Regulatory DNA sequences responsible for diseases characterised 

Scientists have developed a new system to identify and characterise the molecular components that control the activities of regulatory DNA sequences in the human genome. Their findings have been published in the journal Cell.

The system, named CAPTURE (CRISPR Affinity Purification in situ of Regulatory Elements), was developed by researchers in the lab of Dr Jian Xu from the Children’s Medical Center Research Institute at UT Southwestern. It provides an approach to simultaneously isolate genomic sequence-associated proteins as well as their RNA and DNA interactions.

“The ability that CAPTURE gives us to isolate and analyse the entire set of factors that regulate our DNA offers many possibilities to study how different proteins control genome function in cancer and stem cells,” said Dr Xu, senior author of the study and assistant professor in CRI at UTSW and the Department of Pediatrics. “It also opens up a completely new avenue to find new drug targets.”

The method was developed by repurposing the CRISPR genomic editing system, including the CRISPR-associated protein 9 (Cas9) — an RNA-guided enzyme that binds to DNA. CAPTURE works by using guide RNAs to direct a deactivated version of Cas9 (dCas9) to the DNA elements that researchers want to study. Then, dCas9 — along with other proteins, RNA and DNA sequences associated with dCas9’s position on the chromosome (its genomic loci) — can be isolated and studied. This makes it possible to identify and characterise genomic regulatory regions, and their associated proteins, throughout the genome.

Using CAPTURE, Dr Xu’s laboratory successfully identified many known and new human telomere-associated proteins as a proof of principle. Telomeres, which are short, repetitive DNA sequences on the ends of chromosomes, protect our chromosomes from fraying or fusing with neighbouring chromosomes. Next, researchers uncovered new mechanisms regulating aberrant beta-globin gene expression in human blood cells. Beta-globin is a vital part of a larger protein known as haemoglobin that is responsible for the exchange of oxygen and carbon dioxide between our lungs and body tissues. Altered expression of beta-globin genes is associated with inherited haemoglobin disorders such as sickle cell disease, currently affecting 5% of the world’s population.

“The unbiased analysis of the genome by CAPTURE provides biomedical researchers with a powerful new tool to decipher underlying regulatory principles. This new tool will advance our understanding of the human genome and genetic variations in a variety of diseases,” Dr Xu said.