Chapter 16, Regulation of Gene Expression in Eukaryotes Video Solutions, Essentials of Genetics

Problem 1

In this chapter, we focused on the regulation of gene expression in eukaryotes. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter:
(a) How do we know that transcription and translation are spatially and temporally separated in eukaryotic cells?
(b) How do we know that DNA methylation is associated with transcriptionally silent genes?
(c) How do we know that core-promoter elements are important for transcription?
(d) How do we know that the orientation of promoters relative to the transcription start site is important while enhancers are orientation independent?
(e) How do we know that alternative splicing enables one gene to encode different isoforms with different functions?
(f) How do we know that small noncoding RNA molecules can regulate gene expression?

Jennifer Stoner

Numerade Educator

00:45

Problem 2

Review the Chapter Concepts list on p. $302 .$ The third concept describes how transcription initiation requires the assembly of transcription regulatory proteins on DNA sites known as promoters, enhancers, and silencers. Write a short essay describing which types of trans-acting proteins bind to which type of cis-regulatory element, and how these interactions influence transcription initiation.

Jennifer Stoner

Numerade Educator

00:29

Problem 3

What features of eukaryotes provide additional opportunities for the regulation of gene expression compared to bacteria?

Sam Limsuwannarot

Numerade Educator

04:19

Problem 4

Describe the organization of the interphase nucleus. Include in your presentation a description of chromosome territories and interchromatin compartments.

Shiksha Dutta

Numerade Educator

04:19

Problem 5

Describe the organization of the interphase nucleus. Include in your presentation a description of chromosome territories and interchromatin compartments.

Shiksha Dutta

Numerade Educator

04:16

Problem 6

Present an overview of the manner in which chromatin can be remodeled. Describe the manner in which these remodeling processes influence transcription.

Dennis Howard

Numerade Educator

04:14

Problem 7

Distinguish between the cis-acting regulatory elements referred to as promoters and enhancers.

Amy Jackson

Numerade Educator

00:37

Problem 8

Describe the manner in which activators and repressors influence the rate of transcription initiation. How might chromatin structure be involved in such regulation?

Sam Limsuwannarot

Numerade Educator

00:32

Problem 9

Many promoter regions contain CAAT boxes containing consensus sequences CAAT or CCAAT approximately 70 to 80 bases upstream from the transcription start site. How might one determine the influence of CAAT boxes on the transcription rate of a given gene?

Sam Limsuwannarot

Numerade Educator

04:10

Problem 10

Research indicates that promoters may fall into one of two classes: focused or dispersed. How do these classes differ, and which genes tend to be associated with each?

Breanna Kloczkowski

Numerade Educator

07:00

Problem 11

Explain the features of the Initiator (Inr) elements, BREs, DPEs, and MTEs of focused promoters.

Kevin Chimex

Numerade Educator

04:32

Problem 12

List three types of alternative splicing patterns and how theylead to the production of different protein isoforms.

Shiksha Dutta

Numerade Educator

01:12

Problem 13

Consider the $C T / C G R P$ example of alternative splicing shown in Figure $16.9 .$ Which different types of alternative splicing patterns are represented?

Mikayla Stephens

Numerade Educator

03:29

Problem 14

Explain how the use of alternative promoters and alternative polyadenylation signals produces mRNAs with different $5^{\prime}-$ and $3^{\prime}$ -ends.

Sana Riaz

Numerade Educator

00:18

Problem 15

The regulation of mRNA decay relies heavily upon deadenylases and decapping enzymes. Explain how these classes of enzymes are critical to initiating mRNA decay.

Sam Limsuwannarot

Numerade Educator

02:13

Problem 16

Nonsense-mediated decay is an mRNA surveillance pathway that eliminates mRNAs with premature stop codons. How does the cell distinguish between normal mRNAs and those with a premature stop?

John Koskinen

Numerade Educator

02:33

Problem 17

In $1998,$ future Nobel laureates Andrew Fire and Craig Mello, and colleagues, published an article in Nature entitled, "Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans." Explain how RNAi is both "potent and specific."

