UNIT VII – GENOMICS & CANCER Big Campbell – Ch 17, 18, 20 Baby Campbell – Ch 10, 11, 12 Hillis – Chp 12, 13, 141-142

I. EUKARYOTIC GENE EXPRESSION REGULATION, cont Epigenetics Definition study of heritable changes in gene expression that do not involve changes to the DNA sequence; change in phenotype without a change in genotype. Due to: DNA methylation, histone modification and non-coding RNA (ncRNA)-associated gene silencing Illnesses, behaviors, & other health issues have been linked to epigenetic mechanisms, including cancers of almost all types, cognitive dysfunction, respiratory, cardiovascular, reproductive, autoimmune, and neurobehavioral illnesses.

I. EUKARYOTIC GENE EXPRESSION REGULATION, cont Epigenetics

I. EUKARYOTIC GENE EXPRESSION REGULATION, cont Epigenetics

II. GENOMICS Human Genome Project Goals Identify all the approximately 20,000-25,000 genes in human DNA Determine the sequences of 3 billion chemical base pairs that make up human DNA Store information in databases Improve tools for data analysis Transfer related technologies to the private sector Address the ethical, legal, and social issues (ELSI) that may arise from the project. Completed early and under-budget in 2003

II. GENOMICS, cont Chromosome 6, p Arm

II. GENOMICS, cont Transposons DNA sequences that move from one location in the genome to another “Jumping Genes”

II. GENOMICS, cont Human Genome Applications SNPs – single nucleotide polymorphisms Single base-pair that shows variation in a significant % of population SNPs that alter the fragment length following exposure to restriction enzymes called RFLPs (restriction fragment length polymorphisms) Genetic markers

II. GENOMICS, cont Human Genome Applications, cont STRs – short tandem repeats Short segments of DNA that are highly repetitive, polymorphic Repeat patterns are inherited Useful for DNA fingerprinting

III. BIOTECHNOLOGY, cont Tools, cont Polymerase Chain Reaction (PCR) In vitro method of amplifying small amounts of DNA DNA is heated to separate the double helix. Mixture is allowed to cool, DNA primers attach to target Heat-stable polymerase is used to extend the primers in the 5’–3’ direction.

III. BIOTECHNOLOGY, cont Tools, cont Southern Blotting Designed by Dr. Southern Detects particular DNA sequences Northern Blotting Detects particular mRNA sequences Western Blotting Used to detect proteins

III. BIOTECHNOLOGY, cont Tools, cont cDNA - complementary DNA Procedure for “cloning DNA” that uses mRNA, reverse transcriptase

III. BIOTECHNOLOGY, cont Recombinant DNA DNA containing nucleotides from other sources Process utilizes restriction enzymes that make jagged cuts in DNA; creates sticky ends When DNA from different sources treated with same restriction enzyme, sticky ends “mix & match” Often use reporter genes to determine success; for example, ampicillin resistance

III. BIOTECHNOLOGY, cont DNA Microarray Assays AKA DNA Chips Test used to determine gene function, gene interactions May be used to determine agressiveness of cancers, method of treatment, etc

III. BIOTECHNOLOGY, cont Gene Cloning Typically plasmid vector Plasmid isolated from bacterial cell Foreign DNA inserted into plasmid Plasmid returned to bacterial cell; described as recombinant bacterium Foreign gene is cloned as bacteria reproduce Common bacterium used for plants is Agrobacterium tumefactiens

III. BIOTECHNOLOGY, cont A CLOSER LOOK AT GENE CLONING

III. BIOTECHNOLOGY, cont Therapeutic Cloning ES iPS

III. BIOTECHNOLOGY, cont Reproductive Cloning Nuclear Transplantation Process of using unfertilized egg cell & replacing nucleus with DNA In 1997, scientists were able to produce first reproductive clone, “Dolly”, by culturing somatic cells in a nutrient-poor medium to de-differentiate them and force them back to totipotency. Reproductive cloning in animals has enjoyed limited success.

III. BIOTECHNOLOGY, cont Transgenic Organisms

III. BIOTECHNOLOGY, cont RNAi Based on principal of microRNA Exogenous small-interfering RNA (siRNA) synthesized taken up by cells or gains entrance via a viral vector Complementary to mRNA target Translation is blocked Has been used to block production of growth factors in certain cancers