http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/epigeneticsnoncoding-rna-research/Epigenetics-Learning-Center/Chromatin/Histone-Modification.

html

Histone Modifications and Variants

Histones are subject to a wide variety of posttranslational modifications including but not limited to, lysine acetylation, lysine and arginine methylation, serine and threonine phosphorylation, and lysine ubiquitination and sumoylation (Vasquero 2003). These modifications occur primarily within the histone amino-terminal tails protruding from the surface of the nucleosome as well as on the globular core region (Cosgrove 2004). Histone modifications are proposed to affect chromosome function through at least two distinct mechanisms. The first mechanism suggests modifications may alter the electrostatic charge of the histone resulting in a structural change in histones or their binding to DNA. The second mechanism proposes that these modifications are binding sites for protein recognition modules, such as the bromodomains or chromodomains, that recognize acetylated lysines or methylated lysine, respectively. The existence of these modifications and recognition modules led to a well established histone code hypothesis proposed by Strahl and Allis (2000). Overall, posttranslational modifications of histones create an epigenetic mechanism for the regulation of a variety of normal and disease-related processes.

Histone Variant Composition

A histone variant is distinguishable from a core (canonical) histone by a small number of amino acid changes. It is believed that the incorporation of histone variants in place of a core histone contributes to marking regions of the chromatin for specialized functions and to reversing the effects of histone methyltransferases (histone replacement model).
Histone Modification:
The core histones consist of a globular C-terminal domain and an unstructured N terminal tail. Although a variety of modifications occur throughout the histone protein, they occur primarily on the N-terminal tail (Table 1) (2-5). Some of these changes are enzymatically reversible (6). In general, the biological significance of all these modifications is not well understood, but the modifications are known to influence transcription, DNA repair, DNA replication and chromatin condensation. A histone code hypothesis is being tested to determine if combinations of histone modifications can be used to predict changes in gene expression (7-8). For example, lysine acetylation is associated with transcriptionally active DNA, while the effects (i.e., activation or repression of transcription) of lysine and arginine methylation vary by location of the amino acid, number of methyl groups and proximity to a gene promoter (9-11). A comprehensive list of histone-modifying enzymes can be found in a

review of mammalian epigenetic mechanisms by Kim et al (12). Table 1. Types of Histone Modification Amino Acid Lysine Modification Methylation, Acetylation, Ubiquitination, Sumoylation, ADP-Ribosylation Methylation Phosphorylation Phosphorylation

Arginine Serine Threonine

Role of DNA Methylation:

DNA can be modified by methylation of adenine and cytosine bases in a wide variety of prokaryotes and eukaryotes (Table 2). In prokaryotes, DNA methylation is involved in: In higher eukaryotes, DNA methylation is involved in:

determination of DNA-host specificity virulence DNA repair chromosome replication and segregation cell cycle regulation gene expression

gene regulation chromatin structure differentiation imprinting mammalian X chromosome inactivation carcinogenesis complex diseases aging

Table 2. Types of DNA Modifications Methylated Base C5-methylcytosine (12, 14-17) Organism DNA Bacteria Some Fungi, Some Insects, Mammals Plants C5-hydroxymethylcytosine Bacteriophages (18-19) Mammals N4-methylcytosine (2021) N6-methyladenine (21-23) Bacteria Methylation Sequence Varies (e.g., CCAGG, CCTGG) CpG CpG, CpHpG1, CpHpH1 Varies (e.g., CCGG, GATC); Some contain only modified cytosines CpG, CpHpG1, CpHpH1 Varies (e.g., CTCTTC, CCCGGG)

Bacteria, Bacteriophages, Archaea, Varies (e.g., GATC, GANTC, Protists, Some Fungi, Plants GAAGAG) Note: H = Adenine, Cytosine, or Thymine Mammalian DNA is enzymatically modified at the 5th carbon position of cytosine (C) bases to 5-mC,

predominately in the context of CpG dinucleotides. 5-mC is amenable to enzymatic oxidation to 5-hmC by the Tet family of enzymes, which are believed to be involved in development and disease. Currently, the biological role of 5-hmC is not fully understood, but is generating a lot of interest due to its potential as a biomarker. Common research techniques, including bisulfite sequencing methods, are unable to easily distinguish between 5-mC and 5-hmC. The EpiMark 5-hmC and 5-mC Analysis Kit provides a solution for distinguishing between these two modifications at specific loci.