The Histone Code

     First, it is important to start with the basics of DNA organization. The eukaryotic genome is organized in what is known as a nucleosome, the first level of condensation. The nucleosome is composed of 147 base pairs of negatively-charged DNA wrapped twice around an octamer of positively-charged proteins called histones. It consists of two H2A and H2B dimers, and a H3 and H4 tetramer. The nucleosomes are separated by 1,016 base pairs (bp) of  DNA called "linker DNA'',  which constitutes an arrangement referred to as ''beads on a string'', that is around 10nm in diameter. DNA can be further condensed at different points during the cell cycle, forming a 30nm chromatin fiber composed of packed nucleosomes using the histone H1, which binds to the linker DNA. These 30nm fibers can form scaffolds and further condense until chromosomes are formed, which are the highest form of DNA organization within a cell.

     Histones have very dynamic N-terminal ''tails'' extending from the surface of the nucleosome that are rich in basic amino acids. These tails can be modified by post-translational modifications (PTM's) catalyzed by a variety of enzymes, by adding either methyl, acetyl or phosphoryl groups. Aditionally, lysines can be mono, di or tri-methylated, while arginine can accept up to two methyl groups which adds to the complexity.  Methylation of DNA at cytosine residues, as well as PTMs of histones, including phosphorylation, acetylation, methylation and ubiquitylation, contributes to the epigenetic information carried by chromatin. These changes play an important role in the regulation of gene expression by modulating the access of regulatory factors to the DNA. Many modification sites are close enough to each other and it seems that modification of histone tails by one enzyme might influence the rate and efficiency at which other enzymes use the newly modified tails as a substrate.
These modifications seem to be part of a complex scheme where distinct histone modifications act in a sequential manner or in combination to form a “histone code”, read by other proteins to control the structure and/or function of the chromatin fiber.

"The different histone modifications act either in a sequential manner or in combination to form a “histone code",  which is read by other proteins to bring about the specific biological events."

   

   
The so-called histone code is established and maintained by post-translational writers, which are the enzymes that modify the histones post translationally. These modifications can be "read" by post-translational readers, which are the motifs that recognize the histones based on their modification state. Modifications of histones, give signals that are recognized by specific binding proteins, or ''readers'' which can influence gene expression and chromatid organization. Examples of readers will be discussed later on.

     One example of writers are histone acetyltransferases (HATs) and histone deacetylases (HDAC's), responsible for the addition and removal of acetyl groups, respectively. On the other hand, methylation is carried out by histone methyltransferases (HMTs), divided in two classes: K-HMT if it methylates lysine, or arginine (R-HMT). Methylation is a stable modification, unlike acetylation and phosphorylation, which makes it an ideal mark for long-term maintenance of chromatin structure. The existence of histone demethylases (HDMTs, or DNMTs) that counteract the methylations of histones in the cell is unclear. Phosphorylation of histones H1 and H3 is known to  play important roles in both transcriptional regulation and  mitosis, and it has been found that ubiquitination is critical in mitotic and meiotic growth. Finally, biotinylation is a new PTM of histones that has been identified, carried out by biotinidase and holocarboxylase synthetase (HCS).

     The acetylation of lysine weakens the DNA-histone interactions, destabilizing the nucleosome by making it less positively charged. This results in DNA that is more weakly bound to the nucleosome, facilitating the binding of transcription factors to DNA. But histone marks by themselves may not alter the nucleosomal dynamics, which might be brought on by binding of further non-histone proteins.

    While hyperacetylation is linked to gene expression, deacetylation can be related to silencing. Methylation is not as straight-forward, as H3-K9 (histone 3, lysine 9) and can be associated to inactive genes. However. H3-K4 methylation is seen in both active and silenced regions, since trimethylation is specific for active state of transcription, whereas dimethylated K4 exists in both active and repressive genes. The site and the number of methyl groups are both important for biological consequences of these modifications. Additionally, in mammals, DNA methylation is controlled by DNMT1, DNMT3a and DNMT3b enzymes. DNMT1 is involved in de novo methylation, while DNMT3a and DNMT3b are linked to the maintenance of methylation.


''Modified histone tails provide recognition sites for factors involved in either the activation or repression of gene expression.''


     Errors in PTMs of histones and other epigenetic marks may be involved in diseases, which is why it's critical to understand these modifications, as it promises new ways to treat several diseases. Certain modifications can either promote, limit, or have no effect on the depositions of other modifications. The combination of these can regulate in a direct or indirect manner, the state of chromatin organization and gene expression.


More information about the histone code, the following article can help:

Munshi, A., Shafi, G., Aliya, N., & Jyothy, A. (2009). Histone modifications dictate specific biological readouts. Journal of Genetics and Genomics, 36(2), 75-88.

It can be downloaded from:
https://www.researchgate.net/publication/24030126_Histone_modifications_dictate_specific_biological_readouts