CDCA7, a gene whose mutations disrupt DNA methylation and lead to immunodeficiency, has been identified as a potential sensor for a specific type of methylated DNA.
DNA methylation is the addition of a methyl group to the cytosine base in DNA, serving as a crucial method of epigenetic tagging. These epigenetic alterations function like switches to control gene activity, enabling the creation of different cell types without altering the DNA sequence itself. This process ensures, for instance, that genes associated with brain function remain inactive in heart cells.
Maintaining the DNA methylation pattern is vital for the proper functioning of different cell types. However, this is challenging as DNA methylation can fluctuate over time and is associated with various diseases. One such condition is known as immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, which features symptoms like frequent respiratory infections and delays in growth and cognitive development.
While it’s established that mutations in the CDCA7 gene result in ICF syndrome, the specific molecular role of the gene was not well understood. Now, the Funabiki lab at Rockefeller University, in collaboration with researchers at the University of Tokyo and Yokohama City University, has uncovered a significant functional property of CDCA7 that is crucial for properly passing on DNA methylation.
The research team found that CDCA7 can detect hemimethylation in eukaryotic cells, which is critical because this task was previously believed to be exclusively managed by a protein named UHRF1. Their findings were published in Science Advances.
“This is an astonishing discovery,” says Isabel Wassing, a co-first author and postdoctoral researcher in the Laboratory of Chromosome and Cell Biology led by Hiro Funabiki. “Understanding that CDCA7 also functions as a sensor illustrates why its mutations lead to conditions like ICF syndrome and fills a crucial knowledge gap in the epigenetics field. However, this also raises new questions, such as why the cell requires two different hemimethylation sensors.”
A transitional state
Through extensive cell division cycles, one parent cell divides into two identical daughter cells, resulting in the trillions of cells in the human body. Precise replication and distribution of DNA, organized into chromosomes, allow for accurate transmission of genetic information to each new daughter cell.
DNA replication is a complex process. Inside the cell nucleus, chromatin—a combination of double-stranded DNA and histone proteins—structures DNA like a string on a yo-yo to form nucleosomes. During replication, the double-stranded DNA unwinds from the histone, separating into two single strands. DNA polymerases then assemble corresponding nucleotides along each strand, creating two new double-stranded DNA molecules.
However, methyl groups do not automatically transfer to the newly synthesized DNA, resulting in a temporary hemimethylated state: the original parent DNA strand carries the methylation, while the newly incorporated nucleotides do not, signaling that DNA methylation maintenance is necessary. The detection of hemimethylation by UHRF1 is the crucial first step, as this protein then recruits and activates the DNA methyltransferase DNMT1, which adds the methyl mark to the new DNA strand.
Timeliness is critical, as cells must sense hemimethylation promptly; otherwise, the epigenetic methylation mark could be permanently lost before the next replication round.
The chromatin problem
Researchers understand that many DNA-binding proteins and enzymes crucial for introducing methylation face accessibility issues due to chromatin. Previous studies by Funabiki’s lab revealed that CDCA7 interacts with the protein from the HELLS gene, whose mutations also contribute to ICF syndrome. HELLS serves as a nucleosome remodeler that can temporarily unwrap DNA from nucleosomes.
“We hypothesized that the CDCA7-HELLS complex is essential for the cell to navigate the tightly packed heterochromatin, making DNA accessible for methylation,” explains Funabiki. “However, numerous nucleosome remodelers can expose DNA in this manner. It was previously unclear why the CDCA7-HELLS complex is uniquely associated with the maintenance of DNA methylation. Now that we have demonstrated that CDCA7 selectively recruits HELLS to hemimethylated DNA, we can finally provide an answer.”
In this new model, CDCA7 identifies hemimethylated DNA within chromatin and brings HELLS to the location, allowing this nucleosome remodeler to slide the nucleosome aside and expose the hemimethylation site to UHRF1.
This transfer of hemimethylation sensing highlights that CDCA7 is more effective at detecting hemimethylation in the dense heterochromatin compared to UHRF1. It also clarifies the reason for needing two distinct sensors. “For these sensors to identify hemimethylation, they must be able to bind directly and specifically to the hemimethylated DNA,” Wassing explains. “CDCA7 appears to have a unique ability to do this even when the DNA is wrapped around the nucleosome. If it weren’t for CDCA7, UHRF1 would not be able to perceive the hemimethylation signal within the nucleosome.”
This newfound knowledge may help clarify the mechanisms behind diseases caused by faulty methylation. Future research will explore possible functions of hemimethylation sensors beyond just maintaining DNA methylation.
“Since some chromosomal regions are known to retain hemimethylation, CDCA7’s recognition of these areas could have broader implications for gene regulation and chromosome organization,” Funabiki says. “This is an exciting prospect.”
