One of the most well known epigenetic mechanisms that proline isomerization plays a role in is the modification of histone tails, specifically those of histone H3. Fpr4 is a PPIase, in the FK507BP group, that exhibits catalytic activity at the proline positions 16, 30, and 38 (also written P16, P30, and P38 respectively) on the N-terminal region of histone H3 in Saccharomyces cerevisiae. Fpr4s binding affinity is strongest at the P38 site, followed by P30 and then P16. However the catalytic efficiency, or the increase in isomerization rates, is highest at P16 and P30 equally, followed by P38 which exhibits a very small change in isomerization rates with the binding of Fpr4. Histone H3 has an important lysine residue at the 36 position (also written K36) on the N-terminal tail which can be methylated by Set2, a methyltransferase. Methylation of K36 is key to normal transcription elongation. Due to P38s proximity to K36, cross-talk between P38 isomerization and K36 methylation can occur. This means that isomer changes at the P38 position can affect methylation at the K36 position. In the cis position, P38 shifts the histone tail closer to the DNA, crowding the area around the tail. This can cause a decrease the ability of proteins to bind to the DNA and to the histone tail, including preventing Set2 from methylating K36. Also, this tail movement can increase the number interactions between the histone tail and the DNA, increasing likelihood of nucleosome formation and potentially leading to the creation of higher-order chromatin structure. In trans, P38 leads to the opposite effects: allowing for Set2 to methylate K36. Set2 is only affected by isomerization of P38 when creating a trimethylated K36 (commonly written as K36me3), however, and not K36me2. Fpr4 also binds to P32 in H4, though its effects are minimal.
In mammalian cells, the isomerization of H3P30 interacts with the phosphorylation of H3S28 (serine in the 28 position of histone H3) and the methylation of H3K27. hFKBP25 is a PPIase that is a homolog for Fpr4 in mammalian cells and is found to commonly be associated with the presence of HDACs. Cyp33 is a cyclophilin that has the ability to isomerize H3 proline residues at P16 and P30 positions. Histones H2A and H2B also have multiple proline residues near amino acids that when modified affect the activity surrounding the histone.