Help
Options
Didn't know it?
click below
click below
Knew it?
click below
click below
Don't Know
Remaining cards (0)
Know
retry
shuffle
restart
0:00
Embed Code - If you would like this activity on your web page, copy the script below and paste it into your web page.
Normal Size Small Size show me how
Normal Size Small Size show me how
14
Gene regulation in Eukaryotes
| Question/Answer | Term/Definition |
|---|---|
| How does bacteria perform gene regulation in response to an environment that lacks glucose yet contains lactose? | The lac operon |
| lac operon | Gene regulation involves activator protein (CAP), and a repressor protein (lac repressor). Effector molecules (cAMP and allolactose) regulate CAP and the lac repressor binding to regulatory DNA sequences (CAP site operator) near promoter for lac operon. |
| What do the CAP and lac repressor proteins determine? | It determines if the sigma factor protein and the RNA polymerase core enzyme activate transcription. |
| What do both prokaryotes and eukaryotes have in common through gene regulation? | Both involve activator proteins, repressor proteins, effector molecules, and regulatory DNA sequences. |
| Difference between eukaryote and prokaryote gene regulation? | Eukaryote gene regulation is a lot more complex. |
| Why is Eukaryote gene regulation so complex? | It needs to produce multicellular organisms with cells in each tissue having unique phenotypes. Ex: white blood cell (leukocyte) and muscle cell have same collection of structural genes. |
| Why is gene regulation so important in Eukaryotes? | It ensures that leukocyte expresses leukocyte-specific proteins, while a muscle cell expresses muscle-specific proteins. Many eukaryotic organisms progress from a fertilized egg through complex development stages to produce the mature adult. |
| What does gene regulation do in Eukaryotes? | It ensures that embryonic genes are expressed only during embryonic development, while other genes are expressed in an adult. |
| What does regulation of a typical eukaryotic gene involve? | Combinatorial control |
| A single eukaryotic gene can be regulated by... (1st one of combinatorial control) | Activator proteins binding to enhancer DNA sequences. |
| A single eukaryotic gene can be regulated by... (2nd one of combinatorial control) | Repressor proteins binding to silencer DNA sequences. |
| A single eukaryotic gene can be regulated by... (3rd one of combinatorial control) | Regulation of activator and repressor protein function. This regulation of activator and repressor protein involves effector molecules, covalent modification, and protein-protein interactions. |
| A single eukaryotic gene can be regulated by... (4th one of combinatorial control) | Modifying the structure of chromatin to activate or repress transcription. Modifying chromatin involves chemically modifying histone proteins or altering the arrangement of nucleosomes near the core promoter of a gene. |
| A single eukaryotic gene can be regulated by... (5th one of combinatorial control) | DNA methylation to silence transcription. The methylation of cytosine bases near the core promoter region of a gene inhibits transcription. |
| Combinatorial control | Provides mechanism by which relatively small numbers of transcription factors can control the expression of a much larger number of genes with a finely tuned temporal and spatial patterns. |
| Core promoter in transcription of eukaryotes | Determines where RNA polymerase II will bind to the DNA and begin transcription. |
| What is included in the core promoter? | The TATA box (-25 sequence), which serves as the binding site for the general transcription factor protein TFIID and the +1 site, the first base in the template DNA strand that is transcribed by RNA polymerase II. |
| What has to happen for transcription to occur? | The TATA box and the +1 site must be present. If those are the only sequences present upstream of a gene, the gene will be transcribed at a low yet constant rate (the so-called basal level of transcription). |
| What is an addition to the core promoter? | Regulatory promoter. |
| Regulatory promoter | Required for transcription levels higher than the basal level provided by the core promoter. |
| What is a common regulatory promoter component that's present in many eukaryotic genes? | The CAAT box. |
| The CAAT box | located -80 and has a sequence 5'-GGCCAATCT-3' The CAA is underlined. |
| What is another common regulatory component that is present in eukaryotic genes? | GC box |
