growth in mouse xenografts. These results provide the first demonstration of an lncRNA’s three-dimensional coordinating role in facilitating cancer-related gene expression in human melanomas.

SPRIGHTLY RNA secondary structure and its binding partners

(A) The secondary structure of SPRIGHTLY was determined by RNA structure with the constraints of SHAPE-seq reactivity data. (B) Histogram of normalized SHAPE-seq reactivities as a function of nucleotide position of SPRIGHTLY. (C) The distribution of RNA sequences within gene bodies corresponding to dChIRP MACS peaks pulled down by the three sets of SPRIGHTLY probes, D1, D2, and D3.  (D) SPRIGHTLY binding partner RNAs determined by common MACS peaks. (E) SPRIGHTLY dChIRP specifically enriches the intronic regions of six genes.  (F) The integrated network of six RNA molecules that bind to SPRIGHTLY was constructed by querying integrated gene interaction network data.