You are working on a newly described transcription factor that appears to have an important role in the differentiation of embryonic stem cells into neural lineage. Deleting your transcription factor is resulting in upregulation of some genes and downregulation of some genes. a. Speculate 2 mechanisms by which your transcription factor is responsible for the regulation of both these set of genes. b. Describe a combination of 2 different techniques you will utilize to distinguish direct targets versus indirect targets.

You are working on a newly described transcription factor that appears to have an important role in the differentiation of embryonic stem cells into neural lineage. Deleting your transcription factor is resulting in upregulation of some genes and downregulation of some genes. a. Speculate 2 mechanisms by which your transcription factor is responsible for the regulation of both these set of genes. b. Describe a combination of 2 different techniques you will utilize to distinguish direct targets versus indirect targets.

Human Anatomy & Physiology (11th Edition)

11th Edition

ISBN:9780134580999

Author:Elaine N. Marieb, Katja N. Hoehn

Publisher:Elaine N. Marieb, Katja N. Hoehn

Chapter1: The Human Body: An Orientation

Section: Chapter Questions

Problem 1RQ: The correct sequence of levels forming the structural hierarchy is A. (a) organ, organ system,...

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The transcription factor Pax6 is required continuallyduring the life of a mouse (or a human) for the development and maintenance of the retina. HomozygousPax6 knockout mice die soon after birth because Pax6protein is also required in essential organs, such as thepancreas.a. In order to study the role of Pax6 in eye development, a researcher wants to generate a mouse thatexpresses Pax6 everywhere except in its eyes.Describe how you could construct such a mouse.b. Suppose the scientist wants to create a mousesimilar to that in part (a), but in which the eye cellsfrom which Pax6 function has been removed nowexpress GFP. Marking the cells in this way willallow the investigator to see the shapes of the Pax6−eye cells more easily than if they did not expressGFP. Diagram a Pax6 gene construct that wouldenable her to do this experiment.
MyoD is a transcriptional activator that turns on theexpression of several muscle-specific genes in humancells. The Id gene product inhibits MyoD action.a. One possibility is that the Id protein directly represses the expression of these muscle-specificgenes. Explain how Id would function if it were arepressor.b. Another possibility is that Id inhibits musclespecific gene transcription indirectly, by preventingMyoD function. Explain how Id could function asan indirect repressor.c. Suppose you know the amino acid sequence ofthe Id protein. How might this information supportthe hypothesis in part (a) or in part (b)?
a. Would you expect a cell to continue or to stopdividing at a nonpermissive high temperature if itis a temperature-sensitive Ras mutant whose protein product is fixed in the GTP-bound form atnonpermissive temperature?b. What would you expect if you had a temperaturesensitive mutant in which the Ras protein staysin the GDP-bound form at high temperature?
For each of the terms in the left column, choose thebest matching phrase in the right column.a. basal factors 1. organizes enhancer/promoter interactionsb. repressors 2. pattern of expressiondepends on which parenttransmitted the allelec. CpG 3. activates gene transcriptiontemporal- and tissue-specificallyd. imprinting 4. site of DNA methylatione. miRNA 5. identifies DNA-binding sitesof transcription factorsf. coactivators 6. bind to enhancersg. epigenetic effect 7. bind to promotersh. insulator 8. bind to activatorsi. enhancer 9. prevents or reduces geneexpression posttranscriptionallyj. ChIP-Seq 10. heritable change in geneexpression not caused byDNA sequence mutation
a. How do bacteria increase the efficiency of gene expression? Is this possible in eukaryotes? b. A mutation in the promoter of Gene K disrupts an enzyme binding site and results in the loss of Gene K expression. Is this change in gene expression likely happening at the transcriptional or the translational level? Explain. c. Propose three different mutations to prevent initiation, elongation, and termination of bacterial transcription, respectively. Explain how/why each mutation would prevent its respective step. (Hint: mutations can be in genes that encode proteins or regulatory DNA sequences)