| GC box | 5'-GGGCGG-3' the GC is underlined. It is located at -100 |
| What is the function of the GC box and CAAT box? | They are the binding sites for certain activator proteins. Thus the CAAT and GC boxes can be considered enhancers adjacent to many eukaryotic structural genes. |
| Eukaryotic transcription factors | Proteins that influence the ability of RNA polymerase II to bind to a eukaryotic core promoter. |
| What is the first category of transcription factor proteins? | General Transcription factor proteins (GTF's) |
| What does GTF include? | TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH proteins |
| TFIID | Bind to core promoter by recognizing the TATA box (-25) DNA sequence, It is a multi-subunit protein "machine" composed of at least ten protein subunits. One of those proteins is TATA-binding protein (TBP) that binds directly yo the TATA box (-25) |
| TFIIA | Helps TFIID bind to the TATA box (-25) DNA sequence |
| TFIIB | Binds to TFIID and recruits the RNA polymerase II/TFIIF complex to the core promoter. |
| TFIIF | Always associated with RNA polymerase II. When the TFIIF protein binds to TFIIB, RNA polymerase II is located at the +1 site in the DNA. |
| TFIIE | Assists to separate the two DNA strands activating transcription |
| TFIIH | MultisubunitproteincomplexSubunitofTFIIHisDNAhelicase formsopencomplex,breakshydrogenbondsatTATA box(-25)sequence in DNA. Subunit Kinase phosphorylates RNA polymerase II to activate transcription. Uses chemical energy in ATP to activate RNA polymerase II. |
| What does GTF do that influences the ability of RNA polymerase II to bind to a eukaryotic core promoter? | Function, recruit RNA polymerase II to the core promoter to begin transcription.Required for all transcription events. If GTF's are the only ones involved, gene is transcribed at basal level.GTF are required for transcription rates above this basal level. |
| What is the second category of transcription factor proteins? | Regulatory Transcription factor proteins. |
| What does Regulatory transcription factor proteins do that influence the ability of RNA polymerase II to bind to a eukaryotic core promoter? | Regulatestranscriptionitincreasesordecreasesbasallevel.ActivatorandRepressorproteinsdothis.Theproteinsareonlyexpressed in certain tissues or certain times during development. Thus playing a critical role in tissue-specific ot time-specific gene expression |
| Activator protein | Increases level of transcription above basal level |
| Repressor protein | Decreases level of transcription below basal level. |
| What are the transcription factor proteins? | Trans-acting factors, and cis-acting elements. |
| Trans-acting factors | Can regulate genes found throughout the genome and bind to the DNA sequence called Cis-acting elements. |
| Cis-acting elements | The DNA binding sites for these transcription factors tend to be near the genes they control. They do not need to be immediately adjacent to the core promoter. Some binding sites can be within the gene they control or can be thousands of bp away |
| Mediator protein | Communicate signals from activator and repressor proteins to RNA polymerase II. Mediator thus serves as a link between regulatory transcription factors, the GTF proteins, and RNA polymerase II thereby determining the overall rate of transcription. |
| enhancer DNA sequences | Stimulate transcription of controlled gene above the basal level. They are the binding site for activator proteins. |
| Silencer DNA sequences | Down-regulate transcription of the controlled gene below the basal level. The binding site for repressor proteins. |
| What can binding of the regulatory transcription factors to the DNA sequences do? | Increase the rate of transcription, and Decrease the rate of transcription. |
| How can binding of the Regulatory transcription factor to the DNA sequences increase the rate of transcription? | Transcription can increase 10 to 1000-fold when activator proteins bind to enhancer DNA sequence (up-regulates). Activator proteins and enhancer DNA sequences are generally responsible for tissue-specific expression of a gene. |
| How can binding of the regulatory transcription factor to the DNA sequences Decrease the rate of transcription? | Transcription can decrease below the basal level when repressor proteins bind to silencer DNA sequence (down-regulation). Repressor proteins and silencer DNA sequences are generally responsible for tissue-specific repression of a gene. |
