Genome analysis

Genome analysis

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  Genome Analysis
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  Importance A gene issequenced to predict its function or to manipulate its activity/ expression. Availability of genome sequence provides, - The sequences of all the genes of an organism. So that , - Important genes and - Disease process can be studied.
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  Goals and Challenges Goals: 1.Identification of genes that are predicted to have a function 2. Design of experiments to test that prediction Challenges: 1. Gene prediction 2. Phylogenetic history 3. Presence of repetitive sequences 4. Genome rearrangements
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  Hapmap project One ofthe efforts to identify the important sequence variations in humans that can be used to identify disease risk or sensitivity to drugs. It tracks the size and the location of common blocks and haplotype variations of each block.
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  Genome anatomy
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  Prokaryotic genomes sequencing project -First bacterial genome to be sequenced - Size 1.8 X 106 - Hemophilus influenza 58% of 1743 predicted genes matched to E.coli K-12 genes of known function Once the assembled genome was available, ORFs were identified and compared to known protein sequences.
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  Criteria for selection 1.They had been subjected to significant biological analysis e.g., E.coli and B.subtilis 2. They were an important human pathogen e.g., M.tuberculosis and M.pneumoniae 3. They were of phylogenetic interest and likely to reveal information about the evolution of bacteria.
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  Eukaryotic genomes Differ fromprokaryotic genomes by having, - Chromosomes within a nucleus - Large genomes - Tandem repeats of sequences - Introns in protein coding genes
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  Sequence repeats Eukaryotic genomesoften have many tandem repeats of the same sequence. They vary in, - Size - Number - Location in the genome - Location in specific regions Some times they may be present on movable elements
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  Satellite DNA Repeats aremade of the same sequence Skewing effect DNA with different buoyant densities Satellite DNA
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  Heterochromatin and Euchromatin Heterochromatin - Dueto compact configuration, take light stain - Role: Centromeres and Telomeres found near heterochromatin Euchromatin - Due to less compact configuration darkly stained - Region to be transcribed
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  Types of SatelliteDNA Satellites: - Composed of repeats of 1000 to several 1000 bases in very large tandem arrays up to 100 million bases long. - Present typically near centromeres and telomeres Minisatellites: - Made up of repeats of approximately 15 bases in length in arrays highly variable in length. - typically located in the euchromatin Microsatellites: - Made up of repeats of 2–6 bases long in arrays that are highly variable in length. - typically present in euchromatin and centromere
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  Transposable elements
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  Eukaryotic TEs 1. ClassI: - LTR (Long Terminal Repeats) - Retrosposons (SINES, LINES) - Retro virus like elements with LTRs 2. ClassII: 3. MITES (Miniature, Inverted repeat TEs)