Transcription is the process of creating a complementary RNA copy of a sequence of DNA.^[1] 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. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. Also unlike DNA replication where DNA is synthesised, transcription does not involve an RNA primer to initiate RNA synthesis.

Transcription is explained easily in 4 or 5 steps, each moving like a wave along the DNA.

1. RNA polymerase moves the transcription bubble, a stretch of unpaired nucleotides, by breaking the hydrogen bonds between complementary nucleotides.
2. RNA polymerase adds matching RNA nucleotides that are paired with complementary DNA bases.
3. RNA sugar-phosphate backbone forms with assistance from RNA polymerase.
4. Hydrogen bonds of the untwisted RNA + DNA helix break, freeing the newly synthesized RNA strand.
5. If the cell has a nucleus, the RNA is further processed (addition of a 3′ poly-A tail and a 5′ cap) and exits through to the cytoplasm through the nuclear pore complex.

Transcription is the first step leading to gene expression. The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene transcribed encodes aprotein, the result of transcription is messenger RNA (mRNA), which will then be used to create that protein via the process of translation. Alternatively, the transcribed gene may encode for either non-coding RNA genes (such as microRNA, lincRNA, etc.) or ribosomal RNA (rRNA) or transfer RNA (tRNA), other components of the protein-assembly process, or other ribozymes.^[2]

A DNA transcription unit encoding for a protein contains not only the sequence that will eventually be directly translated into the protein (the coding sequence) but also regulatory sequences that direct and regulate the synthesis of that protein. The regulatory sequence before (upstream from) the coding sequence is called the five prime untranslated region (5’UTR), and the sequence following (downstream from) the coding sequence is called the three prime untranslated region (3’UTR).^[2]

Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication.^[3]

As in DNA replication, DNA is read from 3′ → 5′ during transcription. Meanwhile, the complementary RNA is created from the 5′ → 3′ direction. This means its 5′ end is created first in base pairing. Although DNA is arranged as two antiparallel strands in a double helix, only one of the two DNA strands, called the template strand, is used for transcription. This is because RNA is only single-stranded, as opposed to double-stranded DNA. The other DNA strand is called the coding (lagging) strand, because its sequence is the same as the newly created RNA transcript (except for the substitution of uracil for thymine). The use of only the 3′ → 5′ strand eliminates the need for the Okazaki fragments seen in DNA replication.^[2]

Transcription is divided into 5 stages: pre-initiation, initiation, promoter clearance, elongation and termination.^[2]

Major steps

Stage I: Pre-initiation

In eukaryotes, RNA polymerase, and therefore the initiation of transcription, requires the presence of a core promoter sequence in the DNA. Promoters are regions of DNA that promote transcription and, in eukaryotes, are found at -30, -75, and -90 base pairs upstream from the transcription start site (abbreviated to TSS). Core promoters are sequences within the promoter that are essential for transcription initiation. RNA polymerase is able to bind to core promoters in the presence of various specific transcription factors.^{[citation needed]}

The most characterized type of core promoter in eukaryotes is a short DNA sequence known as a TATA box, found 25-30 base pairs upstream from the TSS.^{[citation needed]} The TATA box, as a core promoter, is the binding site for a transcription factor known as TATA-binding protein (TBP), which is itself a subunit of another transcription factor, called Transcription Factor II D (TFIID). After TFIID binds to the TATA box via the TBP, five more transcription factors and RNA polymerase combine around the TATA box in a series of stages to form a preinitiation complex. One transcription factor, Transcription factor II H, has two components with helicase activity and so is involved in the separating of opposing strands of double-stranded DNA to form the initial transcription bubble. However, only a low, or basal, rate of transcription is driven by the preinitiation complex alone. Other proteins known as activators and repressors, along with any associated coactivators or corepressors, are responsible for modulating transcription rate.^{[citation needed]}

