tRNA-overlapping long non-coding RNAs loci repress codon-biased genes

The functions of most long non-coding RNAs (lncRNAs) are not known. Here, we define a group of 'tRNA-Overlapping LncRNA' (tROL) genes that are upregulated during in vitro cartilage development. Deletions of tROLs result in changes in the expression of codon-biased genes, where downregulated genes are enriched in codons corresponding to tRNAs overlapping disrupted tROLs. tROL loci are located in gene-dense regions and interact extensively between chromosomes, and tROL whole-gene deletions result in the upregulation of significantly overlapping subsets of genes in the vicinity of tROL loci. Inhibiting the lncRNA transcription and degrading the lncRNA transcripts of a tROL gene downregulates tRNA expression. Taken together, the results suggest that tROL loci coalesce and are dependent on each other's transcription to repress genes in spatial proximity and to activate tRNA expression. Our investigation thus provides insight into a previously uncharacterized role for tROLs as a regulatory bridge between the non-coding and coding genomes. Overall design: To investigate lncRNAs during in vitro cartilage development, we differentiated primary human mesenchymal stem cells (MSCs) into chondrocytes over 14 days. We then performed gene expression profiling analysis of data from RNA-seq of MSCs from two donors (female and male), differentiated in replicate, at 5 time points. To investigate the function of the tROL LINC00324 in cartilage development, we generated two isogenic deletions (KOs) in C-28/I2 chondrocytes. We then performed gene expression profiling analysis of data from RNA-seq of WT and LINC00324 KO clones. To investigate the function of additional tROLs and their interdependence, we generated two isogenic deletions (KOs) for the tROLs LINC00324, LINC01962, ENSG00000284607, and ENSG00000287264 in HEK-293 cells. We then performed gene expression profiling analysis of data from RNA-seq of WT and tROL KO clones.