Control+of+gene+expression

Control of gene expression: Transcription factors, epigenetics, trans cript processing by: Tana, Rachel W, and Rachel B Transcription Processing

** The history behind the discovery of transcription **  In 1909, Archibald Gerrod was the first to suggest that genes dictate phenotype through enzymes that catalyze specific chemical reactions in the cell. He suggested that the symptoms of an inherited disease reflect a person’s inability to synthesize a particular enzyme. He referred to such diseases as “inborn errors of metabolism. ” Gerrod speculated that alkaptonuria, a hereditary disease, was caused by the absence of an enzyme that breaks down a specific substrate, alkapton. Research conducted several decades later supported Gerrod’s hypothesis. In the 1930s, George Beadle and Boris Ephrussi speculated that each mutation affecting eye color in //Drosophila// blocks pigment synthesis at a specific step by preventing production of the enzyme that catalyzes that step. However, neither the chemical reactions nor the enzymes that catalyze them were known at the time. Beadle and Edward Tatum were finally able to establish the link between genes and enzymes in their exploration of the metabolism of a bread mold, //Neurospora crassa//. They did this by exposing the mold to x-rays, thereby causing some of the DNA to mutate. Their results provided strong evidence for the //one gene–one enzyme// //hypothesis.//

** What is transcription? **  Transcription, or RNA synthesis, is the process of converting DNA into messenger RNA (mRNA), which is used later in translation to create proteins used by the cell. Transcription is used by both prokaryotes and eukaryotes in virtually the same process. During transcription, one DNA strand, the template strand**,** provides a template for ordering the sequence of nucleotides in an RNA transcript. A given DNA strand can be the template strand for some genes along a DNA molecule, while for other genes in other regions, the complementary strand may function as the template. The complementary RNA molecule is synthesized according to base-pairing rules, except that uracil is the complementary base to adenine. Like a new strand of DNA, the RNA molecule is synthesized in an antiparallel direction to the template strand of DNA. The mRNA base triplets are called **codons,** and they are written in the 5’ to 3’ direction.

** Why can’t proteins be translated directly from DNA? **  The use of an RNA intermediate provides protection for DNA and its genetic information. Using an RNA intermediate allows more copies of a protein to be made simultaneously, since many RNA transcripts can be made from one gene. Also, each gene transcript can be translated repeatedly.

The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes. Because bacteria lack nuclei, their DNA is not segregated from ribosomes and other protein-synthesizing equipment. This allows the coupling of transcription and translation. Ribosomes attach to the leading end of an mRNA molecule while transcription is still in progress. In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs at ribosomes in the cytoplasm. The transcription of a protein-coding eukaryotic gene results in //pre-mRNA.// The initial RNA transcript of any gene is called a primary transcript. RNA processing yields the finished mRNA. Basically, genes program protein synthesis via genetic messages in the form of messenger RNA.





**There are THREE steps to transcription: ** ** Step One: RNA polymerase binds to DNA ** <span style="background-color: #ffffff; display: block; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 120%;">Initiation: After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand. The start point is called the promoter site. <span style="background-color: #ffffff; display: block; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 120%;">In prokaryotes, there is only one RNA polymerase. In eukaryotes, there are three different types that all aid in gene expression. Transcription in eukaryotes uses RNA polymerase II. <span style="background-color: transparent; display: block; font-family: 'Trebuchet MS',Helvetica,sans-serif;">** Step Two: Elongation: ** <span style="background-color: transparent; display: block; font-family: 'Trebuchet MS',Helvetica,sans-serif;"> Elongation occurs once RNA polymerase is bound at the promoter site. Once there, transcription factors work to unwind the DNA double helix, leaving two unbound strands. <span style="background-color: transparent; color: #000000; font-size: 16px; text-decoration: none; vertical-align: baseline;">As RNA polymerase moves along the DNA, it continues to untwist the double helix, exposing about 10 to 20 DNA bases at a time for pairing with RNA nucleotides.
 * 1) <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">** RNA polymerase binds to DNA **
 * 2) <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">** Elongation **
 * 3) <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">** Termination **



<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">** Step Three: Termination ** <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 120%;">This phase differs in prokaryotes and eukaryotes.

