Temporarily disabling a protein complex that organizes DNA into loops inside the cell’s nucleus drastically disrupted the three-dimensional structure of the genome, but surprisingly most genes continued to function as usual, Weill Cornell Medicine researchers found. However, they also discovered a small group of affected genes that play a critical role in guiding cells to become specific types, for example heart, brain, or liver cells.
The study, published April 13 in Nature Genetics, helps resolve a long-standing paradox in biology about genome architecture and cell function, which may provide insights into certain developmental disorders and cancers.
The protein complex, called cohesin, plays a key role in shaping the three-dimensional structure of DNA inside the nucleus. This organization not only helps DNA fit inside the nucleus but brings distant regulatory elements into contact with the genes they control, influencing which genes are turned on or off to maintain cell identity and function.
Intriguingly, previous research suggested that removing cohesin—and the loops it forms—had little effect on overall gene activity. At the same time, mutations in cohesin are commonly found in cancers and in disorders, known as cohesinopathies, that affect physical and cognitive development.
The researchers revisited the interplay between cohesin and gene activity employing stem cells in a unique experimental system. “We wanted to test this paradox under the most challenging conditions: right after cell division, when the entire genome architecture and gene expression program must be rebuilt from scratch,” said senior author Dr. Effie Apostolou, associate professor of molecular biology in medicine and a member of the Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine.
The study was led by graduate student UkJin Lee in the Apostolou lab, who performed the experiments and computational analysis.
Dividing Stem Cells Make Critical Decisions
To better understand how cohesin operates, Dr. Apostolou’s group studied mouse embryonic stem cells, which can develop into many different cell types in the body. When stem cells divide, the resulting two daughter cells must decide whether to remain stem cells or activate new programs to become specialized. That developmental selection is made immediately after cell division is complete, and scientists can guide this decision in the lab.
Dr. Effie Apostolou
When the researchers removed cohesin at that point, they confirmed that it is essential for maintaining how the DNA is folded. Without cohesin, the overall genomic structure was severely disrupted, with most DNA loops failing to re-form, as shown by techniques that map different DNA interactions in three dimensions.
“But then came the big surprise,” Dr. Apostolou said. “Most genes were largely unaffected.” Even without normal DNA organization, cells were able to restore their regular gene activity, particularly those that remained stem cells.
“This points to a resilient molecular memory that persists through cell division and allows reactivation of the stem cell program in the absence of this critical architectural protein,” said first author Lee. The researchers suspect that additional factors come into play, forming a complex molecular memory that ensures the right genes are activated at the right time.
A Small but Crucial Set of Vulnerable Genes
However, there was more to the story. When the researchers “pushed” stem cells to differentiate into specialized types after cell division, they found that a small group of genes failed to turn on properly without cohesin.
UkJin Lee
“The vulnerable genes tend to be developmentally important—such as those encoding transcription factors that direct cell identity,” Dr. Apostolou said. These genes are often sequestered in isolated areas of the genome and rely on cohesin to bring them in contact with distant DNA elements that enhance their activity.
Inhibiting these interactions can derail normal development, preventing genes from turning on when they should or turning on incorrect genes. “Therefore, the unique vulnerability of these genes to cohesin loss might have long lasting effects on proper development and differentiation,” Dr. Apostolou said.
Moving forward, Dr. Apostolou and her lab will continue to study what makes some genes dependent on cohesin, while others can function normally without it. They will also pursue genes vulnerable to cohesin loss and assess how even slight perturbations in their activity can lead to profound effects, including cancer or developmental impairment.
“The key is identifying these genes and understanding why they are affected and under what conditions,” Dr. Apostolou said.
This study was funded in part by the Tri-Institutional Stem Cell Initiative by the Starr Foundation; the National Institute of General Medical Sciences grants RM1GM139738, R01GM138635 and R01GM144508; the National Institute of Neurological Disorders and Stroke R01NS136475; the Human Genome Research Institute grant HG012103; and the National Cancer Institute grant P30CA008748.