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. Author manuscript; available in PMC: 2020 Jun 4.
Published in final edited form as: Annu Rev Biomed Eng. 2019 Mar 27;21:443–468. doi: 10.1146/annurev-bioeng-060418-052139

Table 1.

Prominent technologies for elucidating mechanotransduction mechanisms

Technique Description References
Detection techniques
Superresolution microscopy Imaging techniques (i.e., SIM, dSTORM, cryo-ET) with protein-level resolution. Useful for examining nuclear organization, binding partners, and supramolecular structure. 14, 17, 18
BioID Proteins are biotinylated when in proximity to an engineered fusion protein (such as Lamin A) to label and identify novel binding partners with mass spectrometry. Can be used to examine protein interactions in mechanically stressed or lamin-mutant nuclei. 18, 169
4D nucleome Genome mapping techniques (i.e., 4C, 5C, Hi-C, and ChIA-PET), for observing spatial organization and condensation states of chromatin. 147
Genomic labeling Fluorescence tagging of chromatin using gene editing for tracking mechanosensitive reorganization of (multiple) gene loci. 82, 151, 152
FRAP A target protein is fluorescently tagged, a small area is photobleached, and time of recovery of fluorescence to the area is measured to understand the recovery dynamics, such as for chromatin histone organization or modifications. 153–156
FRET Visual monitoring of the interaction between fluorescently tagged proteins, which creates a FRET signal. Diverse applications to mechanotransduction, such as monitoring force-dependent protein interactions, chromatin modification/condensation, actin assembly, or measuring tension forces. 77, 121, 157–159, 170
FLIM Through fluorescence tagging of chromatin and examining fluorescence lifetime, which corresponds to viscosity due to degree of chromatin packing, can be used for high-throughput spatial tracking of chromatin condensation in the nucleoplasm. 159, 160
Mechanical manipulation techniques
Isolated nuclei Removal of the nucleus from a cell for the direct study of the nucleus and its constituents, eliminating any confounding effects from the cytoplasm and/or cytoskeleton. Force can be directly applied to the nucleus, such as for LINC complex force measurement or examination of nuclear changes. 121, 169
LINC complex disruption Depletion or deletion of LINC complex proteins via gene editing. By examining any subsequent defects resulting from force application, the role of LINC complex proteins in mechanotransduction may be better understood.
Tissue engineering techniques
Engineered (muscle) tissues Cells are suspended in an ECM solution, compact to form a tissue between two flexible pillars, and tissues contract to deflect the pillars. Useful for examining cell and tissue structures, tissue generated forces, and improving maturity of tissues. 161–168
Micropatterning, structured, and engineered substrates Cells are cultured on micrometer- or nanometer-scale geometries/architectures. Examining the subsequent nuclear changes and cellular signaling, behavior, or phentoype can give an understanding of the role of the nucleus in matrix sensation, such as in stem cell differentiation. 72, 73

Abbreviations: ChIA-PET, chromatin-interaction analysis by paired-end tag sequencing; cryo-ET, cryo electron tomography; dSTORM, direct stochastic optical reconstruction microscopy; ECM, extracellular matrix; FLIM, fluorescence lifetime imaging microscopy; FRAP, fluorescence recovery after photobleaching; FRET, Förster resonance energy transfer; LINC, linker of the nucleoskeleton and cytoskeleton; SIM, structured illumination microscopy.