| How can a particular gene be regulated? | Can be regulated by transcription factor proteins bound to different combinations of enhancer and silencer DNA sequences. Combination of the transcription factor proteins and regulatory DNA sequences involved determines transcription pattern of the gene. |
| a-helicase (how it is formed) (info with it and transcription factor proteins) | Most transcription factor proteins contain a-helicase, a type of protein secondary structure. A a-helix is produced when certain amino acids in the polypeptide sequence interact through hydrogen bonding to produce a helical structure. |
| a-helicase (what it is) | Is the proper width to bind to the major groove in DNA. It is often used by transcription factors proteins to recognize specific base pair sequences located in the major groove of the DNA. |
| Where have transcription factor proteins been identified in? | It has been identified in many organisms, including viruses, bacteria, fungi, plants, and animals. |
| What do all transcription factor proteins contain? | They contain conserved structural features that are important in either binding to regulatory DNA sequences, effector molecules, or other transcription factor proteins. |
| What are four of the common structural motifs? (based on the a-helix structure) | Helix-turn-helix (HTH) motif, Basic helix-loop-helix (bHLH) motif, Zinc finger motif, Leucine zipper motif. |
| Where are structural motifs found in? | They are found in transcription factor proteins. |
| What is the first structural motif and how does it work? (part 1) | The HTH motif includes two a-helicase separated by a "turn" of 3-4 amino acids. One a-helix is called the recognition helix and functions to bind to specific base pair sequences in the DNA major groove. |
| What is the first structural motif and how does it work? (part 2) | The recognition helix also includes basic (positively charged) amino acids that bind to the negatively charged DNA backbone. The helix-turn-helix motif is found in both prokaryotic and eukaryotic transcription factor proteins. |
| What is the first structural motif and how does it work? (part 3) Example | For example many of the transcription factor proteins that we have discussed previously contain the HTH motif including sigma factor, the lac repressor protein, and the catabolite activator protein (CAP) |
| What is the second structural motif and how does it work (part 1) | Basic helix-loop-helix (bHLH) motif. it is similar to the helix turn-helix motif containing a recognition helix that binds to the DNA major groove. However instead of a turn bHLH transcription factors have a long amino acid loop to connect two a-helicases |
| What is the second structural motif and how does it work? (part 2 | bHLH transcription factors play a important role in cell division and differentiation. For example the MyoD and e-mye proteins are transcription factor proteins that contain the bHLH motif. |
| MyoD protein | activates the muscle-specific genes |
| e-myc protein | activates genes involved in cell division |
| What is the third structural motif and how does it work? (part 1) | Zinc finger motif is composed of a finger-like structure composed of an a-helix (i.e, the recognition helix) and two B strands (another type of protein secondary structure). |
| What is the third structural motif and how does it work? (part 2) | Electrostatic interactions between zinc ions (Zn 2+) and negatively charged amino acid chains within the transcription factor protein stabilize the zinc finger motif. |
| What is the third structural motif and how does it work? (part 3) | Steroid hormone receptors, including the glucocorticoid receptor protein testosterone receptor protein and the estrogen receptor protein contain zinc finger motifs |
| What is the fourth structural motif and how does it work? (part 1) | Leucine zipper motif not only contains a recognition helix, but also contains a second a-helix with many hydrophobic leucine amino acids. |
| What is the fourth structural motif and how does it work? (part 2) | When the leucine-rich a-helicase of two leucine zipper transcription factors interact they form a coiled cell to exclude water. The coiled-coil resembles a zipper with interlocking leucine amino acids. |
| What is the fourth structural motif and how does it work? (part 3) | The DNA sequence is bound by recognition helices that extend from the coiled-coil region of these two transcription factor proteins. The CREB protein contains a leucine zipper motif. |
