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• Functional Genomics


  The development and application of global (genome-wide or system-wide) experimental approaches to assess gene function by making use of the information and reagents provided by structural genomics

  
• Functional Genomics


  A method of assessing phenotype that differs from more classical approaches primarily with respect to the scale and automation of biological investigations

  
• Modern functional genomics approaches examine how 1,000 to 10,000 genes are expressed as a function of development

  
• Comparative Genomics


  A comparison of gene numbers, gene locations & biological functions of genes, in the genomes of different organisms, one objective being to identify groups of genes that play a unique biological role in a particular organism
• Reasons for Comparative Genomics

  • Studying evolutionary changes among organisms
  • To identify genes that are conserved or common among species
  • To identify genes that give each organism its unique characteristics

  
• The vast numbers of species and the much larger size of some genomes makes the entire sequencing of all genomes a non-optimal approach for understanding genome structure

  
• Within a given species most individuals are genetically distinct in a number of ways, so "sequencing a human genome" does not mean the genomes of two individuals who are genetically distinct

  
• Because all modern genomes have arisen from common ancestral genomes, the relationships between genomes can be studied with this fact in mind

  
• Commonality of genomes means that information gained in one organism can have application in other even distantly related organisms
• Comparative genomics enables the application of information gained from facile model systems to agricultural and medical problems

  
• The nature and significance of differences between genomes provides a powerful tool for determining the relationship between genotype and phenotype through comparative genomics and morphological and physiological studies

  
• Genomes that have been sequenced

  • Human
  • Chimpanzee
  • Mouse
  • Rat
  • Puffer fish
  • Fruit fly
  • Sea squirt
  • Roundworm
  • Baker's yeast
  • Escherichia coli
  • Chicken
  • Cow
  • Dog
  • Honey bee
  • Sea urchin
  • Rhesus macaque monkey
• Together with over 1,000 prokaryote genomes, a total of over 1,300 species have been completely sequenced and published and this number continues to grow at a prodigious rate, providing a rich source of genomic data for comparison

  
• Synteny


  A situation in which genes are arranged in similar blocks in different species
• Comparison of the human and mouse genomes shows the level of synteny between these two mammals, with human chromosome 20 corresponding entirely to a portion of mouse chromosome 2, and human chromosome 17 corresponding entirely to a portion of mouse chromosome 11

  
• Other chromosomes show evidence of more extensive interchromosomal rearrangement between the human and mouse genomes
• Comparing homologous DNA from different species allows researchers to locate the signals that represent the location of genes, as well as sequences that may regulate gene expression

  
• Much of the functional parts of the human genome have been discovered or verified by sequence comparison, and it is now a standard component of the analysis of every new genome sequence

  
• Phylogenetic distance


  A measure of the degree of separation between two organisms or their genomes on an evolutionary scale, usually expressed as the number of accumulated sequence changes, number of years, or number of generations

  
• The more distantly related two organisms are, the less sequence similarity or shared genomic features will be detected between them
• Over very large phylogenetic distances (e.g., over one billion years since their separation), only general insights about classes of shared genes can be gathered, and the order of genes and the signatures of sequences that regulate their transcription are rarely conserved

  
• At closer phylogenetic distances (50–200 million years of divergence), both functional and non-functional DNA is found within the conserved segments, and the functional sequences will show signatures of selection by virtue of their sequences having changed less, or more slowly than, non-functional DNA

  
• Comparative genomics is contributing to the identification of general classes of important DNA elements, such as coding exons of genes, non-coding RNAs, and some gene regulatory sites

  
• Very similar genomes separated by about 5 million years of evolution (such as human and chimpanzee) are particularly useful for finding the sequence differences that may account for subtle differences in biological form

  
• Comparison of the fruit fly genome with the human genome reveals that about sixty percent of genes are conserved, and two-thirds of human genes known to be involved in cancer have counterparts in the fruit fly
• Comparative genomics may benefit the broader animal world and ecological studies as well, as sequencing technology grows easier and less expensive, and can be used to find subtle differences among animal and plant species

  
• Comparative genomics may lead to the rearrangement of our understanding of some branches of the evolutionary "tree of life," as well as point to new strategies for conserving rare and endangered species

  
• Functional Genomics


  The study of gene function through parallel expression measurements of a genome
• Microarray analysis


  Can be divided into two main steps: probe production and target (cDNA) production

  
• Gene microarray technology rests on the ability to deposit many (tens of thousands) different DNA sequences on a small surface, usually a glass slide

  
• Gene expression microarray


  A type of microarray

  
• Tissue microarray (TMA)


  A type of microarray
• Microarray or "global expression profiling" looks at orders of magnitude more genes than was possible previously, and has the advantage that the genes examined are not influenced by preselection of genes

  
• mRNA


  An intermediary molecule which carries the genetic information from the cell nucleus to the cytoplasm for protein synthesis
• Whenever some genes are expressed or are in their active state, many copies of mRNA corresponding to the particular genes are produced by a process called transcription
• By assessing the various mRNAs, we can assess the genetic information or the gene expression, which helps in the understanding of various processes behind every altered genetic expression

  
• mRNA acts as a surrogate marker, and since mRNA is degraded easily, it is necessary to convert it into a more stable cDNA form
• Labeling of cDNA is done by fluorochrome dyes Cy3 (green) and Cy5 (red), and the principle behind microarrays is that complementary sequences will bind to each other

  
• How a microarray works

  1. Obtain DNA sample from patient and control

  2. Denature the DNA to separate the strands

  3. Cut the DNA into smaller fragments and label with fluorescent dyes (green for patient, red for control)

  4. Insert the labeled DNA fragments into the microarray chip and allow them to hybridize

  5. If the patient has a mutation, their DNA will not bind properly to the "normal" sequence on the chip, but will bind to the mutated sequence

  
• DNA microarrays are used in clinical diagnostic tests for some diseases, and to determine which drugs might be best prescribed for particular individuals