An introduction to Epigenetics.

Multicellular Eukaryotes are intriguing; from one genome in one cell, they are able to generate a wide range of cells, and consequently tissues, and then organs and organisms. The genes contained in the DNA of these cells are more or less identical, but their expression patterns can be widely divergent. There can be genes that are active in neural tissue, for instance, but not in the tissues of the heart, for instance, and this is found across a whole range of tissues.

These expression profiles, as we know them in the language of molecular biology, are distinctive and unique to tissues and can be used to define the normal physiology of a given tissue type, with aberrations from this being associated with disorders. (See http://www.biomedcentral.com/1471-2164/12/439). This raises questions of how tissue specific expression profiles are developed by cells in a given tissue, and how this is modified during development as an organism takes shape from one single cell at conception.

The ability to regulate gene expression is present in all life, even prokaryote, where transcriptional regulation can be seen in the form of operons, and it is true that gene expression may simply be modulated by transcriptional regulation by various promoters and repressors binding to the promoters of genes in various permutations and combinations (See http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0020164 for a paper discussing the complexities of such architecture) but this solely gene-based process isn’t all there is to it. There is something above the genetic layer and below the proteomic layer, and the field that studies this is called epigenetics.

Epigenetics is a function of chromosome structure; for transcription to actually take place, all the transcription factors and enzymes that are required for gene expression must be able to access the DNA that contains the genes that are to be expressed, but chromosome structure will determine if this can be done or not, and can therefore determine if a gene can be expressed or not.

In Eukaryotes, chromsomes aren’t made of naked DNA; DNA is instead associated with complexes of histone octamers, these complexes, called nucleosomes, are then folded upon themselves to form one of several structures; roughly a loosely packed structure called heterochromatin, and a tightly packed structure called euchromatin. Only genes in euchromatin can be transcribed; a heterochromatin configuration at the locus of a gene is a harbinger of silenced expression.

Left, schematic of various levels of chromatin compaction, from extended nucleosome arrays to folding of secondary chromatin structures exemplified by the 30-nm chromatin fiber to poorly characterized higher-order structures. There are ten histone tails protruding from each nucleosome core. Right, detail of nucleosome surface showing histones H2A (yellow), H2B (light red), H3 (blue) and H4 (green). Image Reference - http://www.nature.com/nsmb/journal/v14/n11/fig_tab/nsmb1107-1056_F1.html

I’m now going to introduce you to some of the common epigenetic mechanisms of gene silencing that have been documented.

Promoter methylation

This is one of the best documented mechanisms of epigenetic silencing we’ve uncovered so far; promoters have regions of cytosine nucleotides followed by guanine nucleotides in multiple stretches. We call these CpG islands. If these are methylated, there is a conversion of Cytosine to 5-methylcytosine, and this basically reduces the affinity that the transcriptional apparatus in a cell has for promoters of the genes in question.

The methylation patterns of a cell’s DNA can be inherited by daughter cells as well; enzymes such as DNMT1 (a DNA methyltransferase) can seek out hemimethylated regions (one of the two copies of a gene in a daughter cell is methylated) and methylate the other, completing inheritance of an expression profile. Other proteins such as Methyl CpG binding proteins lock methylation in and keep genes repressed.

a | Differential silencing by CpG island or promoter methylation. b | Regulation by antisense transcripts in conjunction with CpG island or promoter methylation; c | Allele-specific regulation of neighbouring genes by differential methylation of boundary elements within a CpG island. Factors such as CCCTC-binding factor (CTCF) (red disc) bind to the unmethylated allele and block the access of upstream promoters to downstream enhancers (green), leading to transcriptional repression of the upstream gene. d | Differential methylation results in differential binding of silencing factors (red, in this case methylation-sensitive), which repress the promoter in cis. Image Reference - http://www.nature.com/nrg/journal/v2/n1/fig_tab/nrg0101_021a_F5.html

Promoter methylation can also act in combination with transcription factors; it may well be possible to see cases where an activator binding site is methylated while a repressor can bind to its site in the promoter, resulting in synergistic repression of transcription.  Since this is inherited, tissue transcriptomes can be regulated and shaped during development and differentiation, and that is one of the reasons why tissues have unique expression profiles in a state of normalcy.

