BIOL1020 Module 6 - Genomics

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Dr Paul Ebert

Genomics Genomics and sequencing Gene: a segment of DNA needed to contribute to a function by encoding a protein Genetics: study of the function of individual genes and their effects Genome: the entire DNA content and hereditary material possessed by an organism (may refer to nuclear, mitochondrial or chloroplast genome) Genomics: study of the functions and interactions of all genes in the genome 1977: first DNA genome sequenced (E coli bacteriophage) 2001: first human genome Sequencing before 2001 1. Cloning  Fragment genome into small pieces  Insert each piece into vector (plasmid)  Insert plasmid into bacteria and grow each as individual strain 2. Ordering: Determine position of each clone along chromosome using various techniques (i.e. electrophoresis) 3. Sequencing: determine nucleotide sequence of each fragment 4. Assembling: use computer to manage data Next generation sequencing (2009-2013) Use PCR instead (service sequences purified DNA) – costs about $3000  Massively parallel sequencing occurs in lab Assembling: computational and highly automated Soon the genome sequence of any organism will be known  Personalising treatment and drug administration? Clinical genome sequencing Genome sequencing will become a clinical test at birth Most drugs currently wasted due to incompatibility with patient genotypes  Causes financial waste and harm to patients Every human genome known -- ethical issues must be very well managed Bioinformatics How to find genes amongst nucleotides:  Start and stop codons  Translate from RNA sequence  Look at related species and proteins (available in public domain) Why are amino acid sequences similar? (characteristics preserved as important for protein function)  Regulatory sites on proteins  Amino acids essential for structure  Catalytic sites  Hydrophobic and hydrophilic domains Why aren’t nucleic acid sequences similar?  Non-translated regions  Redundancy of the genetic code  More than one nucleotide sequence that can encode same protein  Many matches by chance alone If sequences of two genes are similar:  Initial assumption is that functions are similar  Phenotypes of mutations will be similar  Knowledge of one organism can be applied to other similar ones ‘omics technologies Genomics: sequence similarity of genes/proteins Transcriptomics: abundance of every transcript – which genes are expressed? Proteomics: abundance of nearly every protein - what proteins are expressed? Metabolomics: abundance of all major metabolites – final output of gene expression Transcriptomics All transcripts are chemically quite similar but:  Not every cell type expresses same type of genes  Splice variants from same transcript  Developmental stages have different transcripts  Environmental stressors change transcripts Bacterial genomics Fewer than 1% of bacteria have been grown in the lab – great diversity Microbial fuel cells: fuel cells powered by bacteria that produce electrons as they eat What makes bacteria conducive to genomic study?  Haploid (only 1 copy of each gene)  Small genome size (4.6 million bp) – correlates to physical size  Easy to genetically manipulate  Short generation times  Asexual reproduction (genotype remains constant)  Can be frozen and stored indefinitely  Great diversity and biosynthetic capacity No clear link between genome size and reproduction rate Genome size correlates with lifestyle  Smaller bact
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