Controlled movement of nano-scale stable magnetic objects has been proposed as the foundation for a new generation of magnetic storage devices. Magnetic skyrmions, vortex-like spin textures stabilized by their topology are particularly promising candidates for this technology. Their nanometric size and ability to be displaced in response to an electrical current density several orders of magnitude lower than required to induce motion of magnetic domain walls suggest their potential for high-density memory devices that can be operated at low power. However, to achieve this, skyrmion movement needs to be controlled, where a key question concerns the coupling of skyrmions with the underlying atomic lattice and disorder (pinning). Here, we use Resonant Ultrasound Spectroscopy (RUS), a probe highly sensitive to changes in the elastic properties, to shed new light on skyrmion elasticity and depinning in the archetypal skyrmion material MnSi. In MnSi, skyrmions form a lattice that leads to pronounced changes in the elastic properties of the atomic lattice as a result of magneto-crystalline coupling. Without an applied current, the shear and compressional moduli of the underlying crystal lattice exhibit an abrupt change in the field-temperature range where skyrmions form. For current densities exceeding $j_c^*$ the changes of elastic properties vanish, signaling the decoupling of skyrmion and atomic lattices. Interestingly, $j_c^*$, which we identify as the onset of skyrmion depinning, is about 20 times smaller than $j_c$ previously measured via non-linear Hall effect. Our results suggest the presence of a previously-undetected intermediate dynamic regime possibly dominated by skyrmion-creep motion with important consequences for potential applications.