Pronoy Sinha

Numerade Educator

02:26

Problem 18

Present an overview of RNA interference (RNAi). How does the silencing process begin, and what major components participate?

Dennis Howard

Numerade Educator

05:02

Problem 19

RNAi may be directed by small interfering RNAs (siRNAs) or microRNAs (miRNAs); how are these similar, and how are they different?

Shiksha Dutta

Numerade Educator

05:43

Problem 20

miRNAs target endogenous mRNAs in a sequence-specific manner. Explain, conceptually, how one might identify potential mRNA targets for a given miRNA if you only know the sequence of the miRNA and the sequence of all mRNAs in a cell or tissue of interest.

Khalida Dawar

Numerade Educator

01:24

Problem 21

In principle, RNAi may be used to fight viral infection. How might this work?

Nicole Smina

Numerade Educator

01:54

Problem 22

Competing endogenous RNAs act as molecular "sponges." What does this mean, and what do they compete with?

Josee Pacheco

Numerade Educator

06:28

Problem 23

How and why are eukaryotic mRNAs transported and localized to discrete regions of the cell?

Shiksha Dutta

Numerade Educator

01:45

Problem 24

How is it possible that a given mRNA in a cell is found throughout the cytoplasm but the protein that it encodes is only found in a few specific regions?

Miwa Wenzel

Numerade Educator

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Problem 25

How may the covalent modification of a protein with a phosphate group alter its function?

James Kiss

Numerade Educator

06:26

Problem 26

The proteasome is a multi-subunit machine that unfolds and degrades proteins. How is its activity regulated such that it only degrades certain proteins?

Brett Donadeo

Numerade Educator

02:11

Problem 27

When challenged with a low oxygen environment, known as hypoxia, the body produces a hormone called erythropoietin (EPO), which then stimulates red blood cell production to carry more oxygen. Transcription of the gene encoding EPO is dependent upon the hypoxia-inducible factor (HIF), which is a transcriptional activator. However, HIF alone is not sufficient to activate EPO. For example, Wang et al. (2010. PLOS ONE 5:
e10002 showed that HIF recruits another protein called p300 to an enhancer for the EPO gene. Furthermore, deletion of p300 significantly impaired transcription of the EPO gene in response to hypoxia. Given that $\mathrm{p} 300$ is a type of histone acetyl transfer-

Rabeya Zahid

Numerade Educator

02:32

Problem 28

The TBX20 transcription factor is important for the development of heart tissue. Deletion of the $T b \times 20$ gene in mice results in poor
heart development and the death of mice well before birth. To better understand how TBX20 regulates heart development at a genetic level, Sakabe et al. (2012. Hum. Mol. Genet. 21:21942204 ) performed a transcriptome analysis in which they compared the levels of all mRNAs between heart cells from wild-type mice and mice with $\mathrm{Tb} \times 20$ deleted.
(a) How might such a transcriptome analysis provide information about how TBX20 regulates heart development?
(b) This study concluded that TBX20 acts as an activator of some genes but a repressor of other genes in cardiac tissue. How might a single transcription factor have opposite effects on the transcription of different genes?

James Kiss

Numerade Educator

00:47

Problem 29

Many viruses that infect eukaryotic cells express genes that alter the regulation of host gene expression to promote viral replication. For example, herpes simplex virus- 1 (HSV-1) expresses a protein called ICP0, which is necessary for successful viral infection and replication within the host. Lutz et al. (2017. Viruses
9: 210 ) showed that ICP0 can act as a ubiquitin ligase and target the redundant transcriptional repressors ZEB1 and ZEB2, which leads to upregulation of the miR-183 cluster (a set of three miRNAs transcribed from the same locus).
(a) What likely happens to ZEB1 and ZEB2 upon HSV-1 infection?
(b) How may ICP0 expression in a host cell lead to upregulation of the miR-183 cluster?
(c) Speculate on how miR-183 cluster upregulation may benefit the virus.

Eleanor Behling

Numerade Educator