Identification and Characterization of Sequence-Specific Trans-Acting Functional lncRNA

The non-protein-coding portion of the human genome has gone from being considered “junk DNA” to “hot spots” in the area of life science. Genome-wide transcriptome studies indicate that this portion covers 75-90% of the genome, whereas only 2% of the human genome comprises protein-coding genes. The non-protein-coding areas in the genome generate non-coding RNAs (ncRNAs) that are subsequently divided according to their function and size. In the human genome, the majority of these ncRNAs are classified as long non-coding RNAs (lncRNAs). lncRNAs have been found to be dysregulated in a number of cancers, affecting several biological processes. Their most witnessed function is their ability to regulate and interact with different types of molecules, such as DNA, proteins, and RNA. Broadly, their functions can be classified as either cis-acting, affecting genes close to their site of transcription, or trans-acting, throughout the whole cell.

In this study, a novel CRISPR-interference (CRISPRi)-based approach for researching and characterizing a cytoplasmic-enriched lncRNA CYTOR that is hypothesized to be functional and trans-acting in leukemia cells is presented. The effect of CYTOR knockdown on the cell transcriptome is tested, hinting towards its function by connecting it to the resulting altered biological pathways. lncRNA CYTOR is further characterized, showing its potential as both trans- and cis-acting molecule, and its connection to the regulation of several genes involved in DNA and histone methylation. A deeper understanding of CYTOR in different cancer types may provide new therapeutic targets, eventually leading to world-changing effects in target therapy and non-coding RNA therapeutics.