What are histone modifications?


histone modifications

Histone modification refers to the process of histone modifications such as methylation, acetylation, phosphorylation, adenylation, ubiquitination, and ADP ribosylation under the action of related enzymes.

Acetylation of H3·H4 opens an open chromatin structure and increases gene expression. Transcriptional co-activators such as CBPÖP300 and PCA F are essentially histone acetyltransferases (HATs) in vivo. On the contrary, histone deacetylases (HDACs) participate in the formation of transcriptional co-repression complexes. The two co-repression complexes SIN3 and Mi22NHRD (nucleosome remodeling protein deacetylases) have been found to contain HDAC1, HDAC2. The composition of S IN 3 is the core (HDAC1, HDAC2, RBA P46ÖRBA P48) + S IN 3AÖS IN 3B, SA P30ÖSA P18. The S IN 3 complex interacts with sequence-specific transcription factors or co-repressors including mael2max, nuclear hormone receptor N 2CORÖSMRT, methylated CPG adhesion proteins (NECP2, MBD2) through component S IN 3A.

Mi22NHRD is composed of core (HDAC1, HDAC2, RBA P46ÖRBA P48) + Mi2, M TA 1ÖM TA 2, MBD3, among which MBD3 contains MBD-like sequences and has low affinity with methylated DNA. The analysis found that MBD3 is related to methylation Amino acids were substituted, and it was speculated that MBD3 interacts with MBD2 to allow Mi22NURD to bind to methylated DNA. It can be seen that DNA methylation and histone deacetylation work together in transcriptional repression. In addition, Mi22NURD also has chromatin remodeling activity, so S IN 3 and Mi22 NURD may play a role in the regulation of long-term and short-term transcriptional repression, respectively.

In mammalian genomes, histones can have many modifications. A nucleosome consists of two H2A, two H2B, two H3, two H4 octamers and 147bp of DNA wrapped around the outside. The state of the core part of the histones that make up the nucleosome is roughly uniform, The free N-terminus can be subjected to various modifications, including histone end acetylation, methylation, phosphorylation, ubiquitination, ADP ribosylation, etc. These modifications will affect the transcriptional activity of genes .
Methylation of histones:
The sites where histones are methylated are lysine and arginine. Lysine can be mono-, di-, and tri-methylated, respectively, while arginine can only be mono- or di-methylated. On histone H3, a total of 5 lysine sites can be modified by methylation. In general, the methylation of histone H3K4 is mainly concentrated in actively transcribed promoter regions. Methylation of histone H3K9 is associated with transcriptional repression of genes and heterochromatin. EZH2 can methylate H3K27, leading to silencing of related genes, and is associated with X-Chromosome inactivation. Methylation of H3K36 is associated with gene transcriptional activation.

⒈ Methylation
Histone methylation is accomplished by histone methyl transferase (HMT). Methylation can occur on lysine and arginine residues of histones, and lysine residues can be mono-, di-, or tri-methylated, while arginine residues can be mono- or di-methylated , these varying degrees of methylation greatly increase the complexity of histone modification and regulation of gene expression. The methylation sites are on the side chain N atoms of lysine (Lys) and arginine (Arg). Positions 4, 9, 27 and 36 of histone H3, Lys at position 20 of H4, positions 2, 17, 26 of H3 and Arg at position 3 of H4 are common sites of methylation. Studies have shown that histone arginine methylation is a relatively dynamic marker, and arginine methylation is associated with gene activation, while loss of H3 and H4 arginine methylation is associated with gene silencing. In contrast, lysine methylation appears to be a more stable marker in the regulation of gene expression. For example, methylation of lysine residues at position 4 of H3 is associated with gene activation, whereas methylation of lysine residues at positions 9 and 27 is associated with gene silencing. In addition, the methylation of H4-K20 is associated with gene silencing, and the methylation of H3-K36 and H3-K79 is associated with gene activation. It should be noted, however, that the number of methylation correlates with the degree of gene silencing and activation.

⒉ Acetylation
Histone acetylation mainly occurs at the relatively conserved lysine position at the N-terminal of H3 and H4, which is coordinated by histone acetyltransferase and histone deacetylase. Histone acetylation is diverse, with multiple sites on the nucleosome providing acetylation sites, but histone acetylation and deacetylation at specific gene sites occurs in a non-random, position-specific manner . Acetylation may regulate gene transcription through effects on histone charge and interacting proteins. In the early classification of chromatin and its characteristic components, it was concluded that histones in the heterochromatin domain were hypoacetylated and histones in the euchromatin domain were hyperacetylated. Recent studies have found that some HAT complexes contain some common transcription factors, and some HDAC complexes contain proven repressor proteins. These findings support the notion that hyperacetylation is associated with activation of gene expression and hypoacetylation with inhibition of gene expression.