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">// Prokaryotes - // <span style="display: block; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 120%; text-align: left;">In prokaryotes, there are two phases, the rho dependent termination and the Rho independent termination. In Rho dependent termination a protein factor called Rho binds to the transcription termination site, and destabilizes the interaction between the DNA template and the RNA polymerase complex, resulting in transcription being ended and the RNA transcript being released. In Rho independent termination, the formation of the hairpin loop in the G-C rich regions of the DNA template makes it inaccessible to the RNA strand the the RNA polymerase, resulting in a termination of transcription.

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">// Eukaryotes - // <span style="display: block; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 120%; text-align: left;">RNA polermase moves along the DNA strand until it reaches the designated termination site. At that point the RNA polymerase will detach from the DNA strand and release the mRNA strand along with the RNA polymer.

<span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 120%; text-align: left;">[|Transcription Demo]

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<span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 200%; text-align: center;">Transcription Factors

=<span style="font-family: Arial,Helvetica,sans-serif; font-size: 12pt;">**__What are Transcription Factors?__** = <span style="font-family: Arial,Helvetica,sans-serif; font-size: 12pt; vertical-align: sub;">Transcription factors are regulatory proteins whose function is to activate transcription of DNA by binding to specific DNA sequences. Many transcription factors act by recognizing //cis//-acting sites that are parts of promoters or enhancers. A factor may also recognize another factor, or may recognize RNA Polymerases. In Eukaryotes, transcription factors, rather than the enzymes themselves, are principally responsible for recognizing the promoter.

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<span style="font-family: Arial,Helvetica,sans-serif; font-size: 12pt;">**__Functions and Biological Roles__** <span style="font-family: Arial,Helvetica,sans-serif;">** Basal transcription complex ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">In eukaryotes, an important class of transcription factors called general transcription factors (GTF) are necessary for transcription to occur. Many of these GTFs don't actually bind DNA but are part of the large basal transcription complex that interacts with RNA polymerase directly. The basal transcription complex binds to promoter regions of DNA upstream to the gene that they regulate. <span style="font-family: Arial,Helvetica,sans-serif;">** Differential enhancement of transcription ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Other transcription factors differentially regulate the expression of various genes by binding to enhancer regions of DNA adjacent to regulated genes. These transcription factors are critical to making sure that genes are expressed in the right cell at the right time and in the right amount, depending on the changing requirements of the organism. <span style="font-family: Arial,Helvetica,sans-serif;">** Development ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Many transcription factors in multicellular organisms are involved in development. Responding to cues (stimuli), these transcription factors turn on/off the transcription of the appropriate genes, which, in turn, allows for changes in cell morphology or activities needed for cell fate determination and cellular differentiation. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> o Ex: The Hox transcription factor family is important for proper body pattern formation in organisms as diverse as fruit flies to humans. <span style="font-family: Arial,Helvetica,sans-serif;">** Response to intercellular signals ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Cells can communicate with each other by releasing molecules that produce cascades within another receptive cell. If the signal requires up regulation or down regulation of genes in the recipient cell, often transcription factors will be downstream in the signaling cascade. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> o Ex: Estrongen signaling is an example of a fairly short signaling cascade that involves the estrogen receptor transcription factor: Estrogen is secreted by tissues such as the ovaries and placenta, crosses the cell membrane of the recipient cell, and is bound by the estrogen receptor in the cell's cytoplasm. The estrogen receptor then goes to the cell's nucleus and binds to its DNA-binding sites, changing the transcriptional regulation of the associated genes. <span style="font-family: Arial,Helvetica,sans-serif;">** Response to environment ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Not only do transcription factors act downstream of signaling cascades related to biological stimuli but they can also be downstream of signaling cascades involved in environmental stimuli. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> o Examples: heat shock factor (HSF), which up regulates genes necessary for survival at higher temperatures, hypoxia inducible factor (HIF), which up regulates genes necessary for cell survival in low-oxygen environments, and sterol regulatory element binding proteir (SREBP), which helps maintain proper lipid levels in the cell. <span style="font-family: Arial,Helvetica,sans-serif;">** Cell cycle control ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Many transcription factors help regulate the cell cycle and as such determine how large a cell will get and when it can divide into two daughter cells <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> o Ex: Myc oncogene, which has important roles in cell growth and apoptosis. <span style="font-family: Arial,Helvetica,sans-serif;">** Pathogenesis ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Transcription factors can also be used to alter gene expression in a host cell to promote pathogenesis. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> o Ex: A well-studied example of this are the transcription-activator like effectors ( TAL effectors ) secreted by Xanthomonas bacteria. When injected into plants, these proteins can enter the nucleus of the plant cell, bind plant promoter sequences, and activate transcription of plant genes that aid in bacterial infection.

