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Ch. 21 - Genomic Analysis

Chapter 20, Problem 29

Although a single activator may bind many enhancers in the genome to control several target genes, in many cases, the enhancers have some sequence conservation but are not all identical. Keeping this in mind, consider the following hypothetical example:

- Undifferentiated cells adopt different fates depending on the concentration of activator protein, Act1.
- A high concentration of Act1 leads to cell fate 1, an intermediate level leads to cell fate 2, and low levels to cell fate 3.
- Research shows that Act1 regulates the expression of three different target genes (A, B, and C) with each having an enhancer recognized by Act1 but a slightly different sequence that alters the affinity of Act1 for the enhancer. Act1 has a high affinity for binding the enhancer for gene A, a low affinity for the gene B enhancer, and an intermediate affinity for the gene C enhancer.

From these data, speculate on how Act1 concentrations can specify different cell fates through these three target genes? Furthermore, which target genes specify which fates?

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Hello everyone and welcome to today's video. So we have a gene called TP 53 is a gene responsible for the production of a protein called a tumor protein. P 53. This protein is a tumor suppressor. So it's going to prevent tumors and can regulate cell division and keeps it from growing uncontrollably. How will they respond if the DNA damage Is irreparable? So normally these p. protein which by the way it's called the Guardian of the cell because it is going to protect it against tumors or mutations of DNA. So when this DNA damage is irreparable, this protein is going to signal the repair of the D. N. A. However in the question it states that the DNA cannot be repaired. So instead this protein is going to signal the cell to undergo apoptosis or basically kill the cell to prevent these mutation from spreading once the cell divides. So P. T. T. Three is going to prevent completely this cell division, it is not going to slow it down. It is going to completely prevent it to prevent the spread of this tumor to prevent the growth of the tumor. That can come from uncontrollable cell division and instead it is just going to signal the cell to undergo apoptosis and by doing so it will kill the cell. So the correct answer choice here is going to be answer choice B. This is what's done once DNA damage in the cell is irreparable. I really hope this video helped you and I hope to see you on the next one
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Textbook Question

Whole-exome sequencing (WES) is helping physicians diagnose a genetic condition that has defied diagnosis by traditional means. The implication here is that exons in the nuclear genome are sequenced in the hopes that, by comparison with the genomes of nonaffected individuals, a diagnosis might be revealed.

What are the strengths and weaknesses of this approach?

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Textbook Question

Whole-exome sequencing (WES) is helping physicians diagnose a genetic condition that has defied diagnosis by traditional means. The implication here is that exons in the nuclear genome are sequenced in the hopes that, by comparison with the genomes of nonaffected individuals, a diagnosis might be revealed.

If you were ordering WES for a patient, would you also include an analysis of the patient's mitochondrial genome?

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Textbook Question

Recall that when the HGP was completed, more than 40 percent of the genes identified had unknown functions. The PANTHER database provides access to comprehensive and current functional assignments for human genes (and genes from other species).

Go to http://www.pantherdb.org/data/. In the frame on the left side of the screen locate the 'Quick links' and use the 'Whole genome function views' link to a view of a pie chart of current functional classes for human genes. Mouse over the pie chart to answer these questions. What percentage of human genes encode transcription factors? Cytoskeletal proteins? Transmembrane receptor regulatory/adaptor proteins?

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Textbook Question

Hereditary spherocytosis (HS) is a disorder characterized by sphere-shaped red blood cells, anemia, and other abnormal traits. Ankyrin-1 (ANK1) is a protein that links membrane proteins to the cytoskeleton. Loss of this activity is associated biochemically to HS. However, Gallagher et al. (2010) (J. Clin. Invest. 120:4453–4465) show that HS can also be caused by mutations within a region from -282 to -101 relative to the transcriptional start site, which lead to constitutive transcriptional repression in erythroid cells due to local chromatin condensation. Propose a hypothesis for the function of the -282 to -101 region of the ANK1 gene.

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Textbook Question

Transcription factors play key roles in the regulation of gene expression, but to do so, they must act within the nucleus. Like most proteins, however, transcription factors are translated in the cytoplasm. To enter the nucleus, transcription factors contain nuclear localization signals, which in some cases can work only when bound to some other molecule such as a steroid hormone. After entering the nucleus, transcription factors must bind to appropriate DNA sites and must interact with other transcription proteins at promoters, enhancers, and silencers. Transcription factors then activate or repress transcription through their activation or repression domains. Many drug therapies target transcription factors. Based on the information provided above, suggest three specific mechanisms through which a successful drug therapy, targeted to a transcription factor, might work.

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