Extracellular Matrix Stiffness Regulates DNA Methylation by PKCα‐Dependent Nuclear Transport of DNMT3L

Abstract

Extracellular matrix (ECM) stiffness has profound effects on the regulation of cell functions. DNA methylation is an important epigenetic modification governing gene expression. However, the effects of ECM stiffness on DNA methylation remain elusive. Here, it is reported that DNA methylation is sensitive to ECM stiffness, with a global hypermethylation under stiff ECM condition in mouse embryonic stem cells (mESCs) and embryonic fibroblasts compared with soft ECM. Stiff ECM enhances DNA methylation of both promoters and gene bodies, especially the 5’ promoter regions of pluripotent genes. The enhanced DNA methylation is functionally required for the loss of pluripotent gene expression in mESCs grown on stiff ECM. Further experiments reveal that the nuclear transport of DNA methyltransferase 3‐like (DNMT3L) is promoted by stiff ECM in a protein kinase C α (PKCα)‐dependent manner and DNMT3L can be binding to Nanog promoter regions during cell–ECM interactions. These findings unveil DNA methylation as a novel target for the mechanical sensing mechanism of ECM stiffness, which provides a conserved mechanism for gene expression regulation during cell–ECM interactions.

Confined migration induces heterochromatin formation and alters chromatin accessibility

“…Although we detected significant increases in global heterochromatin levels in cells migrating through confined microfluidic channels, we did not observe the same global changes in cells migrating through 3D collagen matrices with decreasing average pore sizes. The discrepancy between the microfluidic devices and collagen matrices is likely due to the more complex factors contributing to chromatin changes in collagen matrices, such as matrix stiffness ( Zhao et al., 2021 ) and integrin binding to matrix ligands ( Carley et al., 2021 ), whereas the microfluidic devices allow control of cell confinement without affecting the substrate stiffness or ligand density. This precise control of confinement alone makes microfluidic devices an ideal model for studying confinement-induced biological responses.…”

Confined Migration Induces Heterochromatin Formation and Alters Chromatin Accessibility

“…Although we detected significant increases in global heterochromatin levels in cells migrating through confined microfluidic channels, we did not observe the same global changes in cells migrating through 3D collagen matrices with decreasing average pore sizes. The discrepancy between the microfluidic devices and collagen matrices is likely due to the more complex factors contributing to chromatin changes in collagen matrices, such as matrix stiffness (Zhao et al, 2021) and integrin binding to matrix ligands (Carley et al, 2021), whereas the microfluidic devices allow control of cell confinement without affecting the substrate stiffness or ligand density. This precise control of confinement alone makes microfluidic devices an ideal model for studying confinement-induced biological responses.…”

Mechanoimmunology: Are inflammatory epigenetic states of macrophages tuned by biophysical factors?

“…194 As cells engage in reciprocal interactions with their matrix, it is not surprising that DNA methylation is sensitive to ECM stiffness with global hypermethylation under stiff ECM conditions in mouse embryonic stem cells and embryonic fibroblasts compared with soft ECM. 218 Stiff ECM enhances DNA methylation of both promoters and gene bodies, especially the 5′ promoter regions of pluripotent genes. 218 The enhanced DNA methylation is functionally required for the loss of pluripotent gene expression in mESCs grown on stiff ECM, allowing them to differentiate along a specific lineage.…”

“… 218 Stiff ECM enhances DNA methylation of both promoters and gene bodies, especially the 5′ promoter regions of pluripotent genes. 218 The enhanced DNA methylation is functionally required for the loss of pluripotent gene expression in mESCs grown on stiff ECM, allowing them to differentiate along a specific lineage. 218 Moreover, the altered DNA methylation is driven by ECM-regulated nuclear transport of DNA methyltransferase three-like (DNMT3L), which is promoted by a stiff ECM.…”

“… 218 The enhanced DNA methylation is functionally required for the loss of pluripotent gene expression in mESCs grown on stiff ECM, allowing them to differentiate along a specific lineage. 218 Moreover, the altered DNA methylation is driven by ECM-regulated nuclear transport of DNA methyltransferase three-like (DNMT3L), which is promoted by a stiff ECM. 218 Finally, using gastric cancer cells, it has been shown that the stiffness of the ECM reversibly regulates the DNA methylation of the promoter region of the mechanosensitive protein YAP.…”