Thus, preinitiation complex contains:^{[citation needed]} 1. Core Promoter Sequence 2. Transcription Factors 3. RNA Polymerase 4. Activators and Repressors. The transcription preinitiation in archaea is, in essence, homologous to that of eukaryotes, but is much less complex.^[4] The archaeal preinitiation complex assembles at a TATA-box binding site; however, in archaea, this complex is composed of only RNA polymerase II, TBP, and TFB (the archaeal homologue of eukaryotic transcription factor II B (TFIIB)).^[5][6]

Stage II: Initiation

In bacteria, transcription begins with the binding of RNA polymerase to the promoter in DNA. RNA polymerase is a core enzymeconsisting of five subunits: 2 α subunits, 1 β subunit, 1 β’ subunit, and 1 ω subunit. At the start of initiation, the core enzyme is associated with a sigma factor that aids in finding the appropriate -35 and -10 base pairs downstream of promoter sequences.^[7] When the sigma factor and RNA polymerase combine, they form a holoenzyme.

Transcription initiation is more complex in eukaryotes. Eukaryotic RNA polymerase does not directly recognize the core promoter sequences. Instead, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. Only after certain transcription factors are attached to the promoter does the RNA polymerase bind to it. The completed assembly of transcription factors and RNA polymerase bind to the promoter, forming a transcription initiation complex. Transcription in the archaea domain is similar to transcription in eukaryotes.^[8]

Stage III: Promoter clearance

After the first bond is synthesized, the RNA polymerase must clear the promoter. During this time there is a tendency to release the RNA transcript and produce truncated transcripts. This is called abortive initiation and is common for both eukaryotes and prokaryotes.^[9] Abortive initiation continues to occur until the σ factor rearranges, resulting in the transcription elongation complex (which gives a 35 bp moving footprint). The σ factor is released before 80 nucleotides of mRNA are synthesized.^[10] Once the transcript reaches approximately 23 nucleotides, it no longer slips and elongation can occur. This, like most of the remainder of transcription, is an energy-dependent process, consuming adenosine triphosphate (ATP).^{[citation needed]}

Promoter clearance coincides with phosphorylation of serine 5 on the carboxy terminal domain of RNAP II in eukaryotes, which is phosphorylated by TFIIH.^{[citation needed]}

Stage IV: Elongation

One strand of the DNA, the template strand (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy. Although RNA polymerase traverses the template strand from 3′ → 5′, the coding (non-template) strand and newly-formed RNA can also be used as reference points, so transcription can be described as occurring 5′ → 3′. This produces an RNA molecule from 5′ → 3′, an exact copy of the coding strand (except that thymines are replaced with uracils, and the nucleotides are composed of a ribose (5-carbon) sugar where DNA has deoxyribose (one less oxygen atom) in its sugar-phosphate backbone).^{[citation needed]}

Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from a single copy of a gene.^{[citation needed]}

Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.^{[citation needed]}

Stage V: Termination

Bacteria use two different strategies for transcription termination.1.Rho-independent transcription 2.Rho-dependent transcription. In Rho-independent transcription termination,also called intrinsic termination, RNA transcription stops when the newly synthesized RNA molecule forms a G-C-rich hairpin loop followed by a run of Us. When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds, now filling the DNA-RNA hybrid. This pulls the poly-U transcript out of the active site of the RNA polymerase, in effect, terminating transcription. In the “Rho-dependent” type of termination, a protein factor called “Rho” destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex.^[11]

Transcription termination in eukaryotes is less understood but involves cleavage of the new transcript followed by template-independent addition of As at its new 3′ end, in a process called polyadenylation.^[12]

In molecular biology and genetics, translation is the third stage of protein biosynthesis (part of the overall process of gene expression). In translation, messenger RNA (mRNA) produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. In Bacteria, translation occurs in the cell’s cytoplasm, where the large and small subunits of the ribosome are located, and bind to the mRNA. In Eukaryotes, translation occurs across the membrane of the endoplasmic reticulum in a process called vectorial synthesis. The ribosome facilitates decoding by inducing the binding of tRNAswith complementary anticodon sequences to that of the mRNA. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is “read” by the ribosome in a fashion reminiscent to that of a stock ticker and ticker tape.

