3D chromatin loops in tissue regeneration
Long-range DNA contacts are required for wing regeneration in Drosophila
A paper in Science Advances, published on August 7, describes regeneration of the wing imaginal disc, the larval Drosophila tissue that develops into the adult wing. After injury, two pairs of distant DNA regions came into contact more often in this tissue. The authors separately deleted two short intergenic regions that anchor these contacts. One belonged to a loop that became stronger during regeneration, while the other belonged to a connected loop. Both deletions impaired regeneration.
To repair damaged tissue, cells must coordinate changes in the activity of many genes. This process is influenced by the three-dimensional organization of chromatin, which consists of DNA and its associated proteins inside the nucleus. Genomic regions separated by millions of DNA letters can sometimes come together and form a loop. This allows a gene to interact with a regulatory region located far away in the linear DNA sequence.
The authors induced cell death in part of the wing imaginal disc, the precursor of the adult wing, and compared the injured tissue with a control. Hi-C, a method that shows which DNA fragments frequently come into contact across the nuclei of many cells, identified 27 loops spanning more than one million DNA letters. Contact frequency increased in two of these loops during regeneration. The researchers labeled the ends of these loops with fluorescent markers and measured the distance between them in individual nuclei. For one loop, the ends were close together in 29.6% of nuclei in regenerating tissue and 9.2% of control nuclei. For the other loop, the corresponding values were 33.6% and 9.9%.
The researchers then tested the functions of these contacts genetically. Anchors are short DNA regions at the ends of loops that maintain these contacts. Using CRISPR, which allows precise DNA editing, the authors deleted two intergenic anchors. One belonged to a loop that became stronger during regeneration, while the other belonged to a connected loop. Wings developed normally in larvae carrying either precise deletion. After induced injury, 60% and 57% of wings fully regenerated in the two deletion lines, compared with 87% in the control group. Deleting both anchors at the same time impaired regeneration even further.
The activity of hundreds of genes changed in larval tissues carrying these deletions. The changes were similar in the two precise deletion lines, even though the researchers disrupted different anchors.
The experiment was conducted in wing imaginal discs from Drosophila larvae. In this model, deleting the anchors of long-range loops impaired regeneration. This result indicates that the spatial organization of DNA contributes to tissue repair.