Mapping Chromatin Folding and Enhancer Activation After Exercise Training

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Transcriptional responses are required for proper development in cells and tissues. This response is integrated at gene enhancers and thus are required for responses to developmental cues. However, not much is known regarding how enhancers control the transcriptional responses to physiological adaptation such as after exercise training. We hypothesized that unique exercise responsive enhancers would be activated after exercise training and that these could be identified via specific histone modifications and 3-dimensional chromatin looping. To test this hypothesis, C57BL6J mice were split into an exercise trained or sedentary group. The exercise training consisted of 30 days of voluntary wheel running, while sedentary animals were housed with a locked running wheel. Quadriceps muscle was collected from both groups of animals on the same day, which included a 6hr fast. For the exercise trained group, their wheels were locked 24hrs before tissue collection. Analyses focused on identifying gene enhancers using both histone modifications and 3D genome architecture using Cleavage Under Targets and Tagmentation (CUT&Tag), High-Throughput Chromosome Conformation Capture (Hi-C), Promoter Capture Hi-C (pcHi-C) and RNA-seq. These analyses show unique enhancers that become activated after exercise training as well as condition specific 3-dimensional chromatin loops. Moreover, enhancers that are maintained in both the exercise and sedentary conditions are often activated to a higher degree in the exercise trained group as compared to the sedentary group, suggesting that these enhancers may be used for a more robust transcriptional response to subsequent exercise bouts. These data identify “exercise responsive enhancers” that will be key in understanding how genes are regulated during exercise adaptation in skeletal muscle and will aid future experiments that will test the necessity and sufficiency of these enhancers in controlling the adaptation to exercise. NIH under award number U24DK132746-01, UCLA LIFT-UP, and the A.P. Giannini Foundation. This abstract was presented at the American Physiology Summit 2025 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.

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