<span style="font-family: Arial,Helvetica,sans-serif;">**__ Types of Transcription Factors __**
 * <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">The **general factors** are required for the initiation of RNA synthesis at all promoters. With RNA Polymerase II, they form a complex surrounding the transcription start point, and they determine the site of initiation ; this complex constitutes **the basal transcription apparatus**.
 * <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">The **upstream factors**, which are DNA-binding proteins that recognize specific short consensus elements, are located upstream the transcription start point. These factors are universal and act upon any promoter that contains the appropriate binding site on DNA. They increase the efficiency of initiation.
 * <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">The **inducible factors** function in the same general way as the upstream factors, but have a regulatory role. They are synthesized or activated at specific times and in specific tissues. The sequences that they bind are called response elements.

<span style="font-family: Arial,Helvetica,sans-serif;">**__ Structure __** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Transcription factors are modular in structure and contain the following domains :
 * <span style="font-family: Arial,Helvetica,sans-serif;">** DNA-binding domain ** (**DBD**), which attach to specific sequences of DNA adjacent to regulated genes. DNA sequences that bind transcription factors are often referred to as response elements.




 * <span style="font-family: Arial,Helvetica,sans-serif;">**Trans-activating domain(TAD)**, which contain binding sites for other proteins such as transcription coregulators. These binding sites are frequently referred to as activation functions.
 * <span style="font-family: Arial,Helvetica,sans-serif;">A **signal sensing domain** (**SSD**) which senses external signals and, in response, transmits these signals to the rest of the transcription complex, resulting in up- or down-regulation of gene expression.

<span style="font-family: Arial,Helvetica,sans-serif;">**__ Initiation of transcription __**

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<span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> RNA Polymerase II cannot initiate transcription itself, but is absolutely dependent on supplementary transcription factors (called TFIIX, where "X" is a letter that identifies the individual factor). The enzyme together with these factors constitutes the basal transcriptional complex that is needed to transcribe any class II promoter (coding genes). ====== <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> The first step in the complex formation at a promoter containing a TATA box is binding of the factor TFIID to a region that extends upstream from the TATA sequence. TFIID is solely responsible for recognizing a promoter for RNA Polymerase II. TFIID contains 2 types of components: the TATA-binding protein (TBP), which is responsible for the recognition of the TATA box, and the so-called TAFs (for TBP-Associated Factors). Some TAFs are tissue-specific. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> Transcription factors act in a defined order to build a complex that is joined by RNA polymerase and is needed for the initiation of transcription. Footprinting of the DNA regions protected by the growing complex suggests the following model: commitment to a promoter is initiated when TFIID binds the TATA box; then TFIIA joins the complex. The following step is the addition of TFIIB, which is bound downstream to the TATA box; it may provide the surface that is recognized by RNA polymerase. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> The factor TFIIF consists of 2 subunits. The larger subunit has an ATP-dependent DNA helicase activity that could be involved in melting the DNA at initiation. The smaller subunit has some homology to the regions of bacterial //sigma// factor that contact the core polymerase; indeed, it binds tightly to RNA Polymerase II. TFIIF may bring RNA Polymerase II to the assembling transcription complex. The initiation reaction can occur at this stage. Some further general transcription factors, TFIIE, TFIIH and TFIIJ, are required to allow RNA Polymerase II to start moving away from the promoter. TFIIH has several activities, including an ATPase, a helicase, and a kinase activity that can phosphorylate and activate the RNA Polymerase II; it is also involved in repair of DNA damage. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> Most of the TFII factors are released before RNA Polymerase II leaves the promoter. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;"> The efficiency and specificity with which a promoter is recognized depend upon short sequences, farther upstream the TATA box, which are recognized by upstream and inducible factors. Examples of these are the CAAT box, which plays a strong role in determining the efficiency of the promoter, and is recognized in different promoters by different factors, such as factors of the CTF family, the factors CP1 and CP2, and the factors C/EBP and ACF, and the GC box, which is recognized by the factor Sp1. These factors have the ability to interact with one another by protein-protein interactions. The main purpose of the elements is to bring the factors they bind into the vicinity of the initiation complex, where protein-protein interactions determine the efficiency of the initiation reaction.

