Researchers led by Dubravka Vučićević at the Max Delbrück Center have developed a new method to discover how DNA controls genes. Their technique, published in “Cell Genomics,” can reveal the genetic “switches” that regulate important genes more quickly than existing methods.
Most of the human genome does not code for proteins. Instead, much of it consists of regulatory regions. Like switches that turn lights on and off, these regions of nucleotides –called transcriptional enhancers – determine where and when a gene is active, and largely control how much of the corresponding protein a cell produces. Defects in the genetic code of such regulatory elements can cause developmental defects and disease. But compared to protein-coding regions, they are difficult to identify because they are often located far from the genes they regulate and lack a well-defined genetic code.
Scientists at the Max Delbrück Center led by Dr. Dubravka Vučićević in the Computational and Regulatory Genomics lab of Professor Uwe Ohler have created a powerful new tool to uncover these regions that control our genes. Called TargEted SingLe–cell Activation screen
(TESLA-seq), it combines CRISPR-based gene activation (CRISPRa) – a gene regulation technique that uses an engineered form of the CRISPR-Cas9 system to enhance the expression of specific genes – and targeted single-cell RNA sequencing to identify regulatory regions more quickly and accurately than other methods. The study was published in “Cell Genomics.”
“With this method, we can actually test how thousands of candidate regulatory elements in the genome are capable of switching genes on – and find out exactly what genes they influence,” says Vučićević, lead author of the study.
Mapping regulatory elements
To showcase the technique, the study focused on a gene called PHOX2B, which is essential for nervous system development. Mutations in the gene have been linked to neuroblastoma, a cancer of nervous system tissue that primarily affects children.
Vučićević and her colleagues concentrated on a large area around PHOX2B. They designed two to three guide RNAs (gRNAs) to bind to sections of the DNA, or chunks, each 100 base pairs long. These gRNAs guided the CRISPR system to target locations in the genome. With a total of 46,722 gRNAs, they were able to scan the entire genomic landscape around the PHOX2B gene for potential gene switches.
They then transferred each gRNA into a single human neuroblastoma cell. The CRISPRa system then activated any regulatory regions that might have been present in the “chunk.” They identified more than 600 regions – called CaREs (CRISPRa-responsive elements) – that altered cell growth when activated.
The team then zoomed in on about 200 CaREs in more detail and used targeted single-cell RNA sequencing to read out both the gRNA inside each cell and the RNA expressed from nearby genes. This allowed them to link each CaRE to any of the over 70 genes in the PHOX2B region, whose expression changed in that cell. They also found direct connections between CaREs and important regulators of SHISA3 and APBB2, which are involved in cancer and Alzheimer’s disease.
Surprisingly, many CaREs controlled genes far away, skipping over nearby genes entirely – something other methods often miss. “TESLA-seq doesn’t just capture what’s happening in one cell type, it can reveal potential connections between genes and regulatory regions across different biological systems,” says Ohler.
This is significant because many diseases affect more than a single tissue type, adds Vučićević. “The technique can be used to study the vast, uncharted parts of our DNA that influence health and disease across multiple organ systems and can help us to design more precise and effective therapies.”
Reference: Vučićević D, Hsu CW, Lopez Zepeda LS, et al. Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation. Cell Genomics. 2025:100984. doi: 10.1016/j.xgen.2025.100984
This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source. Our press release publishing policy can be accessed here.