15. Genomes and Genomics

Metagenomics studies generate very large amounts of sequence data. Provide examples of genetic insight that can be learned from metagenomics.

A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay, and the following gel bands are observed.

Match these conditions to a specific lane of the gel.

3.5-kb fragment plus TFIIB and TFIID

A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay, and the following gel bands are observed.

Match these conditions to a specific lane of the gel.

3.5-kb fragment plus TFIIB, TFIID, TFIIF, and RNA polymerase II

A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay, and the following gel bands are observed.

Match these conditions to a specific lane of the gel.

3.5-kb fragment alone

A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay, and the following gel bands are observed.

Match these conditions to a specific lane of the gel.

3.5-kb fragment plus RNA polymerase II

A 3.5-kb segment of DNA containing the complete sequence of a mouse gene is available. The DNA segment contains the promoter sequence and extends beyond the polyadenylation site of the gene. The DNA is studied by band shift assay, and the following gel bands are observed.

Match these conditions to a specific lane of the gel.

3.5-kb fragment plus TFIIB

What are DNA microarrays? How are they used?

A 1.0-kb DNA fragment from the end of the mouse gene described in the previous problem is examined by DNA footprint protection analysis. Two samples are end-labeled with ³²P and one of the two is mixed with TFIIB, TFIID, and RNA polymerase II. The DNA exposed to these proteins is run in the right-hand lane of the gel shown below and the control DNA is run in the left-hand. Both DNA samples are treated with DNase I before running the samples on the electrophoresis gel.

Explain the role of DNase I.

A 1.0-kb DNA fragment from the end of the mouse gene described in the previous problem is examined by DNA footprint protection analysis. Two samples are end-labeled with ³²P, and one of the two is mixed with TFIIB, TFIID, and RNA polymerase II. The DNA exposed to these proteins is run in the right-hand lane of the gel shown below and the control DNA is run in the left-hand. Both DNA samples are treated with DNase I before running the samples on the electrophoresis gel.

Draw a diagram of this DNA fragment bound by the transcriptional proteins, showing the approximate position of proteins along the fragment.

A 1.0-kb DNA fragment from the end of the mouse gene described in the previous problem is examined by DNA footprint protection analysis. Two samples are end-labeled with ³²P and one of the two is mixed with TFIIB, TFIID, and RNA polymerase II. The DNA exposed to these proteins is run in the right-hand lane of the gel shown below and the control DNA is run in the left-hand. Both DNA samples are treated with DNase I before running the samples on the electrophoresis gel.

What length of DNA is bound by the transcriptional proteins? Explain how the gel results support this interpretation.

How would you design a genetic screen to find genes involved in meiosis?

Substantial fractions of the genomes of many plants consist of segmental duplications; for example, approximately 40% of genes in the Arabidopsis genome are duplicated. How might you approach the functional characterization of such genes using reverse genetics?

A substantial fraction of almost every genome sequenced consists of genes that have no known function and that do not have sequence similarity to any genes with known function. How would your approach change if the genes of unknown function were in the human genome?

A substantial fraction of almost every genome sequenced consists of genes that have no known function and that do not have sequence similarity to any genes with known function. Describe two approaches to ascertaining the biological role of these genes in S. cerevisiae.

In conducting the study described in Problem 24, you have noted that a set of S. cerevisiae genes are repressed when yeast are grown under high-salt conditions. How might you approach this question if genome sequences for the related Saccharomyces species S. paradoxus, S. mikatae, and S. bayanus were also available?