Discovering Critical Roles for Sequences that Set the 3D Structure of DNA

Three dimensional DNA strands in a double helix are blue against blue background. In the center is a bright sun-like dot.

Genes can be regulated at the physical level. One example are DNA loops formed by CTCF proteins, which create physical boundaries between enhancers—non-coding DNA that helps promote gene activity or transcription—and the areas of genes where transcription begins, which are known as promoters. However, the overall relevance of CTCF loops is not clear, as previous researchers have only observed mild developmental problems when they are disturbed.

In a study from the Rocha Lab, researchers found that for some domains, altering these boundaries can lead to severe developmental problems, including congenital anomalies.
The researchers used a mouse model to evaluate a very small sequence (20 base pairs) in a non-coding region of DNA that affects binding of the CTCF protein near three developmental genes called FGF. Variations in this sequence disrupted CTCF binding and chromatin structure, rewired chromatin interactions between genes and regulatory regions, and as a result, increased the activity of FGF genes that would otherwise have been inactive or less active.
These changes at the DNA level caused problems including orofacial clefts, encephalocele (a severe type of neural tube defect), and fetal death.
The findings show how small sequence variants at certain domain boundaries can have a surprisingly outsized effect and must be considered as potential sources of gene dysregulation during development and disease. Furthermore, the study provides insight into potential origins of encephalocele, and it will be important to investigate whether this mechanism is relevant for cases of human encephalocele.

Reference

Chakraborty S, Wenzlitschke N,Anderson MJ, Eraso A, Baudic M, Thompson JJ, Evans AA, Shatford-Adams LM, Chari R, Awasthi P, Dale RK, Lewandoski M, Petros TJ, and Rocha PP.
Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development. Developmental Cell DOI: https://doi.org/10.1016/j.devcel.2025.02.002 (2025)

Learn more about the Genetics and Epigenetics of Development Group: https://www.nichd.nih.gov/about/org/dir/affinity-groups/GED.