Genes contain instructions for making proteins, and a central dogma of biology is that this information flows from DNA to RNA to proteins. But only two percent of the human genome actually encodes proteins; the function of the remaining 98 percent remains largely unknown. Now, a new study in Cell finds that some noncoding RNAs are not, in fact, junk -- they are functional and play an important role in our cells, including in cancer and human development. Using CRISPR technology that targets RNA instead of DNA, researchers at New York University and the New York Genome Center searched across the genome and found nearly 800 noncoding RNAs important for the function of diverse human cells from different tissues.

 

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. Most CRISPR applications use an enzyme called Cas9 to edit genes on the DNA level. However, a newer technology uses the enzyme Cas13 to more precisely target RNA without disrupting nearby protein-coding genes and other regulatory elements. Sanjana's lab previously demonstrated how a CRISPR-Cas13 platform targeting RNA instead of DNA can be optimized to screen the whole transcriptome, or the genetic information transcribed into RNA molecules. Using CRISPR-Cas13 to edit RNA and avoid off-target activity, the researchers systematically profiled nearly 6,200 gene pairs of long noncoding RNAs (lncRNAs) and nearby protein-coding genes across five human cell lines, including kidney, leukemia, and breast cancer cells. The researchers identified 778 lncRNAs that are essential for cell function, including a core group of 46 lncRNAs that are universally essential and 732 with functions specific to certain cell types. They then compared the essential lncRNAs to protein-coding genes.

 

The team also discovered that essential lncRNAs modulate key pathways for cell proliferation -- a process that is important in both human development and cancer -- and that their loss can impair the progression of cells and drive cell death. Notably, many essential lncRNAs were highly expressed across tissues early during human development and showed lower expression in the later stages, suggesting an important role for certain lncRNAs during development.