Histone code
Encyclopedia
The histone code is a hypothesis
that the transcription of genetic information encoded in DNA
is in part regulated by chemical modifications to histone
proteins, primarily on their unstructured ends. Together with similar modifications such as DNA methylation
it is part of the epigenetic code
. The main role of histones is in associating with DNA
to form nucleosome
s, which themselves bundle to form chromatin
fibers, which in turn make up the more familiar chromosome
. Histones are globular proteins with a flexible N-terminus (taken to be the tail) that protrudes from the nucleosome. Many of the histone tail modifications correlate very well to chromatin structure and both histone modification state and chromatin structure correlate well to gene expression levels. The critical concept of the histone code hypothesis is that the histone modifications serve to recruit other proteins by specific recognition of the modified histone via protein domain
s specialized for such purposes, rather than through simply stabilizing or destabilizing the interaction between histone and the underlying DNA. These recruited proteins then act to alter chromatin structure actively or to promote transcription.
For details of gene expression regulation by histone modifications see table below.
-DNA interactions are guided by combinations of histone modifications. While it is accepted that modifications (such as methylation
, acetylation
, ADP-ribosylation, ubiquitination and phosphorylation
) to histone
tails alter chromatin structure, a complete understanding of the precise mechanisms by which these alterations to histone tails influence DNA-histone interactions remains elusive. However, some specific examples have been worked out in detail. For example, phosphorylation of serine
residues 10 and 28 on histone H3
is a marker for chromosomal condensation. Similarly, the combination of phosphorylation of serine
residue 10 and acetylation of a lysine
residue 14 on histone H3 is a tell-tale sign of active transcription
.
Deacetylation allows tight arrangement of chromatin, preventing gene expression, while acetylation may occur to open up the chromatin.
Methylation of lysines H3K4 and H3K36 is correlated with transcriptional activation while demethylation of H3K4 is correlated with silencing of the genomic region. Methylation of lysines H3K9 and H3K27 is correlated with transcriptional repression. Particularly, H3K9me3 is highly correlated with constitutive heterochromatin.
The histone code can be summarized in the following table:
Notes:
Structural determinants of histone recognition by readers, writers and erasers of the histone code are revealed by a growing body of experimental data.
Hypothesis
A hypothesis is a proposed explanation for a phenomenon. The term derives from the Greek, ὑποτιθέναι – hypotithenai meaning "to put under" or "to suppose". For a hypothesis to be put forward as a scientific hypothesis, the scientific method requires that one can test it...
that the transcription of genetic information encoded in DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
is in part regulated by chemical modifications to histone
Histone
In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation...
proteins, primarily on their unstructured ends. Together with similar modifications such as DNA methylation
DNA methylation
DNA methylation is a biochemical process that is important for normal development in higher organisms. It involves the addition of a methyl group to the 5 position of the cytosine pyrimidine ring or the number 6 nitrogen of the adenine purine ring...
it is part of the epigenetic code
Epigenetic code
The epigenetic code is hypothesised to be a defining code in every eukaryotic cell consisting of the specific epigenetic modification in each cell. It consists of histone modifications defined by the histone code and additional epigenetic modifications such as DNA methylation. The base for the...
. The main role of histones is in associating with DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
to form nucleosome
Nucleosome
Nucleosomes are the basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound around a histone protein core. This structure is often compared to thread wrapped around a spool....
s, which themselves bundle to form chromatin
Chromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
fibers, which in turn make up the more familiar chromosome
Chromosome
A chromosome is an organized structure of DNA and protein found in cells. It is a single piece of coiled DNA containing many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions.Chromosomes...
. Histones are globular proteins with a flexible N-terminus (taken to be the tail) that protrudes from the nucleosome. Many of the histone tail modifications correlate very well to chromatin structure and both histone modification state and chromatin structure correlate well to gene expression levels. The critical concept of the histone code hypothesis is that the histone modifications serve to recruit other proteins by specific recognition of the modified histone via protein domain
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
s specialized for such purposes, rather than through simply stabilizing or destabilizing the interaction between histone and the underlying DNA. These recruited proteins then act to alter chromatin structure actively or to promote transcription.
