* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Genomics
Ridge (biology) wikipedia , lookup
Genomic imprinting wikipedia , lookup
Genealogical DNA test wikipedia , lookup
Short interspersed nuclear elements (SINEs) wikipedia , lookup
Zinc finger nuclease wikipedia , lookup
DNA vaccination wikipedia , lookup
Cell-free fetal DNA wikipedia , lookup
Gene expression profiling wikipedia , lookup
Epigenetics of human development wikipedia , lookup
DNA supercoil wikipedia , lookup
Nutriepigenomics wikipedia , lookup
Cancer epigenetics wikipedia , lookup
Point mutation wikipedia , lookup
Primary transcript wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Mitochondrial DNA wikipedia , lookup
Oncogenomics wikipedia , lookup
Nucleic acid double helix wikipedia , lookup
Molecular cloning wikipedia , lookup
Epigenomics wikipedia , lookup
Genetic engineering wikipedia , lookup
Metagenomics wikipedia , lookup
Transposable element wikipedia , lookup
Deoxyribozyme wikipedia , lookup
Genome (book) wikipedia , lookup
Whole genome sequencing wikipedia , lookup
Cre-Lox recombination wikipedia , lookup
Public health genomics wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Extrachromosomal DNA wikipedia , lookup
Microsatellite wikipedia , lookup
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing wikipedia , lookup
Pathogenomics wikipedia , lookup
Microevolution wikipedia , lookup
Designer baby wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Site-specific recombinase technology wikipedia , lookup
Human genome wikipedia , lookup
Human Genome Project wikipedia , lookup
Minimal genome wikipedia , lookup
Genomic library wikipedia , lookup
Non-coding DNA wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
History of genetic engineering wikipedia , lookup
Helitron (biology) wikipedia , lookup
LECTURE 1. The Genome Age Lecture 1 MG701 The AGE of DNA: Three Notions Converged in the Construction of the Double Helix Model for DNA by Watson and Crick (1953) Nobel Laureates: 1962 Francis Crick James Watson Maurice Wilkins 1. X-ray diffraction data showed that DNA has the form of a regular helix, making a complete turn every 34 Å (3.4 nM), with a diameter of ~20 Å (2 nM). Since previous studies indicated that the distance between adjacent nucleotides is 3.4 Å, there must be 10 nucleotides per turn of the helix. Maurice Wilkins Rosalind Franklin 1920-1958 2. The density of DNA suggests that the helix must contain two polynucleotide chains. The constant diameter of the helix can be explained if the bases in each chain face inward and are restricted so that a purine is always opposite a pyrimidine 3. Irrespective of the actual amounts of each base, the proportion of G is always the same as the proportion of C, and the proportion of A is always the same as that of T. Thus the composition of any DNA can be described by the proportion of its bases that is G + C, which ranges from 26% to 74% for different species. The Watson-Crick Model: 1. TWO ANTI-PARALLEL DNA STRANDS 2. COMPLEMENTARY A:T AND G:C BASE PAIRS 3. BACKBONE FORMS A RIGHT HANDED DOUBLE HELIX 4. BASES LIE PERPENDICULAR TO THE AXIS OF THE HELIX AND ARE "STACKED" 5. PITCH OF THE HELIX IS 10 BP/TURN Double-stranded DNA can be MELTED and REANNEALED T(M)=temperature at which 1/2 of a DNA sequence of known composition will be denatured (single stranded) The T(M) is Directly Proportional to G-C Content of the DNA T(M): DNA Concentration and Time are Critical parameters At equal DNA concentrations, a smaller genome will reanneal more quickly than a larger genome Genome Analysis by Hybridization: C0t1/2 for different Genomes Is Proportional to Genome Size Mammalian Genomes Contain Three Classes of DNA Highly Repetitive 10K-50K copies/cell Middle Repetitive 100-10,000 copies/cell Unique 1. Unique Sequences A. Genes B. Regulatory Sequences 2. Middle Repetitive A. Gene families, e.g. histones B. Ribosomal, tRNAs, other