| What four transcription factor motif structures permit transcription factor proteins to bind to each other? | HTH motif, bHLH motif, zinc finger motif, and leucine zipper motif. |
| homodimer | Two identical transcription factor proteins interact to form this transcription factor homodimer. |
| heterodimer | Two different transcription factor proteins can interact to form a heterodimer. |
| Example of homodimers | Both CAP protein and the lac repressor proteins are homodimers,composed of two identical transcriptional factor protein with HTH motifs. Higher order interactions (trimers, tetramers) are also possible when transcription factor proteins bind to each other |
| What is something that may or may not happen? (activator protein and repressor protein) | If activator is present in a cell it does not always bind to an enhancer DNA sequence and up-regulate transcription. Similarly, a repressor protein does not always bind to a silence DNA sequence and repress transctiption. |
| What three ways does DNA-binding activities of activator and repressor proteins get regulated? | Effector binding, transcription factor dimerization and covalent modification. |
| Describe the first step (effector binding) of DNA binding activities of activator and repressor proteins get regulated (part 1) | Small effector molecules can bind to transcription factor proteins, change the conformation (shape of the transcription factor, and influence the ability of the transcription factor protein to bind to enhancer or silencer DNA sequences. |
| Describe the first step (effector binding) of DNA binding activities of activator and repressor proteins get regulated (part 2) | In animals, steroid hormones such as glucocorticoid, testosterone, and estrogen are effector molecules that regulate the functions of transcription factor proteins. |
| Describe the second step (transcription factor dimerization) of DNA binding activities of activator and repressor proteins get regulated | Transcription factor dimerization is the formation of transcription factor homodimers or heterodimers influence binding to enhancer or silencer DNA sequences. |
| Describe the third step (covalent modification) of DNA binding activities of activator and repressor proteins get regulated. | Covalent modification is the addition of phosphate groups (phosphorylation) to activator or repressor proteins can stimulate binding to enhancer or silencer DNA sequences. |
| When do we use the modifications of DNA binding activities of activator and repressor proteins get regulated? | For a gene one or more of the mechanisms maybe involved in regulating gene expression. |
| Example of when we use modification of DNA binding activities of activator and repressor proteins get regulated? | ex: the glucocorticoid receptor transcription factor protein is regulated by effector binding and dimerization while the CREB transcription factor protein is regulated by dimerization and covalent modification. |
| Through what does eukaryotic regulatory transcription factors influence RNA polymerase II activity? | The activity happens through TFIID, mediator, the enzymes involved in chromatin remodeling, and the enzymes involved in DNA methylation. |
| What do regulatory transcription factor proteins do? | Influence ability ofRNApolymeraseII totranscribeagene.However regulatory transcription factor proteins do not typically bind to RNA polymerase II directly.Instead they communicate DNA binding indirectly to RNA polymerase II through other protein complexes |
| What is up regulated in transcription? | Activator protein encourages TFIID to bind to the TATA box, and TFIID then recruits the other general transcription factor and RNA polymerase II to the +1 site. |
| What is down regulated in transcription? | RepressorproteinbindstosilencerDNAsequenceadjacenttoagene.TherepressorproteinthenpreventsTFIIDfrombindingtotheTATA box.Abscense of TFIID on core promoter prevents other general transcription factors and RNA polymerase II from binding to the core promoter. |
| What is a mediator protein complex? | It is a protein complex that mediated the interaction between the regulatory transcription factors (i.e activator and repressor proteins) and RNA polymerase II |
| Results if mediator activates RNA polymerase II | transcription begins. |
| What happens when an activator protein binds to an enhancer DNA sequence? | The activator protein activates mediator and mediator then activate TFIIH. Which the RFIIH acts as helicase to sperate the strand. It acts as kinase, phosphorylating RNA polymerase II to begin transcription. |