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<span style="font-family: Arial,Helvetica,sans-serif;">**__ Clinical Significance __** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Transcription factors are of clinical significance for at least two reasons: mutations can be associated with specific diseases, and they can be targets of medications. <span style="font-family: Arial,Helvetica,sans-serif;">** Disorders ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Due to their important roles in development, intercellular signaling, and cell cycle, some human diseases have been associated with mutations in transcription factors.Many transcription factors are either tumor suppressors or oncogenes, and, thus, mutations or aberrant regulation of them is associated with cancer. <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Below are a few of the more well-studied examples:
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-align: center;">**Condition** || <span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-align: center;">**Description** || <span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-align: center;">**Locus** ||
 * <span style="color: windowtext; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-decoration: none;">Rett syndrome || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Mutations in the MECP2 transcription factor are associated with Rett syndrome, a neurodevelopmental disorder. || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Xq28 ||
 * <span style="color: windowtext; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-decoration: none;">Diabetes || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">A rare form of diabetes called MODY (Maturity onset diabetes of the young) can be caused by mutations in hepatocyte nuclear factors (HNFs) or insulin promoter factor-1 (IPF1/Pdx1). || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">multiple ||
 * <span style="color: windowtext; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-decoration: none;">Developmental verbal dyspraxia || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Mutations in the FOXP2 transcription factor are associated with developmental verbal dyspraxia, a disease in which individuals are unable to produce the finely coordinated movements required for speech. || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">7q31 ||
 * <span style="color: windowtext; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-decoration: none;">Autoimmune diseases || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Mutations in the FOXP3 transcription factor cause a rare form of autoimmune disease called IPEX || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Xp11.23-q13.3 ||
 * <span style="color: windowtext; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-decoration: none;">Li-Fraumeni syndrome || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Caused by mutations in the tumor suppressor || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">17p13.1 ||
 * <span style="color: windowtext; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-decoration: none;">breast cancer || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">The STAT family is relevant to breast cancer . || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">multiple ||
 * <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">multiple cancers || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">The HOX family are involved in a variety of cancers. || <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">multiple ||

<span style="font-family: Arial,Helvetica,sans-serif;">** Potential drug targets ** <span style="font-family: Arial,Helvetica,sans-serif; font-size: 13px;">Approximately 10% of currently prescribed drugs directly target the nuclear receptor class of transcription factors. Examples include tamoxifen and bicalutamide for the treatment of breast and prostate cancer, respectively, and various types of anti-inflammatory and anabolic steroids. In addition, transcription factors are often indirectly modulated by drugs through signaling cascades. It might be possible to directly target other less-explored transcription factors with drugs.

<span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 180%; text-align: center;">Epigenetics <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: center;">// "DNA is just a tape carrying information, and a tape is no good without a player. Epigenetics is about the tape player" (Denise Barlow, Vienna Australia). //

<span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 140%; text-align: left;">**What is it?** <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">The term Epigenetics was coined in 1942 as the "branch of biology which studies the casual interactions between genes and their products, which brings the __phenotype into being__" (Scientist Conrad Waddington). In other words, the field of Epigenetics has emerged in order to fill the gap between the long standing ideas of nature vs. nurture. How much are we a product of our genes as opposed to a product of our surrounding influences? That's where Epigenetics comes in.

