Today… Review a few items from last class Next week Presentations on Thurs! Guest Speaker In-Class #9

What is genomics? Field of genetics that studies whole genomes Content Organization Function Evolution

What started the field of genomics? 1997 Svante Paabo sequenced 379 bp region of mtDNA from Neanderthal fossil

What genomes were the first to be sequenced? 1995 Haemophilus influenzae (1.8 Mb) 1996 Saccharomyces cerevisiae (12 Mb) 1998 C. elegans (100 Mb) 2000 Drosophila melanogaster (180 Mb) 2001 First draft of Human genome (3000 Mb) 2005 First draft of Chimpanzee 2007 Craig Venter’s Genome Released; Jim Watson’s Genome Sequenced Using High-Throughput Methods

Map of H. influenzae

Creating a Map of the Genome Break genome into pieces Read sequences of small segments Computationally find areas of overlap Assemble contigs

Genome Sequencing is Automated

Two Strategies for Sequencing Whole Genomes: Whole-genome shotgun (WGS) Sequence first, map later Ordered-clone sequencing Map first, sequence later

WGS: Begin with Reads from Inserts Primers are used to sequence 600 bp of insert If both ends of the clone are sequenced paired-end reads are generated

WGS worked well for bacterial genomes….what about eukaryotes? How do we figure out the location of sequences with lots of repetition??

Overview of WGS

Ordered Clone Approach

Once we had the sequence… The field of bioinformatics was born! What information is found in the DNA??? Goal: Annotate the genome!

First look at the Proteome How do we find gene regions in the DNA? Open reading frames (ORFs) Analyze mRNA by creating cDNA Expressed sequence tags (ESTs)

Lots of binding sites to focus on! (from consensus motifs)

Different ways to make gene predictions

Structure of the Human Genome Only 3% codes for proteins 60% of current proteins have splice variations Estimate about 20,000 genes 19,000 pseudogenes

Cytogenetic Map of Chromosome 7 Mapped physical break points related to disease 1600 rearrangement breakpoints have been mapped, 440 have been sequenced

Comparative Genomics Assume that natural selection rejects mutations that decrease fitness Also see conserved sequences over long periods of evolution Genes are conserved from one species to another

Comparative Genomics Used to study evolution of genes across species Used to study conserved sequences among vertebrates Used to study strains of bacteria (E. coli K12 and E. coli O157:H7)

Compare Genomes of Bacteria Common backbone in blue O157:H7 in red K12 in green

What’s with all the -ogs? Homologs: closely related genes Orthologs: homologs that evolved from a common ancestor Paralogs: genes related by gene duplication in the genome

Oh give me a Ome Besides the genome there are new -omes Transcriptome Proteome Interactome PROTEOME SAMPLER from Yeast. shows 1,458 yeast proteins (circles) and their 1,948 interactions (lines). Removing proteins has different effects on the yeast: lethal (red); nonlethal (green); slowed growth (orange); unknown (yellow).  Hawoong Jeong; University of Notre Dame.

DNA Microarrays DNA chips have “spots” of DNA bound to slide One chip can have an entire genome Expose chip to sample of labeled RNA from a cell…RNA will hybridize to areas of complementary DNA

DNA Microarrays

Ways to Study the Interactome Two-hybrid test Detects the physical interaction between proteins Chromatin Immunoprecipitation Assay (ChIP) Study proteins that bind to DNA

Ways to Study the Interactome Two-hybrid test Detects the physical interaction between proteins Chromatin Immunoprecipitation Assay (ChIP) Study proteins that bind to DNA

Reverse Genetics Disrupt gene function and then study the phenotype in native conditions Random mutagenesis Targeted mutagenesis Phenocopying

Phenocopying RNA interference Chemical genetics Generate dsRNA with sequences homologous to gene you want to study Chemical genetics Reduce the activity of target gene by binding inhibitory molecule

Welcome……..our guest speaker Dr. Michael Schlador Illumina Regional Manager, Field Applications