3. Other modifications of histones
Relatively speaking, the methylation modification of histones is the most stable, so it is most suitable as a stable epigenetic information. The acetylation modification has a high dynamic, and there are other unstable modifications, such as phosphorylation, adenylation, ubiquitination, ADP ribosylation and so on. These modifications more flexibly affect the structure and function of chromatin, and exert their regulatory functions through a combination of various modifications. So some people call these modified information that can be recognized as histone code. These histone code combinations vary widely, so histone covalent modification may be a more refined way of gene expression.
In addition, the study found that the ubiquitination of H2B can affect the methylation of H3K4 and H3K79, which also suggests that there is also a correlation between various modifications.

New findings show that globular histone modification patterns predict recurrence risk in low-grade prostate cancer. The results were published in the journal Nature. “This pattern of modification could ultimately be used as a prognostic or diagnostic marker for prostate or other types of cancer, as well as as a predictor of which patients will suffer from a class of histone deacetylase inhibition,” said first author Siavash K. Kurdistani of the University of California, California. An indicator of a response to a new drug.

Kurdistani explained: Certain histone modification patterns affect gene expression at a certain level, but the exact mechanism is unclear. Kurdistani et al. studied five histone modification patterns, including three acetylation and two dimethylation, and used tissue microarray technology to detect histone modification levels in primary prostate cancer tissue samples. The researchers tested 104 samples with a Gleason score of less than 7 for staining histone modifications and divided the subjects into two groups. The risk of recurrence within ten years of the first group was 17%, and the second group was 42%. This predictor was independent of tumor stage, preoperative PSA level, or whether there was extracapsular invasion. The researchers confirmed the pattern of histone modifications in another 39 low-grade prostate cancer samples, also divided into two groups, one with a 4 percent risk of recurrence and the other with a 31 percent risk.

The researchers concluded that, given the diversity of histone modification patterns, information on other histone modification sites will help us to further classify patients, including those in the high-scoring group. The application of immunohistochemistry and an increasing number of antibodies to detect histone modifications will facilitate the application of this assay in other tumors.

Gene regulation
Gene expression is a complex process regulated by multiple factors. Histones are the basic structure of chromosomes—an important part of nucleosomes, and their N-terminal amino acid residues can undergo acetylation, methylation, phosphorylation, and ubiquitination , poly ADP glycosylation and other covalent modifications. The modification of histones can change the loose or cohesive state of chromatin by affecting the affinity between histones and DNA double-strands, or by affecting the relationship between other transcription factors and DNA. The affinity of structural gene promoters plays a role in gene regulation. The regulation of gene expression by histone modifications is similar to the regulation of DNA genetic code.

DNA methyl
How does the silencing signal (DNA methylation, histone modification, chromatin reassembly) proceed in the process of causing gene silencing? Who comes first? This is a “chicken and egg” question that is still being studied stage, no conclusion yet. Studies have found that DNA methylation and histone methylation are a process that promotes and strengthens each other. For example, many HDACs can interact with DNMT1, 3a, and 3b; 2) It can interact with HDAC again. This mode of action suggests that the presence of either modality can trigger the initiation of the other modification modality.

How do silencing signals work? In what order do they occur? Much of the early research came from studies of non-mammalian organisms. Tamaru’s study in Neurospora CTaSSa found that mutations in the H3K9 histone methyltransferase caused the loss of DNA methylation, suggesting that histone methylation can initiate DNA methylation. Tariq also found in Arabidopsis that CpNpG methylation is dependent on histone methylation. All the above evidences imply that histone methylation plays a guiding role in DNA methylation.

In mammalian cells, however, this phenomenon remains to be further studied. Early studies found that after the in vitro methylated CpG fragments are stably integrated into the mammalian genome, they can bind to proteins containing methylated CpG binding domains (methylbinding domain, MBD) (including MeCP-1 and MeCP-2, etc.), and then Inhibitory complexes including HDACs can be recruited. Further research also found that methylation of the human MLH gene can trigger specific histone code combinations to maintain gene silencing. The researchers used the DNA methylase inhibitor 5-azacytidine (5-Aza), but not the histone acetylase inhibitor trichostatin A (trlcostatmA, TSA), can cause histone methylation Lack of chemical modification. From these results, in mammals, histone modification appears to be a subsequent event to DNA methylation. But when Bachman knocked out the p16 gene in mammals, he found that chromatin modifications were not entirely dependent on initial DNA methylation. At the same time, the results of Mutskov and Felsenfeld also support this theory, they believe that histone modification is an early event in ILR2 gene silencing, the methylation of the promoter region is a step-by-step process, and DNA methylation is established for long-term maintenance. Gene silencing, not initiating it.

From the above results, it can be seen that the epigenetic process is complex and multi-layered, and different epigenetic modifications may also have specificity of regions or signaling pathways, and there are many unknown things to be further studied.