13. Gene Regulation in Eukaryotes

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

Outline the roles of RNA in eukaryotic gene regulation.

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?

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?