In many instances, the entire ribosome/mRNA complex bind to the outer membrane of the rough endoplasmic reticulum and release the nascent protein polypeptide inside for later vesicle transport and secretion outside of the cell. Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA, do not undergo translation into proteins.

Translation proceeds in four phases: initiation, elongation, translocation and termination (all describing the growth of the amino acid chain, or polypeptide that is the product of translation). Amino acids are brought to ribosomes and assembled into proteins.

In activation, the correct amino acid is covalently bonded to the correct transfer RNA (tRNA). The amino acid is joined by its carboxyl group to the 3′ OH of the tRNA by an ester bond. When the tRNA has an amino acid linked to it, it is termed “charged”. Initiation involves the small subunit of the ribosome binding to the 5′ end of mRNA with the help of initiation factors (IF). Termination of the polypeptide happens when the A site of the ribosome faces a stop codon (UAA, UAG, or UGA). No tRNA can recognize or bind to this codon. Instead, the stop codon induces the binding of arelease factor protein that prompts the disassembly of the entire ribosome/mRNA complex.

A number of antibiotics act by inhibiting translation; these include anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, and puromycin, among others. Prokaryotic ribosomes have a different structure from that of eukaryotic ribosomes, and thus antibiotics can specifically target bacterial infections without any detriment to a eukaryotic host’s cells.

Basic mechanisms

The basic process of protein production is addition of one amino acid at a time to the end of a protein. This operation is performed by a ribosome. The choice of amino acid type to add is determined by an mRNA molecule. Each amino acid added is matched to a three nucleotide subsequence of the mRNA. For each such triplet possible, only one particular amino acid type is accepted. The successive amino acids added to the chain are matched to successive nucleotide triplets in the mRNA. In this way the sequence of nucleotides in the template mRNA chain determines the sequence of amino acids in the generated amino acid chain.^[1]Addition of an amino acid occurs at the C-terminus of the peptide and thus translation is said to be amino-to-carboxyl directed.^[2]

The mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. The ribonucleotides are “read” by translational machinery in a sequence of nucleotide triplets called codons. Each of those triplets codes for a specific amino acid.

The ribosome molecules translate this code to a specific sequence of amino acids. The ribosome is a multisubunit structure containing rRNA and proteins. It is the “factory” where amino acids are assembled into proteins. tRNAs are small noncoding RNA chains (74-93 nucleotides) that transport amino acids to the ribosome. tRNAs have a site for amino acid attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary to the mRNA triplet that codes for their cargo amino acid.

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodon sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary base pairing to specific tRNA anticodons. The ribosome has three sites for tRNA to bind. They are the aminoacyl site (abbreviated A), the peptidyl site (abbreviated P) and the exit site (abbreviated E). With respect to the mRNA, the three sites are oriented 5’to 3’ E-P-A, because ribosomes moves toward the 3′ end of mRNA. The A site binds the incoming tRNA with the complementary codon on the mRNA. The P site holds the tRNA with the growing polypeptide chain. The E site holds the tRNA without its amino acid. When an aminoacyl-tRNA initially binds to its corresponding codon on the mRNA, it is in the A site. Then, a peptide bond forms between the amino acid of the tRNA in the A site and the amino acid of the charged tRNA in the P site. The growing polypeptide chain is transferred to the tRNA in the A site. Translocation occurs, moving the tRNA in the P site, now without an amino acid, to the E site; the tRNA that was in the A site, now charged with the polypeptide chain, is moved to the P site. The tRNA in the E site leaves and another aminoacyl-tRNA enters the A site to repeat the process.^[3]

