In this chapter, we focused on how eukaryotic gene expression is regulated posttranscriptionally. 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:

How do we know that alternative splicing enables one gene to encode different isoforms with different functions?

In this chapter, we focused on how eukaryotic gene expression is regulated posttranscriptionally. 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:

How do we know that misregulation of mRNA stability and decay is a contributing factor in some cancers?

In this chapter, we focused on how eukaryotic gene expression is regulated posttranscriptionally. 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:

How do we know that double-stranded RNA molecules can control gene expression?

Write a short essay describing how an mRNA may be regulated in three different ways by specific cis-elements and RBPs.

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

Consider the CT/CGRP example of alternative splicing shown in Figure 18.3. Which different types of alternative splicing patterns are represented?

Explain how the use of alternative promoters and alternative polyadenylation signals produces mRNAs with different 5' and 3' ends.

Explain how a tissue-specific RNA-binding protein can lead to tissue-specific alternative splicing via splicing enhancers or splicing silencers.

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

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?

AU-rich elements (AREs) are cis-elements in mRNAs that regulate stability and decay. How is it possible that a single mRNA sequence element can serve to stabilize an mRNA in some cases and lead to its decay in other scenarios?

Explain how the addition of acetyl groups to histones leads to a weaker association of DNA in nucleosomes.

What are processing bodies (P bodies), and what role do they play in mRNA regulation?

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

Enhancers can influence the transcription of genes far away on the same chromosome. How are the effects of enhancers restricted so that they do not exert inappropriate transcriptional activation of non-target genes?

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

While circular RNAs were first described long ago, they have only recently been investigated for function. What are their known and suspected functions in the cell?

How are mRNAs stored within the cell in a translationally inactive state, and how can their translation be stimulated?

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

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?

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

Explain how the following mutations would affect transcription of the yeast GAL1 gene in the presence of galactose.

A point mutation in the GAL1 core promoter that alters the sequence of the TATA box.

Explain how the following mutations would affect transcription of the yeast GAL1 gene in the presence of galactose.

A mutation within the GAL80 gene that blocks the ability of Gal80 protein to interact with Gal3p.

Explain how the following mutations would affect transcription of the yeast GAL1 gene in the presence of galactose.

A deletion of one of the four UASG elements upstream from the GAL1 gene.

What role do ubiquitin ligases play in the regulation of gene expression?

Explain how the following mutations would affect transcription of the yeast GAL1 gene in the presence of galactose.

A deletion within the GAL4 gene that removes the region encoding amino acids 1 to 100.

Explain how the following mutations would affect transcription of the yeast GAL1 gene in the presence of galactose.

A deletion of the entire GAL3 gene.

Much of what we know about gene interactions in development has been learned using nematodes, yeast, flies, and bacteria. This is due, in part, to the relative ease of genetic manipulation of these well-characterized genomes. However, of great interest are gene interactions involving complex diseases in humans. Wang and White [(2011). Nature Methods 8(4):341–346] describe work using RNAi to examine the interactive proteome in mammalian cells. They mention that knockdown inefficiencies and off-target effects of introduced RNAi species are areas that need particular improvement if the methodology is to be fruitful.

How might one use RNAi to study developmental pathways?

Much of what we know about gene interactions in development has been learned using nematodes, yeast, flies, and bacteria. This is due, in part, to the relative ease of genetic manipulation of these well-characterized genomes. However, of great interest are gene interactions involving complex diseases in humans. Wang and White [(2011). Nature Methods 8(4):341–346] describe work using RNAi to examine the interactive proteome in mammalian cells. They mention that knockdown inefficiencies and off-target effects of introduced RNAi species are areas that need particular improvement if the methodology is to be fruitful.

Comment on how 'knockdown inefficiencies' and 'off-target effects' would influence the interpretation of results.