small RNAs C. Non-coding sequences -variable number tandem repeats (minisatellite) -short tandem repeats (microsatellite) 3. Highly Repetitive sequences A. Sequences involved in chromosome structure/stability -centromeric (satellite) and telomeric B. Transposable elements -Long interspersed elements (LINES) -Short interspersed elements (SINES) THE AGE OF CLONING: Restriction Enzymes Allow DNA to be fragmented in a sequence specific fashion Discovery of Restriction in Bacteria(1962): -phage produced in E. Coli K12 could infect K12 but not E. Coli B: K12 phage growth was "restricted" in B strain. Nobel Prize 1978: Arber, Nathans, Smith Subsequently demonstrated that bacteria contained enzymes that were responsible for phage restriction: A) Each bacterial strain produced an endonuclease that cleaved foreign DNA at specific sites: Restriction enzyme. B) The bacteria also produced a methyl transferase that modified it's own DNA, thus protecting against it's cognate restriction enzyme. Restriction Enzymes allow Molecular Cloning of DNA Polymerase Chain Reaction: Molecular Cloning without vectors Nobel Prize 1993 Kerry Mullis, Michael Smith THE AGE OF GENOMICS Genome Size and Gene Number in Model Organisms and Man 50 genes 4100 genes 6000 genes 18,000 genes 35-70,000 genes? 14,000 genes Goals of Genome Projects: 1) Complete Genetic Maps of the entire genome. 2) Complete set of contiguous clones that span the entire genome. 3) Complete Nucleotide sequence of the genome Yeast genome project* http://genome-www.stanford.edu/Saccharomyces/ C. elegans genome project* http://www.sanger.ac.uk/Projects/C_elegans/ Drosophila genome project* http://flybase.bio.indiana.edu/ Mouse Genome Project* http://www.informatics.jax.org/ Human genome project* http://www.ncbi.nlm.nih.gov/genome/guide/ *all three goals completed Future Laureates? Craig Venter(Celera) Francis Collins (NIH) Genomics: 1) Structural genomics: the original Goals of Genome Projects; largely complete for the Human Genome Project What do we do with all this information? 2) Functional Genomics: Development and Application of GenomeWide Experimental Approaches to Assess Gene Function by making use of the information and reagents provided by STRUCTURAL GENOMICS In the Age of Cloning: Identify and Study One Gene at a Time In the Age of Genomics: Study ALL GENES AT THE SAME TIME Genome Projects are the Periodic Table for Biological Sciences: will allow the organization of 30,000-70,000 genes Goals of Functional Genomics: 1)DNA 2)RNA 3) Protein 4) Whole organism 5) Society Lander, E. 1996. The New Genomics: Global Views of Biology. Science 274: 536-539. 1. DNA level: a) Systematic identification of all common variants in human genes, both the coding and non-coding regions. These are the "isotopes" to gene "elements" b) resequencing of entire genomes of individuals c) comparison of fully sequenced genomes of related (and unrelated) species EG: man and chimp This requires sequencing of many genomes. 2. RNA Simultaneous monitoring of the expression of all genes EG: What do gene expression patterns look like in tumor vs. normal cells? What about following chemotherapy? Will reveal Regulatory Networks. 3. Protein a) monitoring the expression and modification state of all proteins in a cell b) systematic catalogs of all protein interactions (e.g., yeast two hybrid interactions). Already underway in yeast. c) application of structural biochemistry to genomics: classifying proteins by their shapes. 4. Whole organism Genetic tools for manipulating cell circuitry Model Systems are especially important. a) systematic knockout and mutation of genes (already underway in yeast): both stable and transient b) transgenic studies c) redesigning of cellular circuits (e.g., drosophila gal4 enhancer traps) 5. Society a) for Scientists: Increased attention to ethical, legal and social issues (ELSI) b) For non-scientists: public education