Chapter 14 Genomes and Genomics Sequencing DNA dideoxy
- Slides: 30
Chapter 14 Genomes and Genomics
Sequencing DNA dideoxy (Sanger) method dd. GTP dd. ATP dd. TTP dd. CTP 5’TAATGTACG TAATGTAC TAATGTA TAATGT TAATG TAAT TAA TA T Fred Sanger, Nobel prize 1980
Sequencing DNA dideoxy (Sanger) method Leroy Hood, Caltech Fluorescence based sequencing Norm Dovici – Capillary electrophoresis
Sequencing DNA dideoxy (Sanger) method
Genomics era: High-throughput DNA sequencing The first high-throughput genomics technology was automated DNA sequencing in the early 1990. TIGR (The Institute for Genomics Research) 1995 – first whole genome sequence, H. influenza Baker’s yeast, Saccharomyces cerevisiae (15 million bp), was the first eukaryotic genome to be sequenced. In September 1999, Celera Genomics completed the sequencing of the Drosophila genome.
Genomics: Completed genomes as 2002 Currently the genome of over 600 organisms are sequenced: http: //www. genomesonline. org/ This generates large amounts of information to be handled by individual computers.
Cloning/libraries BAC, YAC and ESTs • BAC = bacterial artificial chromosome – 150 kb, replicate in E. coli • YAC = yeast artificial chromosome – 150 kb -1. 5 Mb, replicate in yeast
Assembling contigs
Ordered-clone Sequencing Clones ordered by restriction enzyme sites
Annotation • ORF – open reading frame • EST- Expressed sequence tag – Based on m. RNA • Comparative genomics
The trend of data growth 21 st century is a century of biotechnology: Genomics: New sequence information is being produced at increasing rates. (The contents of Gen. Bank double every year) Microarray: Global expression analysis: RNA levels of every gene in the genome analyzed in parallel. Proteomics: Global protein analysis generates by large mass spectra libraries. Metabolomics: Global metabolite analysis: 25, 000 secondary metabolites characterized Glycomics: Global sugar metabolism analysis
How to handle the large amount of information? Drew Sheneman, New Jersey--The Newark Star Ledger Answer: bioinformatics and Internet
Bioinformatics history In 1960 s: the birth of bioinformatics IBM 7090 computer Margaret Oakley Dayhoff created: The first protein database The first program for sequence assembly There is a need for computers and algorithms that allow: Access, processing, storing, sharing, retrieving, visualizing, annotating…
DNA (nucleotide sequences) databases They are big databases and searching either one should produce similar results because they exchange information routinely. -Gen. Bank (NCBI): www. ncbi. nlm. nih. gov -Arabidopsis: (TAIR) www. arabidopsis. org Specialized databases: Tissues, species… -ESTs (Expressed Sequence Tags) ~at NCBI ~at TIGR -. . . many more!
Comparative genomics BLAST – basic local alignment and search tool (http: //www. ncbi. nlm. nih. gov/) Homologs orthologs paralogs
Question You are a researcher who has tentatively identified a human homolog of a yeast gene. You determine the DNA sequence of c. DNAs of both your yeast gene and the human gene and decide to compare the gene sequences, as well as the predicted protein sequence of each, using alignment software. You would expect the greatest sequence identity from comparisons of the: a. b. c. d. e. c. DNA sequences Protein sequences Genomic DNA sequences Both (a) and (b) will give you equivalent sequence similarity All will give equivalent sequence similarity
What is a microarray?
Types of Arrays • Expression Arrays – c. DNA – Genome • Affymetrix (Gene. Chip®) • Agilent • Tiling arrays
Overview of Microarrays
Transcription Profiling of a mutant WT
A “good” microarray plate Red = only in treatment Green = only in normal Yellow = found in both Black = found in neither
Results 100’s of genes identified, those turned on, those turned off
Expression map red = up regulated green= down regulated
Question Microarray technology directly involves: a. b. c. d. e. PCR DNA sequencing Hybridization RFLP detection None of the above
Protein – protein interactions • Ch. IP (chomatin immunoprecipitation) • Yeast two hybrid • Bi Molecular Fluorescence Complementation (BMFC)
Ch. IP and Ch. IP- chip
Yeast two hybrid
Bi Molecular Fluorescence Complementation (BMFC) Citovsky et al. , 2006
Reverse genetics • • Gene knockouts RNAi Overexpression Altered expression
Summary • DNA Sequencing and the rise of genomics • Annotation of genome sequence – Comparative genomics – Functional genomics • Protein-protein interactions • ESTs • Reverse genetics
- Chapter 18 genomes and their evolution
- Computational biology: genomes, networks, evolution
- Sanger vs maxam gilbert sequencing
- 3rd generation dna sequencing
- Dna sequencing methods
- Contigs
- Dna sequencing
- Dna sequencing applications
- Difference between structural and functional genomics
- Difference between structural and functional genomics
- Essnet qsr
- Vcf viewer
- A vision for the future of genomics research
- Igv genome
- Rachel butler genomics
- Harvest genomics
- Genome
- Genomics
- Functional genomics
- Application of genomics
- Types of genomics
- "encoded genomics" -job
- "encoded genomics" -job
- Coding dna and non coding dna
- Replication
- Bioflix activity dna replication dna replication diagram
- What role does dna polymerase play in copying dna?
- Dna rna protein synthesis homework #2 dna replication
- What is sequencing selection and iteration
- Microprogram example
- Loading sequencing and scheduling