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Genomics and proteomics (Bioinformatics)
Genomics is the study of genomes, including sequencing genomes and determining the complete set of proteins and genes in an organism. The first genomes sequenced included Haemophilus influenzae in 1995 and the human genome was completed in 2003, taking 13 years. Genomics provides information on genes, metabolic pathways, and the functioning of organisms through approaches like genome sequencing, structural genomics, functional genomics, comparative genomics, and proteomics.
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Genomics and proteomics (Bioinformatics)
- 1. What do youmean by genomics? GENOMICS & PROTEOMICS
- 2. WHAT DO YOUMEAN BY GENOMICS? The term genome introduced by H. Winkler in 1920 The term genomics coined by T.H. Roderick in 1987 Genome + Omics Genomics Genomics is a an area of life science that deals with the study of the genomes of organisms
- 3. CENTRAL DOGMA OFMOLECULAR BIOLOGY
- 4. • Today genomicsincludes: sequencing of genomes determination of the complete set of proteins encoded by an organism the functioning of genes and metabolic pathways in an organism Where do we get these sequences from? Through genome sequencing projects
- 5. The Genome IsAll The DNA In A Cell • All the DNA on all the chromosomes • Includes genes, intergenic sequences, repeats • Specifically, it is all the DNA in an organelle • Eukaryotes can have 2-3 genomes • Nuclear genome • Mitochondrial genome • Plastid genome • If not specified, “genome” usually refers to the nuclear genome
- 6. How Many TypesOf Genome??? • Prokaryotic genomes • Eukaryotic Genomes • Nuclear Genomes • Mitochondrial genomes • Choloroplast genomes
- 7. GENOME SEQUENCING- HISTORY The first genome to be sequenced was that of Haemophilus influenzae in 1995. The E. coli genome was completely sequenced in 1997. Yeast (Saccharomyces cerevisiae) (12.8 x 106 bp) and worm (Caenorhabditis elegans) genomes were the first eukaryotic genomes to be sequenced in 1999. Genomes of Drosophila melanogaster and Arabidopsis thaliana were sequenced in 2000.
- 8. GENOME SEQUENCING PROJECT HumanGenome project • The Human Genome Project officially began on Oct. 1, 1990. • Completed in 13 years • Mission of HGP: • To understand the human genome and the role it plays in both health and disease. • The U.S. govt. project coordinated by the Department of Energy and the National Institutes of Health • Francis Collins, Director of the HGP and the National Human Genome Research Institute (NHGRI)
- 9. THE GENOME ISOUR GENETIC BLUEPRINT • Nearly every human cell contains 23 pairs of chromosomes 1 - 22 and XY or XX • XY = Male • XX = Female • Length of chr 1-22, X, Y together is ~3.2 billion bases
- 10. • Chromosomes consistof DNA • molecular strings of A, C, G, & T • base pairs, A-T, C-G • Genes • DNA sequences that encode proteins • less than 3% of human genome The genome is who we are on the inside!
- 11. AIMS OF THEPROJECT: • To identify the approximate 100,000 genes in the human DNA. • Determine the sequences of the 3 billion bases that make up human DNA. • Store this information in databases. • Develop tools for data analysis. • Address the ethical, legal, and social issues that arise from genome research.
- 12. • The first10 years of the project were spent improving the technology to sequence and analyze DNA. • Scientists all around the world worked to make detailed maps of our chromosomes and sequence model organisms, like worm, fruit fly, and mouse. Beginning of project
- 13. How was itdone… First there was the Assembly The DNA sequence is so long that no technology can read it all at once, so it was broken into pieces. There were millions of clones (small sequence fragments). The assembly process included finding where the pieces overlapped in order to put the draft together.
- 14. • UCSC putthe human genome sequence on CD in October 2000, with varying results UCSC put the human genome sequence on the web july 7, 2000
- 15. The completion ofthe human genome sequence • In June 2000, White House announced that the majority of the human genome (80%) had been sequenced (working draft). • Working draft made available on the web July 2000 at genome.ucsc.edu. • Publication of 90 percent of the sequence in February 2001 issue of the journal Nature. • Completion of 99.99% of the genome as finished sequence in July 2003.