| What happens when a repressor protein binds to a silencer DNA sequence instead? | Repressor protein inhibits activity of mediator. As a result mediator fails to activate TFIIH. and TFIIH fails to function preventing initiation of transcription. |
| What can form in the DNA between the enhancer/silencer DNA sequences and core promoter? | A loop to permit the proteins that bind each other in regulation of the mediator. |
| What are two example of gene regulation in the human body? | Glucocorticoid hormones (GCs),cAMP response element-binding protein (CREB) |
| glucocorticoid hormones (GCs) | They are released by adrenal glands in response to fasting, as well as physical activity. GC lead to increase in glucose synthesis, an increase in protein metabolism, and increase in fat metabolism and a decrease in inflammation. |
| What do glucocorticoid hormones (GCs) do to transciption? | It can increase the transcription of a gene above the basal level. |
| What is the first step of how glucocorticoid hormone can increase transcription of a gene above the basal level? | Glucocorticoid are steroid hormones which are nonpolar in structure. As a result the glucocorticoid cross the cytoplasmic membrane and enter the cytoplasm of a target cell. |
| What is the second step of how glucocorticoid hormone can increase transcription of a gene above the basal level? | Glucocorticoids act as effector molecules by binding to an activator protein called glucocorticoid receptor that is found in many cell types. Prior to glucocorticoid binding the glucocorticoid receptor is bound to HSP90 proteins. |
| glucocorticoid receptor | They are glucocorticoids act as effector molecules by binding to activator protein which is called glucocorticoid receptor that is found in many cell types. |
| HSP90 protein | helps maintain the properthree-dimensionalshape of the glucocorticoid receptor so the glucocorticoid receptor can bind to glucocorticoid hormones produced by the adrenal glands. HSP90 is released when glucocrticoid hormone binds to glucocorticoid receptor |
| What is the third step of how glucocorticoid hormone can increase transcription of a gene above the basal level? | glucocorticoid binding changes the conformation of glucocorticoid receptor, exposing a nuclear localization signal (NLS( |
| nuclear localization signal (NLS) | It is a polypeptide sequence that help to target the glucocorticoid receptor (with bound glucocorticoid) to the nuclease of the cell. |
| What is the fourth step of how glucocorticoid hormone can increase transcription of a gene above the basal level? | Two glucocorticoid receptors with bound glucocorticoid hormones form a homodimer in the cytoplasm of the cell. |
| What is the fifth step of how glucocorticoid hormone can increase transcription of a gene above the basal level? | The glucocorticoid receptor: glucocorticoid complex travels to the nucleus of the cell |
| What is the sixth step of how glucocorticoid hormone can increase transcription of a gene above the basal level? | The glucocorticoid receptor: glucocorticoid complex binds to two adjacent enhancer DNA sequences called glucocorticoid response elements (GREs). |
| glucocorticoid response elements (GREs) | GREs are common enhancers found adjacent to many genes involved in metabolism. |
| What is the seventh step of how glucocorticoid hormone can increase transcription of a gene above the basal level? | The glucocorticoid receptor: glucocorticoid complex bound to the GRE sequences activates transcription. |
| What other steroid hormones in humans are effector molecules that activate transcription by binding to cytoplasmic transcription factor proteins? | estrogen and testosterone. |
| Unlike glucocorticoid how does cAMP response element binding protein work? | Unlike glucocorticoid many signaling molecules in the body, such as peptide hormones, growth factor proteins, and cytokine proteins, are not able to diffuse through the cytoplasmic membrane into the cytoplasm of the target cell. |
| What happens in cAMP response element-binding protein instead of glucocorticoid? | Signaling proteins bind to cell receptors on the surface of a target cell, and the receptor binding signal is then transmitted to the nucleus to activate transciption. |
| Second example of gene regulation? | It is a gene regulation demonstrates how transcription is up-regulated when receptor binding activates the factor protein cAMP respone element-binding protein (CREB) |
