Sequences enriched in Alu repeats drive nuclear localization of long RNAs

Long noncoding RNAs (lncRNAs) are emerging as key players in multiple cellular pathways, but their modes of action and how those are dictated by sequence remain unclear. lncRNAs tend to be enriched in the nuclear fraction, whereas most mRNAs are overtly cytoplasmic, although several studies have found that hundreds of mRNAs in various cell types are retained in the nucleus. It is thus conceivable that some mechanisms that promote nuclear enrichment are shared between lncRNAs and mRNAs. In order to identify elements that can force nuclear localization in lncRNAs and mRNAs researchers from the Weizmann Institute of Science screened libraries of short fragments tiled across nuclear RNAs, which were cloned into the untranslated regions of an efficiently exported mRNA. The screen identified a short sequence derived from Alu elements and bound by HNRNPK that increases nuclear accumulation. They report that HNRNPK binding to C-rich motifs outside Alu elements is also associated with nuclear enrichment in both lncRNAs and mRNAs, and this mechanism is conserved across species. These results thus detail a novel pathway for regulation of RNA accumulation and subcellular localization that has been co-opted to regulate the fate of transcripts that have integrated Alu elements.

NucLibA analysis and the SIRLOIN element

a, Experimental approach. b, Nyc/Cyt ratios of tiles when cloned into the indicated region of AcGFP. Tiles overlapping repetitive elements are in black and other tiles are in gray. The region that overlaps the SIRLOIN element is shaded. c, Sequence alignment of four of the most effective tiles, the consensus sequence of AluSx repeat family, and the SIRLOIN element. C/T-rich hexamers are in black, and the regions in JPX#9 and PVT1#22 that were mutagenized in NucLibB are underlined. d, qRT-PCR determination of the abundance of AcGFP mRNA with the indicated fragments cloned into the 3’ UTR. n = 10–14 independent fractionations. Mean± SEM is shown. e, Imaging flow cytometry of AcGFP and MALAT1 mRNA, the fraction of the signal overlapping with DAPI signal out of the total signal intensity is displayed. Values above boxes indicate P-values compared to control (two-sided Wilcoxon test). n = 570–3621 independent cells. Boxplots show 5th, 25th, 50th, 75th and 95th percentiles. f-g, Nuc/Cyt ratios for RNAs with the indicated number of SIRLOINs or their antisense in MCF7 cells (f) and each of ten ENCODE cell lines (g). Boxplots show 5th, 25th, 50th, 75th and 95th percentiles. In f P-values are for sense vs. antisense comparisons (two-sided Wilcoxon). Asterisks in g indicate P < 0.01 (two-sided Wilcoxon) when comparing to transcripts without SIRLOINs. n> 185 genes in each group.