Chapter 21 Genomes Genomics Scientific attempt to sequence interpret and compare whole genomes gives a list of genes that are in an organism o Genome Complete DNA Sequence of an Organism Human genome sequence published 2 2001 Functional Genomics Observed when genes are expressed how the products of those genes interact o Humans have 3 billion nucleotides o Genome shotgun sequencing approach Genome is broken up into overlapping fragments that are later sequenced ordered Shotgun sequencing approach Sonication Breaks genome into pieces by using high frequency sound saves 160 kilobases long Each piece inserted into a BAC plasmid artificial chromosomes Inserted into E Coli cells so colonies are grown rapidly BAC library Each DNA segment is broken down into a 1 kilobase segment Each little segment is cloned into a plasmid then inserted into E Coli cells so a colony of shotgun clones can be created Computer programs then sequence analyze cloned fragments Sequences in order reconstruct the BACs Ends of reconstructed BACs are analyzed each 160 kb segment is put in the right place on the chromosome based on overlaps o Pyrosequencing Cheaper faster way than traditional sequencing Works with 1 single DNA fragment instead of multiple copies Only works with fragments that are to small to be reconstructed into a complete genome Compares sequence of individual to a master genome Bioinformatics Manages analyzes and interprets biological information o First genome sequenced was haemophilius influenza bacteria o Most basic task Interpreting a genome to figure out which bases make which genes tough to do in eukaryotes o Computer programs scan genome sequences in both directions and then identify open reading frames ORFs possible genes long stretches of sequence that have NO stop codons Also look for sequences typical of promoters operators and other sites ORF can be proven to be a gene by analyzing product and checking to see if it s homologous to a known gene Identifying genes in eukaryotic genomes o Genes contain introns o Most of genome don t code for a product can t scan for ORFs o Uses reverse transcriptase to make cDNA version of each mRNA then sequence a portion of resulting molecule to produce an expressed sequence tag EST protein coding gene Bacterial Archael genomes Sequencing of genomes of various strains of same prokaryotic species compared to genomes of closely relating organisms that have different ways of life o Bacteria Correlation between size of genome and metabolic capabilities of organisms o Huge genetic diversity between bacteria archaea 15 unique o Redundancy among genes is common even within one prokaryotic o Mutation genetic recombination within species are not only sources Prokaryotic Genomes Multiple chromosomes plasmids are more common o Significant portion of genome was acquired from other distantly genome of genetic variation related species o Lateral gene transfer movement of DNA from one species to another over 50 of archaen species have 1 gene from lateral gene transfer Evidence If a gene is much more similar to genes in distantly related species than closely related species AND when proportion of G C base pairs to A T base pairs in gene or gene series is really different from base composition of the rest of the genome Lateral gene transfer is often a result because genes are carried on plasmids Also occurs through transformation takes DNA fragments from environment Environmental sequencing metagenomics Practice of cataloging all genes present in a community of bacteria archaea o Study of GENES discovery of over 150 types of new bacteria Eukaryotic Genomes Dominated by repeated DNA sequences that occur between genes inside introns don t code for products used by organism o Much larger than bacterial archaeic genomes and have noncoding repetitive sequences Protein sequencing is very small part of human genome Repetitive sequences make up more than 50 of human genome over 90 of prokaryotic genome consists of genes Repeated sequences in human genome often result of transposable elements Transposable elements Segments of DNA that can move from one location in a genome to another o Selfish genes parasitic DNA sequences that survive reproduce but don t increase fitness of host genome BUT they are parasitic can disrupt gene function when they insert in a new location Long interspersed nuclear elements LINEs One type of transposable element o An active LINE contains all sequences required to make copies of itself insert them into a new location in the genome Analyses of human genome have revealed that only a few LINEs appear to be complete potentially active Repeated sequences Eukaryotic genomes have several thousand loci called short tandem repeats STRs small sequences repeated down the length of a chromosome o Hypervariable Vary among individuals more than any other type of sequence o 2 types of STRs Microsatellites simple sequence repeats that are repeating units of 2 6 bases Minisatellites or variable number terminal repeats VNTRs that are units of 6 to 100 bases Hypothesis for why micro mini satellites have so many different alleles Highly repetitive stretches may misalign when chromosomes synapse during meiosis causes unequal crossover different number of repeats DNA Fingerprinting Any individual can be identified by unique genome features micro mini satellite loci are markers of choice for DNA fingerprinting o Process A sample of DNA is acquired from individual PCR performed using primers that flank a region containing an Region is cloned Region can be analyzed to determine number of repeats STR present Gene Family Genes that are extremely similar to each other in structure function considered to be part of the same gene family within species o Genes that make up gene families are hypothesized to have arisen from a common ancestral sequence through gene duplication Major Source of New Genes in Eukaryotes Through duplication of existing genes o When this occurs an extra copy of a gene is added to the genome o Most common type of gene duplication results from unequal crossing over during meiosis Redundancy of duplicated genes may allow one copy to mutate to create a new gene with different function or regulation possibly leading to evolution of new traits o Gene duplication is important because original gene is still functional produces normal product but duplicated gene may retain original function and provide additional quantities of same product OR undergo mutation
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