Genomics is an interdisciplinary field of science within the field of Genomics is an interdisciplinary field of science within the field of molecular biology. A genome is a complete set of DNA within a single cell of an organism, and as such, focuses on the structure, function, evolution, and mapping of genomes. Genomics aims at the collective characterization and quantification of genes, which direct the production of proteins with the assistance of enzymes and messenger molecules. Genomics also involves the sequencing and analysis of genomes.

INTRODUCTION The term genome refers to the total genetic composition of an organism The term genomics refers to the molecular analysis of the entire genome of a species Genome analysis consists of two main phases Mapping Sequencing In 1995, researchers led by Craig Venter and Hamilton Smith obtained the first complete DNA sequence of an organism The bacterium Haemophilus influenzae Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The International Human Genome Sequencing Consortium published the first draft of the human genome in the journal Nature in February 2001 with the sequence of the entire genome's three billion base pairs some 90 percent complete. A startling finding of this first draft was that the number of human genes appeared to be significantly fewer than previous estimates, which ranged from 50,000 genes to as many as 140,000. The full sequence was completed and published in April 2003.

Genomics begins with the mapping of the genome and progresses ultimately to its complete sequencing Functional genomics examines how the interactions of genes produces the traits of an organism Proteomics is the study of all the proteins encoded by the genome and their interactions Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

CHROMOSOME MAPPING There are three common ways to determine the organization of DNA regions 1. Cytogenetic mapping Relies on microscopy Genes are mapped relative to band locations Linkage mapping Relies on genetic crosses Genes are mapped relative to each other Distances computed in map units (or centiMorgans) 3. Physical mapping Relies on DNA cloning techniques Distances computed in number of base pairs Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

and from one region of the chromosome to another Note: Correlations between the three maps often vary from species to species and from one region of the chromosome to another Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Cytogenetic mapping relies on microscopy It is commonly used with eukaryotes which have much larger chromosomes Eukaryotic chromosomes can be distinguished by Size Centromeric locations Banding patterns Chromosomes are treated with particular dyes The banding pattern that results is used for mapping Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

In situ Hybridization In situ hybridization can locate the position of a gene at a particular site within an intact chromosome It is used to map the locations of genes or other DNA sequences within large eukaryotic chromosomes a probe is used to detect the “target” DNA - fluorescence in situ hybridization (FISH). To detect the light emitted by a fluorescent probe, a fluorescence microscope is used The fluorescent probe will be seen as a colorfully glowing region against a nonglowing background The results of the FISH experiment are then compared to Giemsa-stained chromosomes Thus, the location of a probe can be mapped relative to the G banding pattern Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

fluorescence in situ hybridization (FISH).

Linkage Mapping Linkage mapping relies on the frequency of recombinant offspring to map genes Even regions of DNA, which need not encode genes, can be used as genetic markers A molecular marker is a DNA segment that is found at a specific site and can be uniquely recognized As with alleles, the characteristics of molecular markers may vary from individual to individual (polymorphic) Therefore, the distance between linked molecular markers can be determined from the outcome of crosses Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The amplified region is called a sequence-tagged site (STS) The two STS copies in this case are different in length Therefore, their microsatellites have different numbers of CA repeats

PHYSICAL MAPPING Physical mapping requires the cloning of many pieces of chromosomal DNA The cloned DNA fragments are then characterized by 1. Size 2. Genes they contain 3. Relative locations along a chromosome Eukaryotic genomes are very large Physical mapping will require many much smaller pieces Will require a massive, collaborative undertaking In recent years, physical mapping studies have led to the DNA sequencing of entire genomes Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The goal of functional genomics is to elucidate the roles of genetic sequences in a given species In most cases, it aims to understand gene function Transcriptomics is the study of the transcriptome—the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell—using high-throughput methods, such as microarray analysis. The entire collection of proteins that an organism can make is termed the proteome The goal of proteomics is to understand the functional roles of the proteins of a species It aims to understand the interplay among proteins The goal of bioinformatics is to extract information within genetic sequences using a mathematical/computational approach Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Expressed Genes Can be Identified in a cDNA Library A basic goal of genomic research is to identify regions of DNA that actually encode genes One way to do this, is to show that a given region is transcribed into RNA This can be accomplished by the generation of a cDNA library A cDNA library is also called an expressed sequence tag library (EST library) Because the sequences are from expressed sequences and can also be used as markers (tags) in physical mapping studies Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

A Microarray Can Identify Genes That Are Transcribed Researchers have developed an exciting technology called DNA microarrays (also called gene chips) This new technology makes it possible to monitor thousands of genes simultaneously A DNA microarray is a small silica, glass or plastic slide that is dotted with many sequences of DNA Each of these sequences corresponds to a known gene These fragments are made synthetically These sequences of DNA will act as probes to identify genes that are transcribed Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The DNA fragments can be either/or Amplified by PCR and then spotted on the microarray Synthesized directly on the microarray itself A single slide contains tens of thousands of different spots in an area the size of a postage stamp The relative location of each spot is known The technology for making DNA microarrays is quite amazing It involves spotting technologies that are quite similar to the way that an inkjet printer works Once a DNA microarray has been made, it is used as a hybridization tool Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

It is then placed in a scanning confocal fluorescence microscope Array is washed It is then placed in a scanning confocal fluorescence microscope The pattern of fluorescence is analyzed to indicate hybridization Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Development of novel high-throughput DNA sequencing methods has provided a new method for both mapping and quantifying transcriptomes. This method, termed RNA-Seq (RNA sequencing), has clear advantages over existing approaches and is expected to revolutionize the manner in which eukaryotic transcriptomes are analyzed.

PROTEOMICS Proteomics examines the functional roles of the proteins that a species can make The entire collection of a species’ proteins is its proteome Genomic data can provide important information about the proteome 1. DNA microarrays reveal the genes that are transcribed under a given set of conditions 2. Gene homology studies between species can be used to predict protein structure and/or function Genomic insights, however, have to be followed up with research that involves protein analysis directly Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

The Proteome Is Much Larger Than the Genome Sequencing and analysis of an entire genome can identify all the genes that a given species contains The proteome is larger, however, and its actual size is more difficult to determine This larger size is rooted in a number of cellular processes 1. Alternative splicing 2. RNA editing 3. Postranslational covalent modification Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Two-Dimensional Gel Electrophoresis Any given cell of a multicellular organism will produce only a subset of the proteins in its proteome The subset that it makes depends primarily on the Cell type Stage of development Environmental conditions A common technique in the field of proteomics is two-dimensional gel electrophoresis It is a separation technique that can distinguish hundreds or even thousands of different proteins in a cell extract Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

As the name suggests, the technique involves two different gel electrophoresis experiments. The first separates by pH/charge interactions, the second by size. After the slab gel has run, the proteins within the gel can be stained with a dye The end result is a collection of spots, with each spot corresponding to a unique cellular protein This method can resolve two proteins that differ by a single charged amino acid Two-dimensional gel electrophoresis

BIOINFORMATICS The computer has become an important tool in genetic studies Indeed, the marriage between genetics and biocomputing has yielded an important branch of science: bioinformatics Computer analysis of genetic sequences usually relies on three basic components: A computer A computer program Some type of data Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Computer Databases The amount of genetic information that is generated by researchers has become enormous Large numbers of computer data files are collected and stored in a single location, a database The files in a database are typically annotated They contain the genetic sequence and a concise description of it In addition, they contain other features of significance The scientific community has created several large databases containing data from thousands of labs Refer to Table 21.3 Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display