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H3K4me3 is used as a histone code or histone mark in epigenetic studies (usually identified through chromatin immunoprecipitation) to identify active gene promoters. H3K4me3 promotes gene activation through the action of the NURF complex, a protein complex that acts through the PHD finger protein motif to remodel chromatin. [2]
The H3K27me3 mark silences the gene while the H3K4me3 mark allows the gene to not be permanently silenced, and activated when needed. [2] Embryonic stem cells and imprinted genes are associated with both activating (H3K4me3) and repressive (H3K27me3) marks, as they allow a gene to be repressed until activation is needed.
H3K4me1 is a chromatin signature of enhancers, H3K4me2 is highest toward the 5′ end of transcribing genes and H3K4me3 is highly enriched at promoters and in poised genes. H3K27me3 , H4K20me1 and H3K4me1 silence transcription in embryonic fibroblasts, macrophages, and human embryonic stem cells (ESCs).
Methylated lysines are the best understood marks of the histone code, as specific methylated lysine match well with gene expression states. Methylation of lysines H3K4 and H3K36 is correlated with transcriptional activation while demethylation of H3K4 is correlated with silencing of the genomic region.
During development, TrxG proteins maintain activation of required genes, particularly the Hox genes, after maternal factors are depleted. [8] This is accomplished by preserving the epigenetic marks, specifically H3K4me3, established by maternally-supplied factors. [9]
DHSs mark transcriptionally active regions of the genome, where there will be cellular selectivity. So, they used 125 different human cell types. This way, using the massive sequencing technique, they obtained the DHSs profiles of every cellular type. Through an analysis of the data, they identified almost 2.9 million distinct DHSs.
The gene targeting method in knockout mice uses mouse embryonic stem cells to deliver artificial genetic material (mostly of therapeutic interest), which represses the target gene of the mouse by the principle of homologous recombination. The mouse thereby acts as a working model to understand the effects of a specific mammalian gene.
For example, trimethylation of histone H3 at lysine 4 is an active mark for transcription and is upregulated in hippocampus one hour after contextual fear conditioning in rats. However, dimethylation of histone H3 at lysine 9 ( H3K9me2 ), a signal for transcriptional silencing, is increased after exposure to either the fear conditioning or a ...