Summary

Genomics

• Genomics is the study of the genomes—the full sets of genes—of organisms. Because of the large numbers of genes, genomics depends on high-throughput methods to collect data and on advanced information processing to catalog and use data.
• One of the two major goals of genomics is to elucidate the evolution of genes and genomes. In pursuit of this goal, students of genomics seek to understand the mechanisms of evolutionary modification of genes and genomes (e.g., deletion and duplication). They also seek to reconstruct the paths followed by evolution in the past so that, for example, the order of evolutionary events is better defined.
• The second major goal of genomics is to elucidate the current functioning of genes and genomes. In pursuit of this goal, genomics uses information on already-known genes and gene families to predict the likely functions of newly identified genes and the likely ranges of action and competence of newly sequenced genomes.
• Although knowledge of an animal’s genome permits many useful predictions to be made about the animal’s biochemical phenotype, these predictions must ultimately be tested empirically. For example, although the suite of proteins synthesized in an animal’s tissues can be predicted from the genome, the proteins present must ultimately be studied directly, as by proteomic methods.

The Study of Gene Transcription: Transcriptomics

• Transcriptomics or transcription profiling (also sometimes called expression profiling) is the study of which genes are transcribed in a tissue and the degrees to which they are transcribed. Transcription is evaluated by measuring the messenger RNAs (mRNAs) produced in the tissue.
• DNA microarrays are a major tool in modern transcriptomic research. A microarray consists of a grid of thousands of DNA spots, each representing a particular gene. Each mRNA produced by a tissue binds to the DNA that corresponds to the gene that produced the mRNA. The DNA spots that thus become labeled with mRNA when exposed to the mix of mRNAs produced by a tissue collectively mirror the genes being transcribed in the tissue.
• DNA microarrays are often used to carry out a direct comparison of the mRNAs produced by a tissue under two different conditions. The mRNAs produced under the two conditions are labeled with green and red fluors. Gene-specific DNA spots in the microarray then glow with green light, red light, or yellow light (the result of green + red), depending on whether the corresponding genes were transcribed under just one of the two conditions or both.
• Studies using microarrays often identify hundreds of genes that undergo changes of transcription when an animal is exposed to a change in conditions. Many genes also routinely exhibit daily cycles of transcription.
• One way to study gene function is to manipulate gene transcription or translation and observe the consequences. Gene knockout, gene overexpression, RNA interference, and the CRISPR/Cas system are four of the major methods used. All modify the capacities of cells to produce specific proteins.