| Transcription activation via CREB occurs when? 1 | A receptor embedded in the cytoplasmic membrane binds to a peptide hormone, growth factor, or cytokine protein. |
| Transcription activation via CREB occurs when? 2 | Receptor binding activates a G protein. |
| Transcription activation via CREB occurs when? 3 | The G protein activates adenyl cyclase inside the cell, which converts ATP into cAMP |
| Transcription activation via CREB occurs when? 4 | cAMP binds to and activates protein kinase A (PKS) |
| Transcription activation via CREB occurs when? 5 | PKA moves into the nucleus and phosphorylates an inactive CREB protein homodimer. |
| Transcription activation via CREB occurs when? 6 | The phosphorylated CREB protein homodimer binds to two adjacent enhancer sequences called cAMP response elements (CREs) |
| Transcription activation via CREB occurs when? 7 | The phosphorylated CREB homodimer bound to the CRE sequences activates transcription |
| How can arrangement of nucleosomes on DNA influence the transcription of a nearby gene? | For a gene to be transcribed, RNA polymerase II must be able to bind to the core promoter. If core promoter of a gene contains tightly packed nucleosomes (heterochromatin), RNA polymerase II struggles to find the core promoter. |
| What are the different arrangement of nucleosomes and which one is better? | Heterochromatin form of DNA is said to be in a closed conformation and transcription is limited. regions of chromosome with loosely packed or absent nucleosomes are called euchromatin (open conformation). |
| What is the result of euchromatin? | RNA polymerase II can better access a core promoter located in euchromatin and as a result transcription occurs more rapidly. |
| Heterochromatin and euchromatin | Recall that chromatin is a dynamic structure with a specific gene alternating between the closed (heterochromatin) and open (euchromatin) conformations depending on the needs of the cell. |
| When transcription is happening what causes chromatin to be open or closed conformation? | When an activator protein binds to an enhancer DNA sequence, chromatin is converted to the open conformation. When repressor protein binds to a silencer DNA sequence, chromatin is converted to the closed conformation. |
| B-globin gene. How it happens? | human b-globin gene. It encodes the b-globin protein components of hemoglobin, it is not normally expressed in many cell types, including fibroblast cells. |
| fibroblast analyzation from scientists in fibroblasts | When DNA region that encompasses the beta-globin gene from fibroblasts was analyzed with respect to nucleosomes, scientists discovered that nucleosomes were found at 200 base pairs (bp) intervals from -3000 to +1500 region of the gen. |
| What is something to note about fibroblast analyzation? | It is a closed confirmation region from -3000 to +1500 it includes regulatory promoter, core promoter, and the beginning portion of the b-globin gene. |
| What does heterochromatin have to do with fibroblast analyzation? | heterochromatin arrangement of nucleosomes makes the beta globin promoter inaccessible to GTF and RNA polymerase II. As a result b-globin gene is transcriptionally silent in fibroblasts. |
| B-globin gene in erythroblasts (precursor red blood cells). | When nucleosome arrangement surrounding b-globin gene was examined in erythroblasts nucleosome they were displaced from -500 to +200 region of the b-globin gene. |
| Something to note about and what is in erythroblasts | It is open conformation (euchromatin) area includes regulatory promoter, core promoter and beginning portion of b-globin gene. Thus GTF and RNA polymerase II can access the promoter region in erythroblasts leading to transcription of the b-globin gene. |
| What is difference between fibroblast and erythroblasts in arrangement of the b-globin gene? | fibroblast has inactive promoter because the heterochromatin arrangement. It is transcriptionally silent in fibroblasts. Erythrocytes have open conformation (euchromatin) so it is able to have active promoter and is able to transcribe. |
| What does alteration of the nucleosome in chromatin structure to promote transcription involve? | Covalent modification of histone proteins and the rearrangement of nucleosomes by ATP-dependent chromatin remodeling. |
