1. Histone modifications can effect transcription by altering chromatin structure or interaction with other regulatory proteins. Adding positive or negative charges through modifications disrupts the electrostatic interaction between histones and DNA, which modulates chromatin structure and thus the accessibility of DNA to regulatory proteins. DNA methylation is an epigenetic modification that can influence the interaction between transcription factors and CpG dinucleotides, chromatin structure, or binding between methylated DNA and methylation recognition factors. The different types of histone modifications are: Acetylation is mediated by histone acetyltransferases (HATs) that act as coactivators for transcription by interacting with DNA-binding activators. Acetylation catalyzes the transfer of an acetyl group to the ε-amino group of the lysine residue with the use of acetyl CoA as a cofactor. Example: H3K56 acetylation by p300/CBP. HDACs have opposite effects to those of HATs and remove the acetyl group from lysine residues. Phosphorylation is mediated by kinases through the transfer of the phosphate group to the hydroxyl group of the amino acid side chain of histones from ATP and can play an activative or repressive role. This results in the addition of negative charge to histones, thus affecting the structure of chromatin. Example: Phosphorylation of H3 on Ser 10 is associated with transcriptional activation. Phosphorylation of H2A by MSK1 represses transcriptional activation. Phosphatases restore the effect of kinases by removing the phosphate group. Methylation of histones by methyltransferases occurs on lysine or arginine residues, which can undergo mono-, di...... middle of paper ...... level of transcription, protein synthesis, or genome. The effects of RNAi can be contrary to chromatin and DNA modifications in mediating mRNA degradation, translation inhibition, DNA shedding, and the like in heterchromatin formation. RNAi is post-transcriptional, the modification of Histone modification can be transcriptional and post-translational modification and DNA modification is at the transcription level.RNAi can be reversible or irreversible, while histone and DNA modifications are reversible processes.RNAi involves complementary base pairing with l 'target RNA to cause repression, while DNA and chromatin modification requires bromodomains, chromodomains, specific amino acid residues and chemical groups for protein-DNA and -histone interaction. RNAi, DNA, and chromatin modification are involved in heterochromatin formation, gene regulation, and genome stability.