13. Gene Regulation in Eukaryotes

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?

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

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

Compare and contrast promoters and enhancers with respect to their location (upstream versus downstream), orientation, and distance (in base pairs) relative to a gene they regulate.

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?

What is one proposed role for lncRNAs?

What are the sources of dsRNA? Diagram the mechanisms by which dsRNAs are produced and processed into small RNAs.

How does dsRNA lead to posttranscriptonal gene silencing?

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?

The UG4 gene is expressed in stem tissue and leaf tissue of the plant Arabidopsis thaliana. To study mechanisms regulating UG4 expression, six small deletions of the DNA sequence upstream of the gene-coding sequence are made. The locations of deletions and their effect on UG4 expression are shown here. Explain the differential effects of deletions B and F on expression in the two tissues.

The UG4 gene is expressed in stem tissue and leaf tissue of the plant Arabidopsis thaliana. To study mechanisms regulating UG4 expression, six small deletions of DNA sequence upstream of the gene-coding sequence are made. The locations of deletions and their effect on UG4 expression are shown here. Why does deletion E lower expression of UG4 in leaf tissue but not in stem tissue?

The UG4 gene is expressed in stem tissue and leaf tissue of the plant Arabidopsis thaliana. To study mechanisms regulating UG4 expression, six small deletions of DNA sequence upstream of the gene-coding sequence are made. The locations of deletions and their effect on UG4 expression are shown here. Why does deletion D raise UG4 expression in leaf tissue but not in stem tissue?