After the new amino acid is added to the chain, the energy provided by the hydrolysis of a GTP bound to the translocase EF-G (in prokaryotes) and eEF-2 (ineukaryotes) moves the ribosome down one codon towards the 3′ end. The energy required for translation of proteins is significant. For a protein containing n amino acids, the number of high-energy Phosphate bonds required to translate it is 4n-1^{[citation needed]}. The rate of translation varies; it is significantly higher in prokaryotic cells (up to 17-21 amino acid residues per second) than in eukaryotic cells (up to 6-9 amino acid residues per second).^[4]

DNA replication is a biological process that occurs in all living organisms and copies their DNA; it is the basis for biological inheritance. The process starts when one double-stranded DNA molecule produces two identical copies of the molecule. The cell cycle (mitosis) also pertains to the DNA replication/reproduction process. The cell cycle includes interphase, prophase, metaphase, anaphase, and telophase. Each strand of the original double-stranded DNA molecule serves as template for the production of the complementary strand, a process referred to as semiconservative replication. Cellular proofreading and error toe-checking mechanisms ensure near perfect fidelity for DNA replication.^[1][2]

In a cell, DNA replication begins at specific locations in the genome, called “origins”.^[3] Unwinding of DNA at the origin, and synthesis of new strands, forms a replication fork. In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.

DNA replication can also be performed in vitro (artificially, outside a cell). DNA polymerases, isolated from cells, and artificial DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase chain reaction (PCR), a common laboratory technique, employs such artificial synthesis in a cyclic manner to amplify a specific target DNA fragment from a pool of DNA.

DNA structure

DNA usually exists as a double-stranded structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides having the bases:adenine, cytosine, guanine, and thymine (commonly noted as A,C, G & T). A nucleotide is a mono-, di-, or triphosphate deoxyribonucleoside; that is, a deoxyribose sugar is attached to one, two, or three phosphates, and a base. Chemical interaction of these nucleotides forms phosphodiester linkages, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides (bases) are matched between strands through hydrogen bonds to form base pairs. Adenine pairs with thymine (two hydrogen bonds), and cytosine pairs with guanine (three hydrogen bonds) because a purine must pair with a pyrimidine: a pyrimidine cannot pair with another pyrimidine because the strands would be very close to each other; in a purine pair, the strands would be too far apart and the structure would be unstable. If A-C paired, there would be one hydrogen not bound to anything, making the DNA unstable.

DNA strands have a directionality, and the different ends of a single strand are called the “3′ (three-prime) end” and the “5′ (five-prime) end” with the direction of the naming going 5 prime to the 3 prime region. The strands of the helix are anti-parallel with one being 5 prime to 3 then the opposite strand 3 prime to 5. These terms refer to the carbon atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3′ end of a DNA strand.

The pairing of bases in DNA through hydrogen bonding means that the information contained within each strand is redundant. The nucleotides on a single strand can be used to reconstruct nucleotides on a newly synthesized partner strand.^[4]

DNA polymerase

DNA polymerases are a family of enzymes that carry out all forms of DNA replication.^[6] However, a DNA polymerase can only extend an existing DNA strand paired with a template strand; it cannot begin the synthesis of a new strand. To begin synthesis, a short fragment of DNA or RNA, called a primer, must be created and paired with the template DNA strand.

DNA polymerase then synthesizes a new strand of DNA by extending the 3′ end of an existing nucleotide chain, adding new nucleotides matched to the template strand one at a time via the creation of phosphodiester bonds. The energy for this process of DNA polymerization comes from two of the three total phosphates attached to each unincorporated base. (Free bases with their attached phosphate groups are called nucleoside triphosphates.) When a nucleotide is being added to a growing DNA strand, two of the phosphates are removed and the energy produced creates a phosphodiester bond that attaches the remaining phosphate to the growing chain. The energetics of this process also help explain the directionality of synthesis – if DNA were synthesized in the 3′ to 5′ direction, the energy for the process would come from the 5′ end of the growing strand rather than from free nucleotides.

