A new study details the high-throughput process for rapid screening and identification of mysterious long non-coding RNA.

UC Santa Cruz researchers have discovered that LOUP is a multifunctional gene in immune cells called monocytes. LOUP can work inside the nucleus to control its neighbour SPI1. They also discovered that LOUP RNA can leave the nucleus and produce a small peptide in the cytoplasm leading to an increase in the protein SPI1 and causing downregulation of NF-kB, the master controller of inflammation. CREDIT Carpenter Lab, UC Santa Cruz

UC Santa Cruz researchers have discovered a peptide in human RNA that regulates inflammation and may provide a new path for treating diseases such as arthritis and lupus. The team used a screening process based on the powerful gene-editing tool CRISPR to illuminate one of the biggest mysteries about our RNA–the molecule responsible for carrying out genetic information in our DNA.

This peptide originates within a long non-coding RNA (lncRNA) called LOUP. According to the researchers, the human genome encodes over 20,000 lncRNAs, making it the largest group of genes produced from the genome. But despite this abundance, scientists know little about why lncRNAs exist or what they do. This is why lncRNA is sometimes called the “dark matter of the genome.”

The study, published May 23 in the Proceedings of the National Academy of Sciences (PNAS), is one of the few in the existing literature to chip away at the mysteries of lncRNA. It also presents a new strategy for conducting high-throughput screening to rapidly identify functional lncRNAs in immune cells. The pooled-screen approach allows researchers to target thousands of genes in a single experiment, which is a much more efficient way to study uncharacterized portions of the genome than traditional experiments focusing on one gene at a time.

The research was led by immunologist Susan Carpenter, a professor and Sinsheimer Chair of UC Santa Cruz’s Molecular, Cell, and Developmental Biology Department. She studies the molecular mechanisms involved in protection against infection. Specifically, she focuses on the processes that lead to inflammation to determine lncRNAs’ role in these pathways.

“Inflammation is a central feature of just about every disease,” she said. “In this study, my lab focused on determining which lncRNA genes regulate inflammation.”

This meant studying lncRNAs in a type of white blood cell known as a monocyte. They used a modification of the CRISPR/Cas9 technology, called CRISPR inhibition (CRISPRi), to repress gene transcription and find out which of a monocyte’s lncRNA plays a role in whether it differentiates into a macrophage—another type of white blood cell that’s critical to a well-functioning immune response.

In addition, the researchers used CRISPRi to screen macrophage lncRNA for involvement in inflammation. Unexpectedly, they located a multifunctional region that can work as an RNA and contain an undiscovered peptide that regulates inflammation.

Ms Carpenter said that understanding that this specific peptide regulates inflammation gives drugmakers a target to block the molecular interaction behind that response to suppress it. “In an ideal world, you would design a small molecule to disrupt that specific interaction instead of targeting a protein that might be expressed throughout the body,” she explained. “We’re still far from targeting these pathways with that level of precision, but that’s definitely the goal. There’s a lot of interest in RNA therapeutics right now.”