| What does covalent modification include? | Includes the acetylation of histone proteins with nucleosomes. Enzymes called histone acetyltransferases (HATs) add acetyl groups to the tail regions within the histone protein, |
| Acetylation | neutralizes the positive charge on lysine amino acids within the histone tail disrupting the interaction between the histone tail and the negatively charged DNA backbone. |
| What is a result of acetylation in covalent modification? | Neutralization of the positive charges on the histone tails causes the histones to release from the DNA; the DNA is now more accessible for transcription. When transcription needs to be turned off the histones can be modified using histone deacetylase |
| histone deacetylase (HDAC) proteins | Remove acetyl groups from histones, restore positive charge on histone tail. Histone tail once again bind to negatively charged DNA backbone, and chromatin is converted from the open to closed conformation decreasing transcription of the gene. |
| What is to note about histone acetylation? | When activator binds to enhancer DNA sequence, activator recruits HATs to the promoter, activating transcription. Alternatively. when repressor proteins bind to silencer DNA sequences HDACs are recruited to the promoter, silencing transcription. |
| What does ATP-dependent chromatin remodeling process use? | Uses the energy in ATP to alter the spacing of the nucleosome near a gene. |
| What is an example of a ATP-dependent chromatin remodeling enzyme? | The multi-subunit SWI/SNE protein complex. The SWI/SNF protein complex performs at least two types of chromatin remodeling. |
| What is one type of chromatin remodeling? | SWI/SNF can change the distribution of nucleosomes along the DNA, creating larger gaps between adjacent nucleosomes. When these larger gaps between nucleosomes include the core promoter region of a gene transcription is activated. |
| What is the second type of chromatin remodeling? | SWI/SNF can replace the standard histone proteins (H2A, H2B, H3, and H4) within a nucleosome with histone variant proteins. The presence of these histone variant proteins within the modified nucleosome increases transcription. |
| What is histone variant proteins? | Presence of the histone variant proteins within the modified nucleosome increases transcription. |
| Methylation | Silencing of gene expression in many eukaryotes involve the methylation of DNA sequences near the core promoters of genes. |
| What does the methyl group that was added during methylation do? | It blocks the major groove or the DNA, preventing the binding of activator proteins to enhancer sequences in the DNA. Cytosine bases within CG- rich sequences are called CpG Islands and are typical targets for DNA methylation. |
| Where are CpG islands located? | They are located near the core promoter of genes. Typical CpG islands are 1,000-2,000 base pair (bp) long sequences that contain multiple CpG sites.(i.e many 5'-CG-3' dinucleotide sequences in a row. |
| Full methylation | Within CpG islands adding methyl groups to the cytosine bases on both DNA strands is called full methylation. Full methylation inhibits transcription. |
| Housekeeping genes | encode proteins that are required for the maintenance of a cell. For example, the structural genes that produce the enzyme involved in glycolysis are housekeeping genes. |
| What is unique about the promoters in housekeeping genes? | The promoters of housekeeping genes are typically unmethylated and as a result housekeeping genes are always transcribed. |
| Tissue-specific genes | are only expressed in certain cell types. In cell types in which these genes are not expressed the CpG island near promoter is fully methylated. In cell types in which the gene is expressed the CpG island near promoter in unmethylated, |
| The final example about DNA methylation | The inactive X chromosome (barr body) in female mammals contain methylated CpG islands adjacent to most structural genes; this high degree of CpG island methylation renders the Barr body transcriptionally silent. |
| What is the first way that DNA methylation is thought to silence the transcription of a nearby gene? | Methylation at CpG island near promoter of gene can block a activator protein from binding to enhancer DNA sequence |
| What is the second way that DNA methylation is thought to silence the transcription of a nearby gene? | Methyl-CpG-binding protein binds to a methylated CpG island, the methyl-CpG binding proteins recruit histone deacetylase (HDAC). HDAC then removes the acetyl groups from the histone tails, converting promoter region of gene into heterochromatin. |
