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Mechanisms of Epigenetics
Several types of epigenetic inheritance systems
may play a role in what has become known as cell memory
1.DNA methylation and chromatin remodeling
DNA associates with histone proteins to form
chromatin.Because the phenotype of a cell or individual is affected
by which of its genes are transcribed, heritable transcription
states can give rise to epigenetic effects. There are several layers
of regulation of gene expression. One way that genes are regulated
is through the remodeling of chromatin. Chromatin is the complex of
DNA and the histone proteins with which it associates. Histone
proteins are little spheres that DNA wraps around. If the way that
DNA is wrapped around the histones changes, gene expression can
change as well. Chromatin remodeling is accomplished through two
main mechanisms:
1. The first way is post translational modification of the amino
acids that make up histone proteins. Histone proteins are made up of
long chains of amino acids. If the amino acids that are in the chain
are changed, the shape of the histone sphere might be modified. DNA
is not completely unwound during replication. It is possible, then,
that the modified histones may be carried into each new copy of the
DNA. Once there, these histones may act as templates, initiating the
surrounding new histones to be shaped in the new manner. By altering
the shape of the histones around it, these modified histones would
ensure that a differentiated cell would stay differentiated, and not
convert back into being a stem cell.
2. The second way is the addition of methyl groups to the DNA,
mostly at CpG sites, to convert cytosine to 5-methylcytosine.
5-Methylcytosine performs much like a regular cytosine, pairing up
with a guanine. However, some areas of genome are methylated more
heavily than others and highly methylated areas tend to be less
transcriptionally active, through a mechanism not fully understood.
Methylation of cytosines can also persist from the germ line of one
of the parents into the zygote, marking the chromosome as being
inherited from this parent (genetic imprinting).
The way that the cells stay differentiated in the case of DNA
methylation is clearer to us than it is in the case of histone
shape. Basically, certain enzymes (such as DNMT1) have a higher
affinity for the methylated cytosine. If this enzyme reaches a "hemimethylated"
portion of DNA (where methylcytosine is in only one of the two DNA
strands) the enzyme will methylate the other half.
Although histone modifications occur throughout the entire sequence,
the unstructured N-termini of histones (called histone tails) are
particularly highly modified. These modifications include
acetylation, methylation, ubiquitylation, phosphorylation and
sumoylation. Acetylation is the most highly studied of these
modifications. For example, acetylation of the K14 and K9 lysines of
the tail of histone H3 by histone acetyltransferase enzymes (HATs)
is generally correlated with transcriptional competence.
One mode of thinking is that this tendency of acetylation to be
associated with "active" transcription is biophysical in nature.
Because it normally has a positively charged nitrogen at its end,
lysine can bind the negatively charged phosphates of the DNA
backbone. The acetylation event converts the positively charged
amine group on the side chain into a neutral amide linkage. This
removes the positive charge, thus loosening the DNA from the histone.
When this occurs, complexes like SWI/SNF and other transcriptional
factors can bind to the DNA and allow transcription to occur. This
is the "cis" model of epigenetic function. In other words, changes
to the histone tails have a direct affect on the DNA itself.
Another model of epigenetic function is the "trans" model. In this
model changes to the histone tails act indirectly on the DNA. For
example, lysine acetylation may create a binding site for chromatin
modifying enzymes (and basal transcription machinery as well). This
Chromatin Remodeler can then cause changes to the state of the
chromatin. Indeed, the bromodomain — a protein segment (domain) that
specifically binds acetyl-lysine — is found in many enzymes that
help activate transcription, including the SWI/SNF complex (on the
protein polybromo). It may be that acetylation acts in this and the
previous way to aid in transcriptional activation.
The idea that modifications act as docking modules for related
factors is borne out by histone methylation as well. Methylation of
lysine 9 of histone H3 has long been associated with constitutively
transcriptionally silent chromatin (constitutive heterochromatin).
It has been determined that a chromodomain (a domain that
specifically binds methyl-lysine) in the transcriptionally
repressive protein HP1 recruits HP1 to K9 methylated regions. One
example that seems to refute this biophysical model for acetylation
is that tri-methylation of histone H3 at lysine 4 is strongly
associated with (and required for full) transcriptional activation.
Tri-methylation in this case would introduce a fixed positive charge
on the tail.
It has been shown that the histone lysine methyltransferase (KMT) is
responsible for this methylation activity in the pattern of histones
H3 & H4. This enzyme utilizes a catalytically active site called the
SET domain (Supressor of variegation, Enhancer of zeste, Trithorax).
The SET domain is a 130-amino acid sequence involved in modulating
gene activities. This domain has been demonstrated to bind to the
histone tail and causes the methylation of the histone.
Differing histone modifications are likely to function in differing
ways; acetylation at one position is likely to function differently
than acetylation at another position. Also, multiple modifications
may occur at the same time, and these modifications may work
together to change the behavior of the nucleosome. The idea that
multiple dynamic modifications regulate gene transcription in a
systematic and reproducible way is called the histone code.
