Genomes

• FISH


  fluorescence in situ hybridisation
• FISH fluorescently labels nucleic acid probes
• linkage maps


  type of genetic map of genes on a chromosome
• physical mapping


  ordering of overlapping fragments cloned in YAC and BAC vecotrs
• overlapping of fragments allows gene sections to be put into sequential order
• YAC


  yeast artificial chromosomes, a form of DNA cloning that carries fragments of 1 million base pairs long
• BAC


  bacterial artificial chromosomes, carries inserts of 100,000-300,000 base pairs
• whole genome shotgunning approach


  skips linkage and physical maps and used computed to sequence DNA fragments from randomly cut DNA
• metagenomics


  DNA from a group of species is collected from an environmental sample and sequenced
• gene annotation


  identify all protein-coding genes in the sequence and their functions
• gene annotation looks for transcriptional and translational factors, RNA splicing sites, and mRNA
• expressed sequence tags


  transcriptional and translational factors, RNA splicing sites, and mRNA
• cDNA


  copy DNA, synthetic DNA that has been transferred from a specific mRNA through a reaction using reverse transcriptase
• ENCODE


  encyclopedia of DNA elements
• proteins carry out majority of functions of the cell
• bacterial genomes have 1-6 billion base pairs
• E.coli has 4.6 Mb
• Mb stands for megabase
• one Mb is 1 million bases
• archaea genomes are within the same base range as bacteria
• single-celled yeast has 12 Mb
• eukaryotes have a wide range of base pairs which doesn't have a defining characteristic
• bacteria and archaea have fewer genes than eukaryotes
• bacteria and archea have 1500-1700 genes
• eukaryotes have 5000-40000 genes
• typical human gene has 10 exons
• 93% of human exons can be spliced in two different ways
• eukaryotes have larger genomes but fewer genes in a given number of bases
• gene density is lower in humans
• humans have 10000 times more non-coding DNA than bacteria
• gene-related regulatory sequences and introns account for 5-20% of the human genome
• pseudogenes


  former genes that have accumulated mutations over a long time and no longer produce functional proteins
• repetitive DNA


  sequences that are present in multiple copies of the genome
• 75% of repetitive DNA made of transposable elements
• transposable elements


  stretches of DNA that can move from one location to another within the genome
• during transposition, TE moves to a different target site by a type of recombination process
• TE's are brought together by enzymes and other proteins that bind to the DNA
• some TE's never really detach from the old DNA
• there are two types of transportable elements
• What are the two types of transposable elements?

  transposons and retrotransposons