Genomics A Systematic Study of the Locations, Functions and Interactions of Many Genes at Once

Genomics Overview Structural Genomics characterizes the Organization and sequence of the DNA in the whole genome Functional Genomics characterizes the Transcriptome: mRNA production as an indicator of gene expression Proteome: protein production Comparative Genomics compares the structure and functions of genomes of different organisms

Size of the Human Genome Per haploid genome New estimate 32,000 genes

Structural Genomics: Maps Genetic Maps (Linkage Maps) Gene locations relative to other known genes Based on recombination, measured in centimorgans or map units Physical Maps Gene distances measured in numbers of base pairs Based on direct analysis of DNA

Increasing Resolution of Maps

Mapping of Restriction Fragments

Solution

Map-Based Sequencing Approach for the Human Genome Project Contig=uninterrupted stretch of genome derived from two or more partially overlapping cloned DNAs

Whole-Genome Shotgun Sequencing Approach for the Human Genome Project

Other Sequencing Discoveries Single-Nucleotide Polymorphisms Single-base-pair differences between individuals of the same species Can be inherited together in a specific set or haplotype Used to study disease-causing genes

Other Sequencing Discoveries Expressed-Sequence Tags Small sequences derived from cDNA fragments produced from RNA of a specific cell type Act as markers to identify a larger DNA fragment Used to study gene activity

Genomic DNA Transcriptome Proteome DATABASE

Functional Genomics: Microarray Analysis DNA sequences arranged in a matrix Tests for binding to complementary sequences

A cDNA microarray containing 19,200 ESTs was used to identify genes that may be involved in colon tumor metastasis (spreading). cDNA from a colon tumor with low metastatic activity is labeled green. This shows genes that are down-regulated during metastasis. cDNA from a colon tumor with high metastatic activity is labeled red. This shows genes that are up-regulated during metastasis.

Steps in Microarray Analysis Arrange DNA or cDNA in an ordered array on a glass slide (can also build oligonucleotides directly on a slide) Incubate array with fluorescently-labeled probe Detect probe hybridization using a laser Record and store data with computers

Building specific oligonucleotides for microarray analysis

Applying Structural Genomics: Identifying Genotypes at the Molecular Level Lane 2: Deletion Mutation affecting codon 39 BRCA1 Mutations Lane 3: Insertion Mutation affecting codon 40

Functional Genomics: Studying Gene Expression Northern Blotting -separate mRNA from specific cell type by size using gel electrophoresis -transfer mRNA to filter -use DNA probe to detect complementary mRNA sequences

Using Human Genome Information Pharmacogenomics Using DNA Microarrays to select individual drug treatments Mutations in Gene for Affect the following disease conditions Cytochrome P450 Affects rate of metabolizing 30-40 drugs 5-10% of Caucasians and African Americans have low rates Apo E4 Gene dose affects Age of onset for Alzheimer's disease Response to drug Tacrine

Bioinformatics Bioinformatics is an information science focused on -storage of genetic data -organization of data -indexing sequence information

Applications of Bioinformatics DNA -identifying gene sequences -predicting protein sequences -exploring evolutionary relationships Protein -identifying protein products of genes

Databases DNA GenBank (links to protein sequences, scientific literature and genetic information) http://www.ncbi.nlm.nih.gov/ Exons GenScan http://genes.mit.edu/GENSCAN.html Transcriptome Unigene http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene Restriction Sites WebCutter http://www.firstmarket.com/cutter Protein ExPASy= Expert Protein Analysis System http://www.expasy.ch/