15. Genomes and Genomics

Which of the following terms describes the study of physical interactions between DNA, RNA, and Protein?

Which of the following methods is used to study protein interactions in live cells?

Which of the following methods is used to study protein-DNA interactions?

From microarray analysis, how do we know what genes are being expressed in a specific tissue?

In the discussion we focused on the analysis of genomes, transcriptomes, and proteomes and considered important applications and findings from these endeavors. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions?

How have microarrays demonstrated that, although all cells of an organism have the same genome, some genes are expressed in almost all cells, whereas other genes show cell- and tissue-specific expression?

Discuss the similarities and differences between forward and reverse genetic approaches, and when you would choose to utilize each of the approaches.

What is functional genomics? How does it differ from comparative genomics?

What are the advantages and disadvantages of using insertion alleles versus alleles generated by chemicals (as in TILLING) in reverse genetic studies?

Sequencing the human genome, the development of microarray technology, and personal genomics promise to improve our understanding of normal and abnormal cell behavior. How are these approaches dramatically changing our understanding and treatment of complex diseases such as cancer?

Discuss the advantages (and possible disadvantages) of the different approaches to reverse genetics.

What functional information about a genome can be determined through applications of chromatin immunoprecipitation (ChIP)?

Translational fusions between a protein of interest and a reporter protein are used to determine the subcellular location of proteins in vivo. However, fusion to a reporter protein sometimes renders the protein of interest nonfunctional because the addition of the reporter protein interferes with proper protein folding, enzymatic activity, or protein–protein interactions. You have constructed a fusion between your protein of interest and a reporter gene. How will you show that the fusion protein retains its normal biological function?

It can be said that modern biology is experiencing an 'omics' revolution. What does this mean? Explain your answer.

How would you perform a genetic screen to identify genes directing Drosophila wing development? Once you have a collection of wing-development mutants, how would you analyze your mutagenesis to learn how many genes are represented and how many alleles of each gene? How would you discover whether the genes act in the same or different pathways, and if in the same pathway, how do you discover the order in which they act? How would you clone the genes?

A 2-kb fragment of E. coli DNA contains the complete sequence of a gene for which transcription is terminated by the rho protein. The fragment contains the complete promoter sequence as well as the terminator region of the gene. The cloned fragment is examined by band shift assay. Each lane of a single electrophoresis gel contains the 2-kb cloned fragment under the following conditions:

Lane 1: 2-kb fragment alone

Lane 2: 2-kb fragment plus the core enzyme

Lane 3: 2-kb fragment plus the RNA polymerase holoenzyme

Lane 4: 2-kb fragment plus rho protein

Explain the relative positions of bands in lanes 1 and 4.