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h3k4me3: a Commonly Used Histone Modification

h3k4me3: a Commonly Used Histone Modification

1. About h3k4me3

h3k4me3 is an epigenetic modification of the DNA packaging protein histone H3. It is a marker of trimethylation of the fourth lysine residue of histone H3 protein and is often involved in the regulation of gene expression. The name indicates the addition of three methyl groups to lysine 4 on the histone H3 protein.

H3 is used to package DNA in eukaryotic cells, including human cells, and modifications to histones alter the accessibility of genes to transcription. h3k4me3 is often associated with transcriptional activation of nearby genes. H3K4 trimethylation regulates gene expression through chromatin remodeling of the NURF complex. This makes the DNA in chromatin more accessible to transcription factors, allowing genes to be transcribed and expressed in cells. More specifically, h3k4me3 was found to positively regulate transcripts by introducing histone acetylase and nucleosome remodeling enzyme (NURF). h3k4me3 also plays an important role in the genetic regulation of stem cell potency and lineage. This is because this histone modification is more common in regions of DNA involved in development and establishing cellular identity.

2. One of histone modifications: h3k4me3

h3k4me3 is a commonly used histone modification. h3k4me3 is one of the least abundant histone modifications; however, it is highly enriched at active promoters near the transcription start site (TSS) and is positively correlated with transcription. h3k4me3 is used as a histone code or histone mark in epigenetic studies (usually identified by chromatin immunoprecipitation) to identify active gene promoters.

h3k4me3 promotes gene activation through the action of the NURF complex, a protein complex that acts through PHD finger protein motifs to remodel chromatin. This makes the DNA in chromatin available to transcription factors that enable genes to be transcribed and expressed in cells. Since genes important in determining cell fate appear to be adjacent to many h3k4me3 (indicating that this gene is important for a defined cell type), EpiMogrify, an algorithm for predicting the molecules required to induce cells to differentiate into a given type, is well developed.

The genomic DNA of eukaryotic cells is wrapped around special protein molecules called histones. The complex formed by the DNA loops is called chromatin. The basic building block of chromatin is the nucleosome: it consists of a core octamer of histones (H2A, H2B, H3, and H4) and a DNA linking histones and about 180 base pairs. These core histones are rich in lysine and arginine residues. The carboxyl (C) termini of these histones contribute to histone-histone interactions as well as histone-DNA interactions. The amino (N) terminal charged tail is the site of post-translational modification, such as that seen in H3K4me1.