<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Today, Epigenetics is define as the field which seeks to determine how genome function is affected by mechanisms that regulate the way genes are processed, specifically with regards to what is known as the **Epigenome**.

<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> ** What is the Epigenome? ** Epigenome literally means "above the genome." Although the human genome project has been completed, the 25,000+ genes that have been identified need to know what to do, how to do it, and when to do it. The epigenome consists of molecular switches and markers which literally attach to DNA and either shut down or turn on genes. One such example is the mechanism known as DNA methylation, in which a quartet of atoms called a **methyl group** attaches to DNA and shuts down gene, inhibiting expression. See the picture below illustrating this particular phenomenon.



<span style="font-family: Arial,Helvetica,sans-serif; font-size: 140%;">**What does the Epigenome respond to?** <span style="font-family: Arial,Helvetica,sans-serif;">From the outside world...
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Nutritional Factors (especially during early development
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Diet
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Physical Activity
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Culture
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">The general environment in which one lives

<span style="font-family: Arial,Helvetica,sans-serif;">From the cellular world...
 * <span style="font-family: Arial,Helvetica,sans-serif;">Surrounding Cells
 * <span style="font-family: Arial,Helvetica,sans-serif;">Hormonal signals such as stress hormones
 * <span style="font-family: Arial,Helvetica,sans-serif;">Release Factors

<span style="font-family: Arial,Helvetica,sans-serif;">When any of the above signals reach cells, a pathway of interacting molecules and switches occur, known as a signal-transduction pathway. The information is ultimately passed onto a gene regulatory protein which attaches to a

<span style="font-family: Arial,Helvetica,sans-serif;">specific site on DNA. The gene regulatory can do one of two things: <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> <span style="font-family: Arial,Helvetica,sans-serif;"> <span style="font-family: Arial,Helvetica,sans-serif;">1. The gene regulatory protein either shuts down or turns on a gene itself after binding to DNA. (pictured to the left)

<span style="font-family: Arial,Helvetica,sans-serif;">2. The gene regulatory protein summons enzymes to either remove or place epigenetic tags on DNA. <span style="font-family: Arial,Helvetica,sans-serif;">These tags give the cell a "long=term" memory in what it should be doing. For example, neurons will not be expressing the same genes as liver cells because epigenetic tags have specified what genes should and should not be expressed in each of these cell types. Furthermore, these epigenetic tags are copied during cell replication. (pictured to the right)

<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">The epigenome readily responds to numerous influences such as the ones listed above. Unlike DNA, which takes generations to altered, the epigenome in comparison can be altered quite quickly. One can think of the epigenome as the software that runs the genomic hardware of a computer. It is this epigenome that directs a cell to turn into a heart cell or a liver cell, for example.In order to understand the breadth of what the epigenome does, one must first understand histone proteins and their role in DNA and gene expression.

<span style="font-family: Arial,Helvetica,sans-serif;"> <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">** What are Histones? **

<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Histones are proteins that help organize DNA. Within these proteins are high proportions of positively charged amino acids that bind to the relatively negative charge of DNA. This binding plays a large role in chromosome structure.Histone proteins also have "tails that stick out." These tails provide binding for chemical markers that have the potential to shut down genes based on their interactions with histone proteins. Eight wrapped histones make one **nucleosome bead**, which are the basic units of DNA packaging in eukaryotes.

<span style="display: block; font-family: Arial,Helvetica,sans-serif; font-size: 140%; text-align: left;">**Mechanisms by which the Epigenome switches genes on and off: Acetyl Tags and Methyl Tags**

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<span style="font-family: Arial,Helvetica,sans-serif;">** The Role of the Epigenome in... **

