A new study clarifies how the three-dimensional organization of the genome is regulated at the onset of skeletal muscle formation. Although the DNA sequence of the genome is a linear code, like a long sentence, the actual DNA molecule twists and folds in 3D space, with some sequences that are distant from each other in sequence being physically close to each other in space. These 3D interactions are thought to allow proteins that bind DNA to regulate the activity of genes that are distant from where they are binding.

In an article published in Nature Communications, researchers study the activity of one of these DNA-binding proteins, Pax3, a protein that is essential for the development of skeletal muscle. They show that large loops form between DNA sequences where Pax3 binds, and muscle-specific genes that Pax3 regulates, and that are important for the development of muscle.

The same research group had previously mapped all of the sites to which Pax3 binds in the genome of mesoderm cells, a type of embryonic tissue with the capacity to form muscle. They found that when Pax3 binds to DNA, it opens up and loosens the packing of the DNA molecule in the local region. In the current study, they discovered that after this happens, the Pax3 protein brings in a bridging molecule, called Ldb1, which allows 3 dimensional loops to form between distant sequences by forming a bridge between the Pax3 protein and the distant gene that it is regulating.

To prove the requirement of Ldb1 for the changes in genome architecture, the lead author said "they used a genetic trick," as they forced Ldb1 recruitment where Pax3 typically binds in the genome by creating a Pax3-Ldb1 chimera. They also showed that in the absence of Ldb1, muscle does not form properly in mouse embryos.

"Altogether, we demonstrate that Pax3, besides regulating the chromatin architecture, is also manipulating the activation of myogenic enhancers, genomic DNA fragments with important regulatory functions for gene expression," said the lead author.

There is evidence that changes in DNA molecular looping, also called chromatin architecture, can lead to genetic disorders and cancer. "By studying how chromatin architecture is regulated within the nucleus, we will better understand both normal and pathological processes and potentially identify new targets for the treatment of diseases such as cancer," said the lead author.

"Both publications are great examples of how pluripotent stem cells represent a valuable tool to study cell fate specification and dissect transcriptional regulation," says the senior author.

https://www.med.umn.edu/news-events/umn-researchers-discover-how-three-dimensional-organization-genome-regulates-cell-differentiation

https://www.nature.com/articles/s41586-019-1125-3

http://sciencemission.com/site/index.php?page=news&type=view&id=publications%2Fpax3-cooperates-with&filter=22