[Paleopsych] More on histones

[Steve Hovland]

Histone
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In biology, histones are the chief proteins of chromatin. They act as spools
around which DNA winds and they play a role in gene regulation. Histones are
found in the nuclei of eukaryotic cells. Bacteria do not have histones, but
histones are found in certain Archaea, namely Euryarchaea. These archaeal
histones may well resemble the evolutionary precursors to the eukaryotic
histones.

Contents [hide]
1 Classes
2 Structure
3 Functions
3.1 Packing proteins
3.2 Histone modfications in chromatin regulation
4 History
5 See also



[edit]
Classes
Six histone classes are known:

H1 (sometimes called the linker histone or H5.)
H2A
H2B
H3
H4
Archaeal histones
Two each of the class H2A, H2B, H3 and H4 assemble to form one octameric
nucleosome core particle by wrapping 146 base pairs of DNA around the
protein spool in 1.65 left-handed super-helical turn. The linker histone H1
binds the nucleosome and the entry and exit sites of the DNA, thus locking
the DNA into place and allowing the formation of higher order structure. The
most basic such formation is the 10 nm fiber or beads on a string
conformation. This involves the wrapping of DNA around nucleosomes with
approximately 50 base pairs of DNA spaced between each nucleosome (also
referred to as linker DNA). Higher order structures include the 30 nm fiber
(forming an irregular zigzag) and 100 nm fiber, these being the structures
found in normal cells. During meiosis, through the combination of nucleosome
interactions with other proteins, the chromosome is assembled. The assembled
histones and DNA is called chromatin.

[edit]
Structure

Schematic representation of the assembly of the core histones into the
nucleosome.The nucleosome core is formed of two H2A-H2B dimers and two H3-H4
dimers, forming two nearly symmetrical halves by tertiary structure (C2
symmetry; one macromolecule is the mirror image of the other). The H2A-H2B
and H3-H4 dimers themselves also show pseudodyad symmetry.

The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in
structure and are highly conserved through evolution, all featuring a 'helix
turn helix turn helix' motif (which allows the easy dimerisation). They also
share the feature of long 'tails' on one end of the amino acid structure -
this being the location of post-transcriptional modification (see below).

In all, histones make five types of interactions with DNA:
http://en.wikipedia.org/wiki/Histone

lots of good links from this page.  there are other levels of
control/influence :-)


Helix-dipoles from alpha-helices in H2B, H3, and H4 cause a net positive
charge to accumulate at the point of interaction with negatively charged
phosphate groups on DNA.
Hydrogen bonds between the DNA backbone and the amine group on the main
chain of histone proteins.
Nonpolar interactions between the histone and deoxyribose sugars on DNA.
Salt links and hydrogen bonds between side chains of basic amino acids
(especially lysine and arginine) and phosphate oxygens on DNA.
Non-specific minor groove insertions of the H3 and H2B N-terminal tails into
two minor grooves each on the DNA molecule.
The highly basic nature of histones, aside from facilitating DNA-histone
interactions, contributes to the water solubility of histones.

Histones are subject to posttranslational modification by enzymes primarily
on their N-terminal tails, but also in their globular domains. Such
modifications include methylation, acetylation, phosphorylation,
ubiquitination, and ADP-ribosylation. This affects their function of gene
regulation (see functions).

In general, genes that are active have less bound histone, while inactive
genes are highly associated with histones during interphase. It also appears
that the structure of histones have been evolutionarily conserved, as any
deleterious mutations would be severely maladaptive.

[edit]
Functions
[edit]
Packing proteins
Histones act as spools around which DNA winds. This enables the compaction
necessary to fit the large genomes of eukaryotes inside cell nuclei: the
compacted molecule is 50,000 times shorter than an unpacked molecule.

[edit]
Histone modfications in chromatin regulation
Histones undergo posttranslational modifications which alter their
interaction with DNA and nuclear proteins. The H3 and H4 histones have long
tails protruding from the nucleosome which can be covalently modified at
several places. Modifications of the tail include methylation, acetylation
and phosphorylation. The core of the histones (H2A and H3) can also be
modified. Combinations of modifications are thought to constitute a code,
the so-called "histone code". Histone modifications act in diverse
biological processes such as gene regulation, DNA repair and chromosome
condensation (mitosis).

The common nomeclature of histone modifications is as follows:

The name of the histone (e.g H3)
The single letter amino acid abbreviation (e.g. K for Lysine) and the amino
acid position in the protein
The type of modification (Me: methyl, P: phosphate, Ac: acetyl, Ub:
ubiquitin)
So H3K4Me denotes the methylation of H3 on the 4th lysine from the start
(N-terminal) of the protein.

(See also Histone methyltransferase, Histone acetyltransferase)

For a detailed example of histone modifications in transcription regulation
see RNA polymerase control by chromatin structure.

[edit]
History
Histones were discovered in 1884 by Albrecht Kossel. The word "histone"
dates from the late 19th century and is from the German "Histon", of
uncertain origin: perhaps from Greek histanai or from histos. Until the
early 1990s, histones were dismissed as merely packing material for nuclear
DNA. During the early 1990s, the regulatory functions of histones were
discovered.

[edit]
See also
Gene silencing
Genetics
Histone deacetylase
Chromatin