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

A muscle enzyme called ME1 is produced by transcription and translation of the ME1 gene in several muscles during mouse development, including heart muscle, in a highly regulated manner. Production of ME1 appears to be turned on and turned off at different times during development. To test the possible role of enhancers and silencers in ME1 transcription, a biologist creates a recombinant genetic system that fuses the ME1 promoter, along with DNA that is upstream of the promoter, to the bacterial lacZ (β-galactosidase) gene. The lacZ gene is chosen for the ease and simplicity of assaying production of the encoded enzyme. The diagram shows bars that indicate the extent of six deletions the biologist makes to the ME1 promoter and upstream sequences. The blue deletion labeled D is within the promoter whereas the gray bars span potential enhancer/silencer modules. The table displays the percentage of β-galactosidase activity in each deletion mutant in comparison with the recombinant gene system without any deletions.

Given the information available from deletion analysis, can you give a molecular explanation for the observation that ME1 expression appears to turn on and turn off at various times during normal mouse development?

A muscle enzyme called ME1 is produced by transcription and translation of the ME1 gene in several muscles during mouse development, including heart muscle, in a highly regulated manner. Production of ME1 appears to be turned on and turned off at different times during development. To test the possible role of enhancers and silencers in ME1 transcription, a biologist creates a recombinant genetic system that fuses the ME1 promoter, along with DNA that is upstream of the promoter, to the bacterial lacZ (β-galactosidase) gene. The lacZ gene is chosen for the ease and simplicity of assaying production of the encoded enzyme. The diagram shows bars that indicate the extent of six deletions the biologist makes to the ME1 promoter and upstream sequences. The blue deletion labeled D is within the promoter whereas the gray bars span potential enhancer/silencer modules. The table displays the percentage of β-galactosidase activity in each deletion mutant in comparison with the recombinant gene system without any deletions.

Why does deletion D effectively eliminate transcription of lacZ?

A muscle enzyme called ME1 is produced by transcription and translation of the ME1 gene in several muscles during mouse development, including heart muscle, in a highly regulated manner. Production of ME1 appears to be turned on and turned off at different times during development. To test the possible role of enhancers and silencers in ME1 transcription, a biologist creates a recombinant genetic system that fuses the ME1 promoter, along with DNA that is upstream of the promoter, to the bacterial lacZ (β-galactosidase) gene. The lacZ gene is chosen for the ease and simplicity of assaying production of the encoded enzyme. The diagram shows bars that indicate the extent of six deletions the biologist makes to the ME1 promoter and upstream sequences. The blue deletion labeled D is within the promoter whereas the gray bars span potential enhancer/silencer modules. The table displays the percentage of β-galactosidase activity in each deletion mutant in comparison with the recombinant gene system without any deletions.

Does this information indicate the presence of enhancer and/or silencer sequences in the ME1 upstream sequence? If so, where is/are the sequences located? 

Using the components in the accompanying diagram, design regulatory modules (i.e., enhancer/silencer modules) required for 'your' gene to be expressed only in differentiating (early) and differentiated (late) liver cells. Answer the three questions presented below by describing the roles that activators, enhancers, repressors, silencers, pioneer factors, insulators, chromatin remodeling complexes, and chromatin readers, writers, and erasers will play in the regulation of expression of your gene, that is, what factors will bind and be active in each case? Specify which transcription factors need to be pioneer factors. How will expression be prevented in other cell types?

Using the components in the accompanying diagram, design regulatory modules (i.e., enhancer/silencer modules) required for 'your' gene to be expressed only in differentiating (early) and differentiated (late) liver cells. Answer the three questions presented below by describing the roles that activators, enhancers, repressors, silencers, pioneer factors, insulators, chromatin remodeling complexes, and chromatin readers, writers, and erasers will play in the regulation of expression of your gene, that is, what factors will bind and be active in each case? Specify which transcription factors need to be pioneer factors. How will its expression be maintained?

Using the components in the accompanying diagram, design regulatory modules (i.e., enhancer/silencer modules) required for 'your' gene to be expressed only in differentiating (early) and differentiated (late) liver cells. Answer the three questions presented below by describing the roles that activators, enhancers, repressors, silencers, pioneer factors, insulators, chromatin remodeling complexes, and chromatin readers, writers, and erasers will play in the regulation of expression of your gene, that is, what factors will bind and be active in each case? Specify which transcription factors need to be pioneer factors. How will the gene be activated in the proper cell type?

The majority of this chapter focused on gene regulation at the transcriptional level, but the quantity of functional protein product in a cell can be regulated in many other ways as well. Discuss possible reasons why transcriptional regulation or posttranscriptional regulation may have evolved for different types of genes.