Background: Fibroblasts in the skin are highly heterogeneous, both in vivo and in vitro. One intriguing difference between follicular and interfollicular fibroblasts in vitro is their ability to differentiate in response to osteogenic media, or mechanical stimulation. In this study, we asked whether differences in the ability to respond to differentiation stimuli are due to baseline differences in chromatin accessibility.
Results: We performed chromatin accessibility and transcriptional profiling of two fibroblast subtypes found in human skin, which arise from a common progenitor during development yet display distinct characteristics in adult tissue and in vitro. We found that when cells were grown in regular growth media (GM) in culture they had unique chromatin accessibility profiles, however, these profiles control similar functional networks. When we introduced a chemical perturbation and grew cells in osteogenic media (OM) to promote differentiation, we observed a divergence not only in the accessible chromatin signatures but also in the functional networks controlled by these signatures. The biggest divergence was observed when we applied two perturbations to cells; growth in OM combined with mechanical stimulation in the form of a shock wave (OMSW). Here, in one of the fibroblast subtypes we found a number of uniquely accessible promoters which controlled osteogenic interaction networks associated with bone and differentiation functions. This fibroblast subtype also readily differentiates into bone in OMSW conditions, while the other fibroblast subtype under analysis lacks differentiation capability in vitro.
Conclusions: Using ATAC-seq and RNA-seq we found that a combination of two stimuli could result significant and specific changes in chromatin accessibility associated with osteogenic differentiation, but only within the fibroblast sub-type capable of osteogenic differentiation. Our results suggest that these two stimuli elicit this cell specific response by modifying chromatin accessibility of osteogenic related gene promoters.