<span style="font-family: Arial,Helvetica,sans-serif;">**__ Genetic Imprinting and Epigenetic Inheritance __** <span style="font-family: Arial,Helvetica,sans-serif;">Imprinting is one instance where we see the Epigenome come into play. For most genes, we inherit one copy from mom and another from dad. However, with imprinted genes, we still inherit two genes, but only one (either from mom or dad) is a working copy while the other copy is epigenetically silenced. This silencing once again involves DNA methylation of a specific gene (during egg or sperm formation). The methylated allele is said to be the imprinted gene, and the epigenetic tags on this gene stays put for the life of the organism. As a result, the gene that is not imprinted is expressed and used by the animal. <span style="font-family: Arial,Helvetica,sans-serif;">An example of this **genomic imprinting** is shown by two disorders known as //Prader-Willi Syndrome// and //Angelman Syndrome//. The symptoms for these two disorders are different; however, the genetic cause for these two disorders seems to be the same: deletion of a particular segment of chromosome 15. This deleted region contains many crucial imprinted genes. During gamete formation, some of the genes in this region are silenced in the egg while at least one of these genes is silenced in sperm. So depending on whether the defective chromosome 15 is inherited from the mother or father, an offspring will experience very different symptoms. If the abnormal chromosome is derived from the mother, the offspring will have Angelman Syndrome. On the other hand, if the abnormal chromosome is derived from the father, the offspring will show signs of Prader-Willi Syndrome. All in all, the gene silencing during imprinting is very important in the life cycles of mammals and flowering plants. In mammals, about 1% of all genes are imprinted. Prior to gametogenesis, imprints on chromosomes are erased, and genes are re-imprinted all over again in either a maternal or paternal pattern depending on whether the individual is female or male. This genetic reprogramming is depicted to the right:

<span style="font-family: Arial,Helvetica,sans-serif;">Another example of an imprinted gene is the gene that codes for Insulin-like Growth Factor 2 (IGF2), which is an important fetal growth factor. This gene is only expressed from the paternally inherited allele while the maternal allele is epigenetically silenced by methylation.



<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">The evolution of imprinting apparently occurred because of a parental battle between the sexes to control the maternal expenditure of resources to the offspring. Paternally expressed imprinted genes tend to promote growth while it is suppressed by those genes that are maternally expressed. Thus, paternally expressed genes enhance the extraction of nutrients from the mother during pregnancy, whereas, the maternal genome seeks to limit it. This genetic battle between the mother and father appears to continue even after birth since mice that lack paternally expressed genes have reduced maternal nurturing behavior.

<span style="font-family: Arial,Helvetica,sans-serif;">__** X Inactivation **__ <span style="font-family: Arial,Helvetica,sans-serif;">Epigenetics also comes into play during **X inactivation** in Female Mammals. Although female mammals inherit two X chromosomes, the cells of the early embryo randomly silence one X chromosome independently of one another. This silenced X chromosome condeses into what is known as a **Barr Body**. As a consequence, cells within the female organism have either a paternal X chromosome being expressed or a maternal X chromosome being expressed based on its embryonic origins. Approximately half the cells are expressing one X while the other half expresses the other X. X inactivation is also controlled by the attachment of methyl groups to cytosine, one of the nitrogenous bases of DNA nucleotides.

<span style="font-family: Arial,Helvetica,sans-serif;">__** Twin Studies and the Epigenome **__ <span style="font-family: Arial,Helvetica,sans-serif;">Twins develop from a single zygote, and therefore have identical genomes, This erases genetics as a variable when studying differences between the two individuals. It is also safe to assume that the observed differences in individuals is caused only by environmental factors that are exerted over the epigenome. The insight gained from studying twins gives us a better understanding of how nature and nurture work together to shape an individual. Twin studies have shown that some traits are more determined by an individual's genes, with little change caused by his/her environment. Other traits, however, are more strongly influenced by the environment despite having an identical genome.

<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: center;">Dyslexia is one trait that is heavily determined by one's genes, while the debilitating joint disease known as arthritis can be heavily influenced by one's environmental surroundings.

<span style="font-family: Arial,Helvetica,sans-serif;">The graph below shows incidences of both individuals within identical and fraternal twin sets gaining a certain characteristic. Once again, arthritis is a trait that is heavily influenced/brought about by the environment, meaning that it is more likely for just one twin to show signs of arthritis while the other does not. On the other hand, the genes coding for a set of twins' height is highly determined by the pair's genes, regardless of external influences. Allin all, the epigenome is affected to different degrees by the environment on different genetic loci.