For details of gene expression regulation by histone modifications see table below.
The Hypothesis
The hypothesis is that chromatinChromatin
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are; to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis and prevent DNA damage, and to control gene...
-DNA interactions are guided by combinations of histone modifications. While it is accepted that modifications (such as methylation
Methylation
In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...
, acetylation
Acetylation
Acetylation describes a reaction that introduces an acetyl functional group into a chemical compound...
, ADP-ribosylation, ubiquitination and phosphorylation
Phosphorylation
Phosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes....
) to histone
Histone
In biology, histones are highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and play a role in gene regulation...
tails alter chromatin structure, a complete understanding of the precise mechanisms by which these alterations to histone tails influence DNA-histone interactions remains elusive. However, some specific examples have been worked out in detail. For example, phosphorylation of serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
residues 10 and 28 on histone H3
Histone H3
Histone H3 is one of the five main histone proteins involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and a long N-terminal tail, H3 is involved with the structure of the nucleosomes of the 'beads on a string' structure...
is a marker for chromosomal condensation. Similarly, the combination of phosphorylation of serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
residue 10 and acetylation of a lysine
Lysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
residue 14 on histone H3 is a tell-tale sign of active transcription
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
.
Modifications
Possible modifications to the tails are:- AcetylationAcetylationAcetylation describes a reaction that introduces an acetyl functional group into a chemical compound...
- by HATHistone acetyltransferaseHistone acetyltransferases are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA to form ε-N-acetyl lysine....
(histone acetyl transferase); deacetylation - by HDAC (histone deacetylase)
Deacetylation allows tight arrangement of chromatin, preventing gene expression, while acetylation may occur to open up the chromatin.
- MethylationMethylationIn the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom...
Methylation of lysines H3K4 and H3K36 is correlated with transcriptional activation while demethylation of H3K4 is correlated with silencing of the genomic region. Methylation of lysines H3K9 and H3K27 is correlated with transcriptional repression. Particularly, H3K9me3 is highly correlated with constitutive heterochromatin.
- PhosphorylationPhosphorylationPhosphorylation is the addition of a phosphate group to a protein or other organic molecule. Phosphorylation activates or deactivates many protein enzymes....
- Ubiquitination
- ADP-ribosylationADP-ribosylationADP-ribosylation is the addition of one or more ADP-ribose moieties to a protein. These reactions are involved in cell signaling and the control of many cell processes, including DNA repair and apoptosis.-ADP-ribosylation enzymes:...
The histone code can be summarized in the following table:
| Type of modification |
Histone | ||||||
|---|---|---|---|---|---|---|---|
| H3K4 | H3K9 | H3K14 | H3K27 | H3K79 | H4K20 | H2BK5 | |
| mono-methylation Methylation In the chemical sciences, methylation denotes the addition of a methyl group to a substrate or the substitution of an atom or group by a methyl group. Methylation is a form of alkylation with, to be specific, a methyl group, rather than a larger carbon chain, replacing a hydrogen atom... |
activation | activation | activation | activation | activation | activation | |
| di-methylation | repression | repression | activation | ||||
| tri-methylation | activation | repression | repression | activation, repression |
repression | ||
| acetylation Acetylation Acetylation describes a reaction that introduces an acetyl functional group into a chemical compound... |
activation | activation | |||||
Notes:
- H3K4me3 is found in actively transcribed promoters, particularly just after the transcription start site.
- H3K9me3 is found in constitutively repressed genes.
- H3K27me is found in facultatively repressed genes.
- H3K36me3 is found in actively transcribed gene bodies.
- H3K9ac is found in actively transcribed promoters.
- H3K14ac is found in actively transcribed promoters.
Structural determinants of histone recognition by readers, writers and erasers of the histone code are revealed by a growing body of experimental data.