Functional Genomics is a branch of genomics that focuses on understanding the functions, expressions, and interactions of genes and proteins. It encompasses several subdivisions, including transcriptomics, which examines the expression and sequence of RNA transcripts; proteomics, which studies protein expression; and interactomics, which investigates the interactions between DNA, RNA, and proteins. These subdivisions highlight the complexity of gene expression, as not all transcribed genes are translated into proteins due to various regulatory mechanisms.
One of the primary techniques used in Functional Genomics is DNA microarrays. This method allows researchers to determine which genes are active in specific cells under varying conditions. Since gene expression is dynamic and can change based on environmental factors, age, and developmental stages, DNA microarrays provide a snapshot of gene activity at a given time. In an experiment, RNA is extracted from cells, reverse transcribed into complementary DNA (cDNA), and labeled (e.g., cancer cells in red and normal cells in green). The cDNA is then hybridized to a microarray containing probes for numerous genes. The resulting color intensity indicates the level of gene expression in each cell type, allowing for comparisons between cancerous and normal cells.
Another important technique is the two-hybrid test, which is performed in yeast to study protein interactions. This method utilizes a system where two proteins must interact to activate transcription of a reporter gene, such as green fluorescent protein (GFP). If the bait and prey proteins interact, transcription is activated, resulting in a visible green fluorescence. Conversely, if they do not interact, transcription remains inactive, and no fluorescence is observed. This technique is crucial for identifying protein-protein interactions within the cell.
Chromatin immunoprecipitation (ChIP) is another key method that investigates protein-DNA interactions. In this process, genomic DNA is cross-linked to proteins that bind to it, allowing researchers to study which proteins are associated with specific DNA sequences. After cross-linking, the DNA is fragmented, and antibodies specific to the protein of interest are used to isolate the protein-DNA complexes. The DNA can then be sequenced to identify the binding sites of the protein, providing insights into gene regulation and expression.
Lastly, reverse genetics is a technique that starts with a known gene sequence. Researchers introduce mutations to disrupt the gene and observe the resulting phenotypic changes. This approach allows scientists to infer the function of the gene based on the observed effects of the mutation. In contrast, forward genetics begins with a phenotype of interest, such as an organism exhibiting an abnormal trait, and works backward to identify the underlying genotype responsible for that phenotype. Together, these methods enhance our understanding of gene function and regulation, contributing to advancements in fields such as medicine and biotechnology.