- 16. • Where arethe genes? • How do genes work? • How do scientists use this information for scientific understanding and to benefit us? • What do genes do anyway? • We only have ~27,000 genes, so that means that each gene has to do a lot. • Genes make proteins that make up nearly all we are (muscles, hair, eyes). • Almost everything that happens in our body happens because of proteins • (walking, digestion, fighting disease). Next …the Annotation or Eye Color is determined by genes
- 17. From our genomeso far… • Relatively small number of human genes, less than 30,000 • Have a complex architecture (which is yet to be analyzed completely) • We know where 85% of genes are in the sequence. • We don’t know where the other 15% are because we haven’t seen them “on” (they may only be expressed during fetal development). • We only know what about 20% of our genes do so far.
- 18. What Does TheDraft Human Genome Sequence Tell Us? • The human genome contains 3.2 billion chemical nucleotide bases (A, C, T, & G) • Takes 95 years to read
- 20. Sequence Similarity/ Dissimilarity?? 0.001% 95- 98% 7% 36% 90%
- 21. STRUCTURAL GENOMICS • Effortaimed at determining the three-dimensional structures of gene products • Using efficient and high-throughput mode • For Proteins- Structural proteomics! • Understanding novel proteins and 3D structures
- 22. FUNCTIONAL GENOMICS • Identifyfunctions of gene and non-gene sequences • Describe gene & protein functions • Gene & Protein interaction • Genotype- Phenotype
- 23. COMPARATIVE GENOMICS • Comparegenome sequence between different species • To better understand the evolutionary relationships • Determine the function of each genome
- 24. MUTATIONAL GENOMICS • Studyof genome in terms of mutations that occur in the DNA or Genome of an individual • Also termed as gene function determination • Understand the mutations in Coding sequences Non coding sequences • Due to Repeat sequences: Minisatellites Microsatellites • SNP
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- 26. • The setof all RNA molecules including: mRNA rRNA tRNA non-coding RNA produced in one or a population of cells Transcriptomics, is a global way of looking at gene expression patterns
- 27. TRANSCRIPTOME PROFILING • Deepinvestigation of the transcriptome • Study the transcriptional activity • Proteins coded by the RNA transcript • Study gene fusions etc… Annotate the RNA transcript
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- 29. We all aremade up of proteins 29
- 30. WHY PROTEOMICS? Fact: • Genome~ 26,000-31,000 protein encoding genes • Human proteins ≥ 1 million • Proteomics – • Study of the full protein complement of organisms e.g. plasma, cells and tissue
- 31. UNDERSTANDING THE PROTEOMEALLOWS… • Characterisation of proteins • Understanding protein interactions • Identification of disease biomarkers
- 32. MAJOR APPLICATIONS… GENOMICS, TRANCRIPTOMICS,PROTEOMICS • Gene prediction • ORF Finding • Metagenomics • Next Generation Sequencing • Computer Aided Drug Design
- 33. NEXT GENERATION SEQUENCING •DNA sequencing technology which has revolutionised genomic research • Determining the number and order of nucleotides that make up a given molecule of DNA. • Using NGS an entire human genome can be sequenced within a single day. • In contrast to the previous Sanger sequencing technology • A number of different modern sequencing technologies including: Illunmina, Roche 454 sequencing, Ion Torrent , PacBio etc. • Cost
- 34. COMPUTER AIDED DRUGDESIGN
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- 36. PREDICT TERTIARY STRUCTURE Protein sequence Homology modelling Abinitio prediction Threading • Find homologous sequence • Homology > 30% • Keeping in view of the template structure Swiss PDB Viewer , MODELLER If homologous sequence is < 30 % similar we use this method Prediction of structure from scratch using the knowledge of amino acid properties iTASSER, PHYRE ROSETTA 36
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- 38. TIME & MONEY … •10-12 Years • 1 Drug/Year • Rs 400 Crores (=Boeing 747) • 5000 to even 50000 screenings Returns too are striking… • Lipitor, cholesterol reducer from Pfizer sold for 8.6 Billion US$ in 2001 38
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- 40. IMPORTANT TERMS • Target-a molecule important in a disease-usually a protein • Ligand- a small molecule binds to a larger one • Active site- ligand binding site • Hit- a ligand which can geometrically fit to the binding site • Lead- hit with biological activity • DRUG- Ligand that can modulate the function of target in desired way 40
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- 43. ENZYME – SUBSTRATEBINDING: 2 MODELS 43
- 44. • Docking Software- Discovery Studio, Schrodinger Auto Dock. Phyredock, Patch dock • Mostly drug activity is obtained through binding of one molecule to the pocket of another. • ADME Test Absorption, Distribution, Metabolization, & Excretion 44
- 45. MORE IS NOTALWAYS BETTER • Be careful about dosage amounts 45
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