<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: center;">Below is a NOVA video examining different sets of identical twins and how their gene expression has been influenced by their respective environments. media type="custom" key="12922034" align="center" width="159" height="146"

<span style="font-family: Arial,Helvetica,sans-serif;">**__ Nutrition and the Epigenome __** <span style="font-family: Arial,Helvetica,sans-serif;">Diet is a more easily studied extedrnal influence, and therefore is easily evaluated as to how it affects the epigenome more so than stress and behavioral differences between individuals. Since the epigenome constists of the molecular tags such as methyl groups that silence or allow gene expression, there are metabolic pathways that produce these functional molecules which can be traced back to very food we eat and nutrients we take in. Familiar nutrients like folic acid and B-vitamins are critical in methyl production, so depending on whether a person's diet is either high or lacking in these nutrients can quickly alter gene expression. <span style="font-family: Arial,Helvetica,sans-serif;"> <span style="font-family: Arial,Helvetica,sans-serif;">

<span style="font-family: Arial,Helvetica,sans-serif;">Nutrition plays a critical role during early development as a growing embryo. The mother's diet can cause changes that will potentially stick with her offspring into adulthood. If a mother is without nutries that promote methyl production, her child's genome may be "under-methylated" for life. This nutrient deficiency, however can be counteracted to a large extent as long as the offspring eats a normal, healthy diet. <span style="font-family: Arial,Helvetica,sans-serif;">An agouti mouse study shows how the epigenome of mice is affected by their mother's nutrition during pregnancy. The Agouti gene is a gene that when expressed causes yellow coat in mice and obesity. When shut down, this inactive gene allows mice to grow brown coats and remain healthy and lean as long as other variables are controlled for. In this experiment, mothers who ate a healthy diet produced healthy offspring, whereas the ones who were fed BPA, a toxin that affects Agouti gene expression, gave rise to offspring who were obese and yellow in coat color.

<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: center; vertical-align: baseline;">Click [|here] for an auditory slideshow created by a post-doc student at Duke University studying these Agouti mice and how their genes are expressed differently due to exposure to certain chemicals and due to their mother's nutrition when she was pregnant.

<span style="font-family: Arial,Helvetica,sans-serif; font-size: 140%;">**The Essential Questions**
 * <span style="background-color: transparent; color: #000000; font-family: Arial,Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">What accounts for the expression of some genes and not others?
 * <span style="font-family: Arial,Helvetica,sans-serif;">What genetic controls are there in over-seeing gene expression?
 * <span style="font-family: Arial,Helvetica,sans-serif;">How much does the environment play a role affecting gene expression and what is the mechanism by which this may happen?

__**<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 140%;">Powerpoint: **__

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">

<span style="background-color: #ffffff; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 130%; vertical-align: baseline;">__** Review Questions **__ <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">1. Which of the following does epigenetics have a role in? <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">a) histone acetylation/methylation <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">b) genomic imprinting <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">c) DNA synthesis <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">d) a, b, and c <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">e) just a and b

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> 2. The epigenome <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> a) is static and is never prone to changes <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> b) is modified throughout an organism’s life cycle <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> c) is very sensitive during early embryonic as well as fetal development <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> d) is the set of molecular switches and markers that oversees gene expression <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> e) b, c, and d

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">3. The epigenome is most like <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">a) a remote control that turns a tv on and off <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">b) a tape player because a video cannot function without a tape player <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> c) a flock of birds deciding to land near a large lake instead of a small pond <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> d) a person reading a book because the person can choose which page to turn to <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> e) none of the above

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> 4. What signals during early development are present that may affect the epigenome regulatory effects? <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> a) maternal nutrition <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> b) levels of stress hormones in the mother <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> c) cellular signals <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> d) just a and c <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;"> e) a, b, and c

<span style="background-color: white; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 10pt;">5.All of the following are functions of transcription factors EXCEPT: <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;"> a) Formation of basal transcription complex <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;"> b) Turning on/off the transcription of appropriate genes <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;"> c) Regulation of cell cycle <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;"> d) involvement in termination of transcription <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;"> e) They can increase the rate of transcription by themselves