There are other possible combinations for silencing by methylation, too; antisense transcripts (through RNAseH silencing as well as RNAi and miRNA) can act in conjunction with methylation, upstream promoter element methylation can block access to downstream methylation sites and so on.

Histone Modification.

Histones are proteins as well, and the residues that comprise them are subject to posttranslational modifications by enzymes, and the presence of different modifications can alter the shape of the chromatin at the site of modification. This altered conformation then influences how active a gene is by modulating DNA access by transcriptional machinery.

Chromatin remodelling in this way enables the establishment of activation or repression long term and the continued maintenance thereof. One of the rather well studied modifications is histone acetylation/deacetylation at a lysine residue, especially in Histone H3. However, this is not the only known modification, and phosphorylation, ubiquitylation and so on may be of import as well.

Histone modifications occur at selected residues and some of the patterns shown have been closely linked to a biological event (for example, acetylation and transcription). Emerging evidence suggests that distinct H3 (red) and H4 (black) tail modifications act sequentially or in combination to regulate unique biological outcomes. How this hierarchy of multiple modifications extends (depicted as 'higher-order combinations') or how distinct combinatorial sets are established or maintained in localized regions of the chromatin fibre is not known. Relevant proteins or protein domains that are known to interact or associate with distinct modifications are indicated. The CENP-A tail domain (blue) might also be subjected to mitosis-related marks such as phosphorylation; the yellow bracket depicts a motif in which serines and threonines alternate with proline residues. Image source - http://www.nature.com/nature/journal/v403/n6765/fig_tab/403041a0_F2.html

One thing you could carry away from reading the section above is that the mere presence of histones and enzymes that act on and modify them can regulate differentiation, development and tissue homeostasis, and all of that section is somewhat nicely summarised by the following video.

Why does Epigenetics matter and where are we headed?

If there are disorders that are associated with aberrant epigenetic function in a cell, and there is mounting evidence for this already, it would make sense to continue to understand the mechanisms involved and the effects they have, and a range of techniques, ranging from those that map out global methylation to those that look at individual histones, have been, and are, being developed.

Global dysregulation of methylation patterns is a phenomenon in cancer cells and so are aberrations associated with microRNA dysfunction; in fact, this is significant enough that drugs that seek to hit dysregulated epigenetic processes are in development, such as histone deacytlase inhibitors and global methylation modulators (See http://carcin.oxfordjournals.org/content/31/1/27.full for a well-written summary of the field of cancer epigenetics). Sometimes, more complex chromatin remodeling may serve as potential drug targets, too, JQ1 , a drug that tells undifferentiated cancer cells to differentiate into normal cells,being a case in point…

Understanding epigenetics may also have significant impact on regenerative medicine; some cutting-edge work done recently based on the understanding of how miRNA can alter the expression of chromatin remodelling complexes resulted in researchers being able to turn skin fibroblasts into neurons. The relevant paper is brilliant and can be found here http://www.nature.com/nature/journal/v476/n7359/full/nature10323.html .

There are already large scale projects to study epigenetics being put in place, such as the Human Epigenome Project, which is great news for anybody who is interested in the field.There is a Human Epigenome Browser in case you want to play with it, by the way. This has been accompanied by the development of high-throughput screening methods for epigenetic analysis, such as Medip-Seq, which is a natural progression in the evolution of techniques such as ChIP on Chip and ChIP-Seq.

That is all from me this time round. I will be studying cancer epigenetics in about a month’s time on an academic basis so I suggest you stay tuned for more insights into the field.

Cheers,
Exploreable

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One response to “An introduction to Epigenetics.

  1. Pingback: A Bird’s Eye View of Cancer Research… | Exploreable

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