In general, DNA polymerases are extremely accurate, making less than one mistake for every 10⁷ nucleotides added.^[7] Even so, some DNA polymerases also have proofreading ability; they can remove nucleotides from the end of a strand in order to correct mismatched bases. If the 5′ nucleotide needs to be removed during proofreading, the triphosphate end is lost. Hence, the energy source that usually provides energy to add a new nucleotide is also lost.

Replication process

DNA Replication, like all biological polymerization processes, proceeds in three enzymatically catalyzed and coordinated steps: initiation, elongation and termination.

Origins

For a cell to divide, it must first replicate its DNA.^[8] This process is initiated at particular points in the DNA, known as “origins”, which are targeted by proteins that separate the two strands and initiate DNA synthesis.^[3] Origins contain DNA sequences recognized by replication initiator proteins (e.g., DnaA in E. coli’ and the Origin Recognition Complex in yeast).^[9] These initiators recruit other proteins to separate the strands and initiate replication forks.

Initiator proteins recruit other proteins and form the pre-replication complex, which separate the DNA strands at the origin and forms a bubble. Origins tend to be “AT-rich” (rich in adenine and thymine bases) to assist this process, because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair)—in general, strands rich in these nucleotides are easier to separate since less energy is required to break relatively fewer hydrogen bonds.^[10]

All known DNA replication systems require a free 3′ OH group before synthesis can be initiated (Important note: DNA is read in 3′ to 5′ direction whereas a new strand is synthesised in the 5′ to 3′ direction – this is entirely logical but is often confused). Four distinct mechanisms for synthesis have been described.

1. All cellular life forms and many DNA viruses, phages and plasmids use a primase to synthesize a short RNA primer with a free 3′ OH group which is subsequently elongated by a DNA polymerase.

2. The retroelements (including retroviruses) employ a transfer RNA that primes DNA replication by providing a free 3′ OH that is used for elongation by thereverse transcriptase.

3. In the adenoviruses and the φ29 family of bacteriophages, the 3′ OH group is provided by the side chain of an amino acid of the genome attached protein (the terminal protein) to which nucleotides are added by the DNA polymerase to form a new strand.

4. In the single stranded DNA viruses – a group that includes the circoviruses, the geminiviruses, the parvoviruses and others – and also the many phages and plasmids that use the rolling circle replication (RCR) mechanism, the RCR endonuclease creates a nick the genome strand (single stranded viruses) or one of the DNA strands (plasmids). The 5′ end of the nicked strand is transferred to a tyrosine residue on the nuclease and the free 3′ OH group is then used by the DNA polymerase for new strand synthesis.

The best known of these mechanisms is that used by the cellular organisms. In these once the two strands are separated, RNA primers are created on the template strands. To be more specific, the leading strand receives one RNA primer per active origin of replication while the lagging strand receives several; these several fragments of RNA primers found on the lagging strand of DNA are called Okazaki fragments, named after their discoverer. DNA polymerase extends the leading strand in one continuous motion and the lagging strand in a discontinuous motion (due to the Okazaki fragments). RNase removes the RNA fragments used to initiate replication by DNA polymerase, and another DNA Polymerase enters to fill the gaps. When this is complete, a single nick on the leading strand and several nicks on the lagging strand can be found. Ligase works to fill these nicks in, thus completing the newly replicated DNA molecule.

The primase used in this process differs significantly between bacteria and archaea/eukaryotes. Bacteria use a primase belonging to the DnaG protein superfamily which contains a catalytic domain of the TOPRIM fold type. The TOPRIM fold contains an α/β core with four conserved strands in a Rossmann-like topology. This structure is also found in the catalytic domains of topoisomerase Ia, topoisomerase II, the OLD-family nucleases and DNA repair proteins related to the RecR protein.