DNA methylation frequently occurs in repeated sequences, and helps
to suppress the expression and mobility of 'transposable elements':
Because 5-methylcytosine is chemically very similar to thymidine,
CpG sites are frequently mutated and become rare in the genome,
except at CpG islands where they remain unmethylated. Epigenetic
changes of this type thus have the potential to direct increased
frequencies of permanent genetic mutation. DNA methylation patterns
are known to be established and modified in response to
environmental factors by a complex interplay of at least three
independent DNA methyltransferases, DNMT1, DNMT3A and DNMT3B, the
loss of any of which is lethal in mice. DNMT1 is the most abundant
methyltransferase in somatic cells, localizes to replication
foci, has a 10–40-fold preference for hemimethylated DNA and
interacts with the proliferating cell nuclear antigen (PCNA). By
preferentially modifying hemimethylated DNA, DNMT1 transfers
patterns of methylation to a newly synthesized strand after DNA
replication, and therefore is often referred to as the ‘maintenance'
methyltransferase. DNMT1 is essential for proper embryonic
development, imprinting and X-inactivation.
Histones H3 and H4 can also be manipulated through demethylation
using histone lysine demethylase (KDM). This recently identifited
enzyme has a catalytically active site called the Jumonji domain (JmjC).
The demethylation occurs when JmjC utilizes multiple cofactors to
hydroxylate the methyl group, thereby removing it. JmjC is capable
of demethylating mono-, di-, and tri-methylated substrates.
Chromosomal regions can adopt stable and heritable alternative
states resulting in bistable gene expression without changes to the
DNA sequence. Epigenetic control is often associated with
alternative covalent modifications of histones. The stability and
heritability of states of larger chromosomal regions are often
thought to involve positive feedback where modified nucleosomes
recruit enzymes that similarly modify nearby nucleosomes. A
simplified stochastic model for this type of epigenetics is found
here.
Because DNA methylation and chromatin remodeling play such a central
role in many types of epigenic inheritance, the word "epigenetics"
is sometimes used as a synonym for these processes. However, this
can be misleading. Chromatin remodeling is not always inherited, and
not all epigenetic inheritance involves chromatin remodeling.
It has been suggested that the histone code could be mediated by the
effect of small RNAs. The recent discovery and characterization of a
vast array of small (21- to 26-nt), non-coding RNAs suggests that
there is an RNA component, possibly involved in epigenetic gene
regulation. Small interfering RNAs can modulate transcriptional gene
expression via epigenetic modulation of targeted promoters.
RNA transcripts and their encoded proteinsSometimes a gene, after
being turned on, transcribes a product that (either directly or
indirectly) maintains the activity of that gene. For example, Hnf4
and MyoD enhance the transcription of many liver- and
muscle-specific genes, respectively, including their own, through
the transcription factor activity of the proteins they encode. RNA
signalling includes differential recruitment of a hierarchy of
generic chromatin modifying complexes and DNA methyltransferases to
specific loci by RNAs during differentiation and development.[24]
Other epigenetic changes are mediated by the production of different
splice forms of RNA, or by formation of double-stranded RNA (RNAi).
Descendants of the cell in which the gene was turned on will inherit
this activity, even if the original stimulus for gene-activation is
no longer present. These genes are most often turned on or off by
signal transduction, although in some systems where syncytia or gap
junctions are important, RNA may spread directly to other cells or
nuclei by diffusion. A large amount of RNA and protein is
contributed to the zygote by the mother during oogenesis or via
nurse cells, resulting in maternal effect phenotypes. A smaller
quantity of sperm RNA is transmitted from the father, but there is
recent evidence that this epigenetic information can lead to visible
changes in several generations of offspring.
2. Prions
Prions are infectious forms of proteins. Proteins
generally fold into discrete units which perform distinct cellular
functions, but some proteins are also capable of forming an
infectious conformational state known as a prion. Although often
viewed in the context of infectious disease, prions are more loosely
defined by their ability to catalytically convert other native state
versions of the same protein to an infectious conformational state.
It is in this latter sense that they can be viewed as epigenetic
agents capable of inducing a phenotypic change without a
modification of the genome.
Fungal prions are considered epigenetic because the infectious
phenotype caused by the prion can be inherited without modification
of the genome. PSI+ and URE3, discovered in yeast in 1965 and 1971,
are the two best studied of this type of prion. Prions can have a
phenotypic effect through the sequestration of protein in
aggregates, thereby reducing that protein's activity. In PSI+ cells,
the loss of the Sup35 protein (which is involved in termination of
translation) causes ribosomes to have a higher rate of read-through
of stop codons, an effect which results in suppression of nonsense
mutations in other genes. The ability of Sup35 to form prions may be
a conserved trait. It could confer an adaptive advantage by giving
cells the ability to switch into a PSI+ state and express dormant
genetic features normally terminated by premature stop codon
mutations.
3. Structural inheritance systems
In ciliates such as Tetrahymena and Paramecium,
genetically identical cells show heritable differences in the
patterns of ciliary rows on their cell surface. Experimentally
altered patterns can be transmitted to daughter cells. It seems
existing structures act as templates for new structures. The
mechanisms of such inheritance are unclear, but reasons exist to
assume that multicellular organisms also use existing cell
structures to assemble new ones.
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