The human genome contains about 20,000 protein-coding genes, but that only accounts for roughly two percent of the genome. For many years, it was easier for scientists to simply ignore all of that extra genetic material, and it was written off as junk DNA that served no purpose. But in recent decades, the importance of some of that non-coding DNA has been revealed. As genetic and computational tools are improving, more discoveries are being made.
Reporting in Cell, scientists have determined that there are hundreds of crucial, long-non-coding RNA (lncRNA) molecules that are transcribed from DNA, and which play an important biological role in cells. Some of these lncRNAs function in human development, while others are related to cancer, showing the wide range of impacts they may have.
In this study, the investigators used the CRISPR gene editing tool to delete various genetic sequences, and identified about 800 noncoding RNAs in various cell types in different tissues. However, instead of using the Cas9 enzyme that is often used to edit DNA molecules, the investigators relied on a different enzyme called Cas13, which cuts RNA. This way, they could target RNA molecules directly, without disrupting regulatory elements in DNA.
While sequencing all of the RNA molecules in cells can be done, even at the single-cell level, those approaches are less likely to reveal much about the function of those molecules. By individually targeting lncRNAs for removal, scientists can see what the effect is on cell function.
"This survey of functional noncoding RNAs advances our understanding of the human genome and demonstrates the potential of CRISPR screens that specifically target RNA, even those that don't code for proteins," said senior study author Neville Sanjana, associate professor of biology at NYU, among other appointments.
The researchers assessed about 6,200 pairs of lncRNAs and protein-coding genes in five different cell types. This can provide some insight into the impact of an individual lncRNA. The approach identified 778 lncRNAs that are crucial to the normal function of various cells. This includes 46 essential lncRNAs that are required for normal cell function across cell types, and 732 lncRNAs that are more specialized to function in specific types of cells.
The study indicated that many crucial lncRNAs function independently of the protein-coding genes that may sit nearby in the genome.
Many critical lncRNAs were found to be expressed during developmental stages, with lower levels of expression as development proceeded. Many of these essential lncRNAs help control various pathways related to cell growth, which is relevant to both development and cancer.
"These noncoding RNAs may yield new biomarkers and therapeutic targets for cancer treatment, a potential opportunity for personalized medicine given their cell type-specific expression," added Sanjana.
Sources: New York University, Cell