Simon Elsasser’s group developed a better method to map these structures in the genome while investigating the G quadruplex DNA structure (G4). G4 CUT&Tag discovered many G4s in both the mouse and human genomes that had not been previously detected. The study was published in Nucleic Acid Research. These findings could be used to develop drugs for cancer therapy. They also provide an important tool for evaluating drug safety and action.

The individual DNA strands can take on alternative folds when the double-stranded canonical helix of the DNA is melted. The G quadruplex structure has four guanine bases arranged in a planar quartet, instead of pairing with the cytosine as usual. G4 is a structure that consists of several G quartets, stacked on top each other. G4s were first discovered at the ends chromosomes of so-called “telomeric repeat DNA” chromosomes 20 years ago. Researchers have discovered that G4s can be found in many variations and are also common in other parts of the human genome.

G4s function, location, and formation are yet to be determined

Researchers are still unsure where exactly G4s can be found, how they form and what they might be useful for. Jing Lyu, a doctoral student in Simon Elsasser’s group has created a new method of mapping G4 structures genome-wide and at high resolution.

“While genome-wide G4 mapping methods were available earlier, we were concerned about the fact that the protocols did not preserve the fragile G4 structures and therefore only allowed us to identify the most stable and abundant G4s in our genome. We used an in-situ approach in which antibodies against G4 structures are diffused to lightly permeabilized cells. This allowed us to “mark” the DNA sequences that made up a G4, says Jing Lyu (Ph.D. student) in Simon Elsasser’s Department of Medical Biochemistry and Biophysics.

CUT&Tag method to more accurately identify G4

CUT&Tag is a method that uses a transposase enzyme to recruit the antibody. It inserts an oligonucleotide in the genome sequence, which can be used later to amplify and sequence the targeted locations. Lyu was able to detect many G4s in his genome using the G4 CUT&Tag technique. This method had a better signal-to noise ratio than other methods.

Lyu was the first to map G4s in mouse embryonic cells and discovered that enhancers bound to pluripotency factor also contained G4s. G4 formation seemed to be a clear distinction between tissue-specific enhancers and enhancers that activated during differentiation.

Implications of Drug action and safety

Simon Elsasser is principal investigator and researcher at the Department of Medical Biochemistry and Biophysics. He says, “In the future, we would like to examine if and how enhancer G4s can play a role regulating gene activity and 3D genomic organization.”

Drug development for Cancer Therapy is a hot topic. Genome-wide mapping of G4s will be an important tool to assess drug safety and action.