The primase used by archaea and eukaryotes in contrast contains a highly derived version of the RNA recognition motif (RRM). This primase is structurally similar to many viral RNA dependent RNA polymerases, reverse transcriptases, cyclic nucleotide generating cyclases and DNA polymerases of the A/B/Y families that are involved in DNA replication and repair. All these proteins share a catalytic mechanism of di-metal-ion-mediated nucleotide transfer, whereby two acidic residues located at the end of the first strand and between the second and third strands of the RRM-like unit respectively, chelate two divalent cations.

As DNA synthesis continues, the original DNA strands continue to unwind on each side of the bubble, forming a replication fork with two prongs. In bacteria, which have a single origin of replication on their circular chromosome, this process eventually creates a “theta structure” (resembling the Greek letter theta: θ). In contrast, eukaryotes have longer linear chromosomes and initiate replication at multiple origins within these.^{[citation needed]}

In biology, and specifically genetics, epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence – hence the name epi- (Greek: επί– over, above, outer) -genetics. It refers to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence. Examples of such changes areDNA methylation and histone modification, both of which serve to regulate gene expression without altering the underlying DNA sequence.

These changes may remain through cell divisions for the remainder of the cell’s life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism;^[1]instead, non-genetic factors cause the organism’s genes to behave (or “express themselves”) differently.^[2]

One example of epigenetic changes in eukaryotic biology is the process of cellular differentiation. During morphogenesis, totipotent stem cells become the various pluripotent cell lines of the embryo, which in turn become fully differentiated cells. In other words, a single fertilized egg cell – the zygote – changes into the many cell types including neurons, muscle cells, epithelium, endothelium of blood vessels, etc. as it continues to divide. It does so by activating some genes while inhibiting others.^[3]

In 2011, it was demonstrated that the methylation of mRNA has a critical role in human energy homeostasis. The obesity associated FTO gene is shown to be able to demethylate N6-methyladenosine in RNA. This opened the related field of RNA epigenetics.^[4][5]

Etymology and definitions

Epigenetics (as in “epigenetic landscape”) was coined by C. H. Waddington in 1942 as a portmanteau of the words genetics and epigenesis.^[6]Epigenesis is an old^[7] word that has more recently been used (see preformationism for historical background) to describe the differentiation of cells from their initial totipotent state in embryonic development. When Waddington coined the term the physical nature of genes and their role in heredity was not known; he used it as a conceptual model of how genes might interact with their surroundings to produce a phenotype.

Robin Holliday defined epigenetics as “the study of the mechanisms of temporal and spatial control of gene activity during the development of complex organisms.”^[8] Thus epigenetic can be used to describe anything other than DNA sequence that influences the development of an organism.

The modern usage of the word in scientific discourse is more narrow, referring to heritable traits (over rounds of cell division and sometimes transgenerationally) that do not involve changes to the underlying DNA sequence.^[9] The Greek prefix epi- in epigenetics implies features that are “on top of” or “in addition to” genetics; thus epigenetic traits exist on top of or in addition to the traditional molecular basis for inheritance.

The similarity of the word to “genetics” has generated many parallel usages. The “epigenome” is a parallel to the word “genome”, and refers to the overall epigenetic state of a cell. The phrase “genetic code” has also been adapted—the “epigenetic code” has been used to describe the set of epigenetic features that create different phenotypes in different cells. Taken to its extreme, the “epigenetic code” could represent the total state of the cell, with the position of each molecule accounted for in an epigenomic map, a diagrammatic representation of the gene expression, DNA methylation and histone modification status of a particular genomic region. More typically, the term is used in reference to systematic efforts to measure specific, relevant forms of epigenetic information such as thehistone code or DNA methylation patterns.