| What is the results of the first way that DNA methylation is thought to silence the transcription of a nearby gene? | DNA methylation inhibits activator binding because methyl group on cytosine prevents activator protein from binding to DNA major groove in enhancer sequence. So transcription is inhibited. |
| What is the results of the second way that DNA methylation is thought to silence the transcription of a nearby gene? | Transcription of nearby genes are inhibited. |
| de novo methylation? what is it a process of? | The DNA methylation pattern in a cell is established by a process called de novo methylation |
| What does de novo do? | De novo methylation converts unmethylated DNA to fully methylated DNA (i.e., both DNA strands are methylate). It is a highly regulated process that is thought to occur during embryonic development or the differentiation of cells to form tissues. |
| What is unfortunate about de novo? | Details of de novo methylation are poorly understood. |
| What happens to the DNA methylation pattern established during de novo methylation? | It is preserved during cell division; If CpG island is fully methylated in a cell prior to mitosis, the same CpG island is fully methylated in the two daughter cells at the conclusion of mitosis. |
| Maintenance methylation | ensures that daughter cells produced by mitosis maintain the same methylation pattern as the parental cell. |
| Example of maintenance methylation | suppose that fully methylated DNA is replicated. Because DNA replication machinery does not methylate nitrogenous bases in the DNA during replication, the daughter DNA strands produced do not contain methylated cytosine bases. |
| What happens because of maintenance methylation? | daughter double-stranded DNA molecules are initially hemi methylated, with a methylated parental strand and a unmethylated daughter DNA strand. |
| What is the hemi methylated DNA recognized by? | The hemi methylated DNA is recognized by DNA methyltransferase, which subsequently methylates the cytosine bases on the daughter DNA strands, thus preserving the DNA methylation pattern established in the parental cell. |
| What does methylation of DNA explain? | A genetic phenomenon called genomic imprinting. |
| oogenesis | egg cell formation |
| spermatogenesis | sperm cell formation |
| genomic imprinting | oogenesis or spermatogenesis a specific gene can be methylated by de novo methylation. Following fertilization the methylation pattern is maintained as the fertilized egg begins to divide. |
| Example of genomic imprinting | If paternal allele for a gene is fully methylated by genomic imprinting that parental allele remains fully methylated in the cells of the offspring. |
| What do not necessarily influence the regulation of an adjacent gene? | the process that regulate expression of one structural gene such as activators/repressor proteins binding, histone acetylation, and DNA methylation |
| Insulator DNA sequences | define boundaries between genes; an insulator DNA sequence ensures that the gene regulation processes that affect one gene do not affect nearby genes |
| What are the two insulator DNA sequences? | Serve as the binding sites for proteins that act as a physical barriers for the HATs, HDACs and SWI/SNF protein complexes. and Serve as the binding sites for proteins that limit the effects of enhancer/silencer sequences. |
| Describe the first insulator DNA sequence | Serve as binding sites for proteins that act as physical barriers for HATs, HDACs and SWI/SNF protein complexes. For example, suppose a gene is flanked by two insulator DNA sequences, and HATs modify histone tails and activate transcription of the gene |
| Why does the first insulator DNA sequence have two insulator DNA sequences? | Because the proteins bound to insulators serve as physical barriers to the HATs, genes beyond the insulator sequences are not activated. |
| Describe the second insulator DNA sequence | Serve as the binding sites for proteins that limit the effects of enhancer/silencer sequences. Suppose Gene A has adjacent enhancer DNA sequence. Gene B is also near the enhancer DNA sequence. |
| Why is there a protein between gene a and b? | A protein bound to the insulator DNA sequence between Genes A and B ensures that the enhancer only activates Gene A; the transcription of Gene B is unaffected. Insulators can limit the effects of silencer DNA sequence in a similar way. |
Created by:
myliemilliemoo