Trichostatin A is widely used in biological research as a potent inhibitor of histone deacetylases (HDACs). By inhibiting these enzymes, it increases histone acetylation, leading to a more open chromatin structure and activation of gene expression. This property makes it a valuable tool for studying epigenetic regulation, cell differentiation, and gene silencing.

It is commonly applied in cell culture studies to induce cell cycle arrest, apoptosis, and differentiation in various cancer cell lines. Due to its ability to reactivate silenced tumor suppressor genes, Trichostatin A has been investigated in preclinical models for cancer therapy, particularly in combination with other epigenetic drugs or conventional chemotherapeutics.

Additionally, it is used in stem cell research to improve the efficiency of somatic cell reprogramming and to maintain pluripotency. Its role in modulating chromatin dynamics also makes it useful in studies of DNA repair, aging, and neurodegenerative diseases.