The hunchback gene contains a 5′ transcriptional regulatory region, a 5′ UTR, a structural region (the coding sequences), and a 3′ UTR.a. What important sequences required to controlhunchback gene expression are found in the transcriptional regulatory region of hunchback?b. What sequence elements that encode specific protein domains are found in the structural region ofhunchback?c. Another important kind of sequence is located inthe 3′ UTR of the hunchback mRNA. What mightthis sequence do?
Genes in both prokaryotes and eukaryotes are regulated by activators and repressors.a. Compare and contrast the mechanism of functionof a prokaryotic repressor (for example, Lac repressor) with a typical eukaryotic repressor protein(a direct repressor).b. Compare and contrast the mechanism of functionof a prokaryotic activator (for example, CAP) witha typical eukaryotic activator protein.
A single UASG regulates the expression of threegenes, all of which are adjacent: GAL7 and GAL10 asdescribed in Problem 8, and also GAL1.a. Would you expect these genes to be transcribedinto individual transcripts, or to be cotranscribed asone mRNA? Explain.b. How could you determine experimentallywhether each gene is transcribed separately orinstead that the three are cotranscribed into asingle mRNA?c. GAL1 and GAL10 are not only adjacent to eachother, but also are transcribed divergently with asingle UASG between them. Describe experimentsusing GFP and RFP transgenes that would allowyou to determine which of the four GAL4 bindingsites in this UASG element is (are) important for thetranscription of GAL1 and/or GAL10.
The chart below is a position specific scoring matrix (PSSM, a logarithmic transformed matrix) for a transcription factor binding site. (1). Evaluate a sequence “GACATTCA” to find out which segment of the sequence fits the binding site best. (2) What is the max score that a sequence can have with this PSSM? (3) What is the minimum score a sequence can have with this PSSM?
Wilms tumor 1, or nephroblastoma, is caused by mutations in the WT1 gene, which encodes a transcription factor. You have identified a novel variant in WT1: Arg422Pro. You have control cells and cells that have been engineered to carry the homozygous WT1 p.Arg422Pro mutation. You want to assess effects of this mutation on a variety of endpoints. For each endpoint listed below, choose the one technique is best suited to answer the question. Choose from: array CGH, qRT-PCR, qPCR, RNA-seq, FISH, in situ hybridization, western blot, immunostaining, WT1 ChIP-seq, WT1 ChIP-PCR, ATAC-seq, 3C Endpoint Technique? WT1 protein amount (quantitative) Western blot WT1 protein binding to all enhancers, genome-wide Chip-seq WT1 mRNA amount (quantitative) WT1 protein subcellular localization Quantitative assessment of all mRNAs in these cells (genome-wide) RNAseq Chromatin interactions between a specific WT1 chromatin binding site (identified above)…
a) hours: 0 2 567 DMC1 SPS1 hours: 0 2 5 6 7 9 11 DIT1 SPS100 Oxygen level (% normal) b) 120 100 FIGURE 4.6. Comparison of Northern blots with DNA microarray data. a) Results from four individual Northern blots examining four different genes and measuring mRNA production over time, as indicated. b) Results from a series of microarrays for the same four genes of interest. Note the color scale on the bottom of b), where bright green indicates a 20-fold repression and bright red indicates a 20-fold induction. Black indicates no change in transcription (i.e., the merged microarray spot would have appeared yellow). 80 60 40 20 0 1 2 gene X gene Y gene Z 3 1 hour 1.0 1.0 b) 1.0 hours: 0.5 2 5 7 9 11 DMC1 SPS1 DIT1 SPS100 fold repressed >20 10x 3x3x10x >20 1:1 fold induced 4 5 6 7 8 9 10 11 Time (hours) 3 hour 2.2 4.5 1.5 5 9 hour hour 1.0 0.15 0.95 0.05 2.0 2.0 FIGURE 4.7 Transcriptional response of three genes to the gradual loss of oxygen. a) Graph of oxygen con- sumption over time by…
. a. Mice engineered to block expression of the geneencoding the telomerase protein age at a muchfaster rate than normal and have decreased lifespans. When expression of the telomerase proteinis turned back on in mice that are prematurely old,many negative effects of this aging are rapidly anddramatically reversed. Provide a possible explanation for these results.b. The results of these mouse experiments have ledsome researchers to propose that treatments thatcould lead to overexpression of the telomerase genemight serve as a “fountain of youth” leading to reversal of aging in humans. Why do you think weshould be very cautious about trying such treatments? Your argument should address why it mightbe advantageous to multicellular organisms for mostof their somatic cells not to express telomerase.