Highly efficient method to identify the genetic “switches” that control gene expression

Scientists at St. Jude Children’s Research Hospital have created an integrated, high-throughput method to help explain and potentially regulate gene expression for the treatment of diseases like beta-thalassemia and sickle cell disease. The findings were published in the journal Nature Genetics.

Corresponding author Yong Cheng, PhD, of the St. Jude Departments of Hematology and Computational Biology, helped develop a highly efficient method in identifying the genetic switches that regulate gene expression. Image Credit: St. Jude Children’s Research Hospital.

The system was used by researchers to classify dozens of DNA regulatory elements that work together to orchestrate the shift from fetal to adult hemoglobin expression. The approach may also be used to investigate other diseases including gene control.

Regulatory components, also known as genetic switches, are found in non-coding regions of DNA. These regions, which account for about 98% of the genome, do not encode genes.

The elements are known by various names—repressor, enhancer, insulator, among others—but the specific genes they control, how the regulatory elements interact, and responses to other questions remain unknown.

Without the high-throughput system, identifying key regulatory elements is often extremely slow.”

Yong Cheng, PhD, Study Corresponding Author, Departments of Hematology and Computational Biology, St. Jude Children’s Research Hospital

Mitchell Weiss, MD, PhD, Hematology chair, is the co-corresponding author of the study.

“For example, despite decades of research, fewer than half of regulatory elements and the associated genetic variants that account for fetal hemoglobin levels have been identified,” said Cheng.

Precision editing provides key details about the regulation of gene expression

The new method integrates bioinformatic prediction algorithms with an adenine base editing platform, as well as experiments to determine how base gene editing influences gene expression.

Base editing is more accurate than traditional gene-editing tools like CRISPR/Cas9 since it changes a single letter in the four-letter DNA alphabet at a high efficiency without causing bigger deletions or insertions.

The research team used the ABEmax base editor to make 10,156 unique edits in 307 regulatory elements expected to affect fetal hemoglobin expression. The expression has the potential to alter the severity of hemoglobin diseases like sickle cell disease.

The DNA bases thymine and adenine were modified to cytosine and guanine because of the edits. The researchers concentrated on regulatory elements in the genes BCL11A, MYB-HBS1L, KLF1, and beta-like globin.

The researchers used this method to validate the few recognized regulatory elements of fetal hemoglobin expression while also discovering several new ones.

Using this system, Dr. Cheng and our colleagues have identified a regulatory ‘archipelago’ of dozens of regulatory elements that act together to orchestrate a developmental switch from fetal to adult hemoglobin expression. A deeper understanding of this switch is important for human genetics in general. It may also have implications for treating hemoglobin disorders such as sickle cell disease and beta thalassemia.”

Mitchell Weiss, Hematology Chair, St. Jude Children’s Research Hospital

The hemoglobin mutation that causes sickle cell disease has little effect on fetal hemoglobin. The mutation induces sickle cell disease red blood cells to transform from pliable disks that migrate effortlessly across small blood vessels to fragile, sickle-shaped cells that obstruct blood supply and cause pain, organ damage, and higher risk of death.

After birth, fetal hemoglobin synthesis normally, but not always, decreases significantly. Because of genetic differences, certain people produce fetal hemoglobin during their lives with no ill effects. In sickle cell disease patients, fetal hemoglobin persistence may eliminate symptoms.

Base editing increased fetal hemoglobin and reduced sickling

In this research, the researchers used the base editing method to destroy one of the recently discovered hemoglobin regulatory elements. Researchers working on developing blood cells from sickle cell patients discovered elevated fetal hemoglobin in the edited cells.

These cells were therefore less likely to sickle when exposed to low oxygen levels, which would usually cause the shape to change.

The St. Jude Sickle Cell Genome Project, which included gene editing and analytic expertise, was critical to this study. The research involved the whole-genome sequencing of almost 1,000 people with sickle cell disease.

The sequencing information is valuable because many of the regulatory elements found in this study are rare and may have gone undetected otherwise.