SCOPE Tool Expands Protein Discovery at Genomic Sites

Weill Cornell Medicine investigators developed a molecular tool that significantly advances the detection and study of proteins regulating gene activity inside cells. The activity of genes depends largely on proteins that can switch them on or off, or alter their rates of activity by binding directly to DNA. Until now, pinpointing these regulatory DNA-binding proteins has posed major challenges, due to a lack of sufficiently precise techniques. The newly developed tool, described in the Proceedings of the National Academy of Sciences, makes it possible to target nearly any site on the genome and capture proteins in the vicinity, allowing for their identification and functional study. The method enabled the researchers to identify new protein regulators responsible for stem cell gene functions in humans.

According to Dr. Shuibing Chen, co-senior author of the study, the group expects this tool to become widely used in laboratories and is already making plans to apply it to studies of diseases such as type 1 diabetes.

The tool, called SCOPE, is composed of two main elements. The first is a protein that incorporates a guide RNA—an engineered RNA molecule able to direct the protein complex to almost any DNA sequence in the genome. The second component is a unique amino acid, which serves as a protein building block that only becomes reactive when exposed to ultraviolet light, forming a stable bond with nearby proteins. With this design, researchers can isolate proteins "captured" by SCOPE and identify them using widely available techniques such as mass spectrometry.

This special amino acid, known as AbK, is derived from microbes known as archaea and does not react with naturally occurring amino acids in mammalian or bacterial cells unless UV light is applied. “This reduces the chances of unwanted interactions between the SCOPE tool and other proteins, which effectively gives SCOPE a high sensitivity, enabling it to detect proteins that are DNA-bound only weakly and/or transiently,” notes Dr. Jiajun Zhu, the study’s first author.

The SCOPE tool can be integrated into the genomes of various cells, even stem cells, so that it functions inside living cells, binding to proteins at targeted genomic locations. In their research, the scientists used SCOPE on human embryonic stem cells and determined the roles of three DNA-binding proteins: two maintained the cells’ stem-like state, while the third promoted their differentiation. The team aims to use SCOPE to discover gene-regulating proteins in diverse cell types and disease models, including those related to the heart, diabetes, and neurological disorders.