The psychologist Erik Erikson used the term epigenetic in his book Identity: Youth and Crisis (1968). Erikson writes that the epigenetic principle is where “anything that grows has a ground plan, and that out of this ground plan, the parts arise, each part having its time of special ascendancy, until all parts have arisen to form a functioning whole.”^[10] That usage, however, is of primarily historical interest.^[11]

Molecular basis of epigenetics

Epigenetic changes can modify the activation of certain genes, but not the sequence of DNA. Additionally, the chromatin proteins associated with DNA may be activated or silenced. This is why the differentiated cells in a multi-cellular organism express only the genes that are necessary for their own activity. Epigenetic changes are preserved when cells divide. Most epigenetic changes only occur within the course of one individual organism’s lifetime, but, if gene disactivation occurs in a sperm or egg cell that results in fertilization, then some epigenetic changes can be transferred to the next generation.^[12]This raises the question of whether or not epigenetic changes in an organism can alter the basic structure of its DNA (see Evolution, below), a form of Lamarckism.

Specific epigenetic processes include paramutation, bookmarking, imprinting, gene silencing, X chromosome inactivation, position effect, reprogramming, transvection, maternal effects, the progress ofcarcinogenesis, many effects of teratogens, regulation of histone modifications and heterochromatin, and technical limitations affecting parthenogenesis and cloning.

Epigenetic research uses a wide range of molecular biologic techniques to further our understanding of epigenetic phenomena, including chromatin immunoprecipitation (together with its large-scale variantsChIP-on-chip and ChIP-Seq), fluorescent in situ hybridization, methylation-sensitive restriction enzymes, DNA adenine methyltransferase identification (DamID) and bisulfite sequencing. Furthermore, the use ofbioinformatic methods is playing an increasing role (computational epigenetics).

Figure 2.

Intracellular signaling pathways regulating growth. PI3K/TOR, Hippo, and MAPK pathways regulate growth by modulating protein translation, cell cycle progression, and apoptosis. Schematic of pathways showing key components. Genes highlighted in red are mutated in human genetic syndromes that manifest growth deficiency or overgrowth. (A) Growth hormone acts systemically through its regulation of IGF-1, which activates phosphotidyl-inosine-3 kinase (PI3K) by binding the IGF-1 receptor (IGF-1R). Subsequent activation of downstream kinases results in increased protein translation and ribosome biosynthesis, leading to cellular growth. The pathway is inhibited by the phosphatase PTEN and integrates multiple other signals, such as nutrient/energy levels, through the master kinase target of rapamycin (TOR). TOR activates the ribosomal S6 kinase and facilitates eIF4E activity to promote translation and transcription initiation. (B) The Hippo pathway restricts growth to control organ size and prevent tissue overgrowth and tumorigenesis. The pathway is currently best defined in Drosophila, where the cell polarity protein Crumbs (Crb) and the protocadherins Fat and Dachsous (Ds) activate Hippo kinase, which in turn activates Warts kinase. The signaling cascade negatively regulates the transcriptional coactivator Yorkie (Yki) by retaining Yki in the cytoplasm. This restricts cell proliferation and promotes cell death, as Yki promotes G1 progression over G0 cell cycle exit through transcriptional up-regulation of Cyclin E (CycE) and the E2F transcription factor. Yki also has an anti-apoptotic effect by inducing inhibitor of apoptosis protein (IAP). The core pathway is conserved in mammals: Mst1/2 (Hippo), Lats (Warts), and Yap (Yki). Homologs to Fat and Ds or the target gene bantam have not yet been identified in mammals. (C) The MAPK (ERK) signaling cascade transduces mitogen signals, driving cellular proliferation by promoting G1-to-S-phase progression (Meloche and Pouysségur 2007). Downstream, ERK kinase activates the proproliferative transcription factors Myc and E2F as well as decreases levels of the cyclin-dependent kinase inhibitors p21 and p27. Rather than being entirely discrete signaling pathways, these three signaling pathways (A–C) overlap; for instance, Akt inhibits Hippo activity, while ERK phosphorylates, and thus activates, TOR.

Fig. 4.