REGULATION 2: Processes in Eukaryotes

Regulation of gene expression in multicellular eukaryotes is in general more complex than in bacteria, and is still an area of very active research.. In general, most regulation is of a positive type, and may involve "remodeling" the chromatin (#1 below) to allow transcription to occur. For some genes, there is more than one promotor (#2 below). For many of our genes, "alternative splicing" of the primary transcript is used either as a regulator of expression levels or as a way to make different versions of the protein in different tissues (#3 below). Because the study of the regulation of gene expression in eukaryotes is a very active area of current research, we will be able to just introduce the subject by looking briefly at the three examples mentioned above.


1. In general for expression of genes in eukaryotes, how might "chromatin-remodeling" be involved in the formation of any specific transcription initiation complex?

We have already looked at Figure 11.25, which shows in general how the eukaryotic transcription initiation complex forms, involving DNA regions called enhancers to which a transcriptional activator protein binds, thus starting a recruitment process that gets a transcription complex containing RNA polymerase onto the promoter, ready to start transcription of the gene. In order for this to work, the enhancer and promoter sites in the DNA need to be "accessible" to the proteins that bind to them.

Figure 11.27 shows the involvement of "chromatin-remodeling complexes" to convert inaccessible sites into accessible sites for transcription to begin.


2. What is an example of the use of alternative promoters during development?

Figure 11.28 shows the use of alternative promoters in the gene coding for the enzyme alcohol dehydrogenase in Drosophila. By this mechanism, the regulation of expression of this gene can be different in larvae and adults.


3. How is "alternative splicing" used to get a gene to be expressed at different levels in different tissues or to get somewhat different versions of a protein made from the same gene?

Figure 11.33 shows the use of alternative splicing during the expression of the insulin receptor gene in humans. There are a total of 20 exons in this gene. In cells in the liver, all 20 exons end up in the mRNA. In skeletal muscle cells, however, the mRNA has 19 exons, with exon #11 missing. The two versions of the insulin receptor synthesized from these two mRNAs have different binding affinities for insulin.

Analysis of the human genome indicates that alternative splicing occurs during expression of over half of our genes. This is the major reason why it is correct to say that the number of proteins we can make is greater than the number of genes we have.



Problem S-9: Alternative Splicing

Assume that the human gene alpha codes for a protein we'll call PA (for "protein alpha"), of which there are two versions, PA1 and PA2. Protein PA1 consists of just two domains, while protein PA2 has these same two domains plus a third (internal) domain. Assume that the domains are each 200 amino acids long, and that each domain is coded for by a different exon. Assume that gene alpha is known to be 6200 base pairs (significantly smaller than the average of about 15,000), that the introns in this gene are each 2000 base pairs in length, and that the untranslated 5' region is the same length as the untranslated 3' region.

Figure out the structure of the gene (base pair lengths of all parts of the gene).

What is the length of the translated region of the mRNA for PA2?

What is the length of the untranslated 5' region of the mRNA for PA2?

What is the total length of the mRNA for PA1?