6. Upstream Factors a) Increase the efficiency of transcription by themselves b) Form the basal transcription complex c) Decrease the rate of transcription by themselves e) Are located downstream the transcription start point d) all of the above

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">7.The assembly of transcription factors on the DNA strand begins at which sequence? <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">a) TAAT <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">b) TATA <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">c) TTAA <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">d) ATAT <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">e) AATT

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">8. The one gene-one enzyme theory was proposed and proven by <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;"> a) Archibald Gerrod <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">b) George Beadle <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">c) Boris Ephrussi <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">d) Charles Darwin <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">e) b and c

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">9. Which stage(s) are used for prokaryotic termination? <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">a) elongation <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">b) translation <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">c) Rho independent termination <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">d) Rho dependent termination <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">e) c and d

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">10. The purpose of RNA polymerase II is all of the following EXCEPT: <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">a) To use DNA to make a string of tRNA <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">b) To use DNA to make a string of mRNA <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">c) To bind to the promoter site on a DNA strand <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">d) To create uracil to bind with adenine instead of thymine <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">e) none of the above

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">** __Essay__ **

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 110%; text-decoration: none; vertical-align: baseline;">a. Define and explain the general mechanisms by which transcription and translation work.

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 110%; text-decoration: none; vertical-align: baseline;">b. Describe how the following parts of transcription and translation facilitates gene expression in a eukaryotic cell. Choose two out of the four options below.

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 110%; text-decoration: none; vertical-align: baseline;"> 1. RNA polymerase <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 110%; text-decoration: none; vertical-align: baseline;"> 2. Start/Stop codons <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 110%; text-decoration: none; vertical-align: baseline;"> 3.General Transcription Factors <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 110%; text-decoration: none; vertical-align: baseline;"> 4.Upstream Transcription Factors

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 110%; text-decoration: none; vertical-align: baseline;">c. (i)Explain what the epigenome is and (ii) discuss the molecular mechanisms by which it controls gene expression.

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">__ **Annotated Bibliography** __

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">**Transcript Processing:** <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">[] <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">[] <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">[]

<span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">**Transcription** **Factors** <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">transcription factors and role in initiation- [] <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">different types of transcription factors-[|http://www.ndsu.edu/pubweb/~mcclean/plsc731/transcript/transcript1.htm] <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">transcriptional regulation in eukaryotes-[] <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">function of transcription factors, structure and clinical signigicance-[|http://en.wikipedia.org/wiki/Transcription_factor#cite_note-pmid9570129-0] <span style="font-family: 'Trebuchet MS',Helvetica,sans-serif;">role in initiation-[]

<span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">**Epigenetics** <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] examines identical twins and how environmental factors impact the epigenome. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] examines the impact of nutritional influences upon the epigenome, especially during prenatal development. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] explores the phenomenon of epigenetic inheritance, and how some epigenetic tags either stay in place or are erased and re-imprinted during early development <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] provides a concise, clear description of gemonic imprinting and the reasons why evolutionarily imprinting came to be. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] also describes genomic imprinting and provides very useful examples of how imprinting errors can cause serious diseases (Prader-Willi and Angelman’s Syndrome). <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] provides an in-depth description of what DNA methylation is. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link]provides an overview of epigenetics, genomic imprinting, and DNA methylation. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] provides the historical roots of how epigenetics came to be along with very helpful analogies/quotes describing what epigenetics is comparable to. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This[| link]describes the impact of epigentics in biology and how it is shaping the way scientists look at gene expression with respect to other variable factors. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] provides a auditory video about an Agouti mice study, providing a clear example of how nutritional factors affect the epigenome. <span style="background-color: transparent; color: #000000; font-family: 'Trebuchet MS',Helvetica,sans-serif; font-size: 13px; text-decoration: none; vertical-align: baseline;">This [|link] provides an interactive activity that gives the crucial basics of DNA, histone proteins, acetylation, methylation, and gene expression in general.