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BPS3101 Genomics Fall 2012

BPS3101 Genomics Fall 2012 . Textbook: Genomes 3 rd edition by T.A. Brown (Garland, 2007) in U. of O. bookstore and Agora bookstore. Access to Genomes 2 nd edition (Wiley, 2002) at: NCBI PubMed ( www.ncbi.nlm.nih.gov/ ) Search under “Books” with key words of interest.

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BPS3101 Genomics Fall 2012

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  1. BPS3101 Genomics Fall 2012 Textbook: Genomes 3rd edition by T.A. Brown (Garland, 2007) in U. of O. bookstore and Agora bookstore Access to Genomes 2nd edition (Wiley, 2002) at: NCBI PubMed (www.ncbi.nlm.nih.gov/) Search under “Books” with key words of interest Website notes & practice questions at: Virtual campus http://137.122.151.31/bps3101/

  2. When large-scale... DNA Genome transcription Transcriptome RNA translation PROTEIN Proteome What kind of cell is this? GENOMICS - study of complete set of genes in organism FUNCTIONAL GENOMICS - study of complete set of mRNAs (transcriptome) in cell/ tissue/ organism PROTEOMICS - study of complete set of proteins in cell/ tissue/organism “Today, we refer to genomics as a discipline that studies the structure, function and inheritance of the genome”. Biotechnology Focus “We are living in a Genomic World, July/August 2012, p.11 Fig.1.1 & 1.2

  3. ENVIRONMENTAL GENOMICS (METAGENOMICS) - study of collective genomes in an environmental community Venter et al. Science 304:66, 2004 “…identified over one million new genes and almost 150 new typesof bacteria” from ocean water microbial populations

  4. HUMAN MICROBIOME (METAGENOMICS) - study of microbes in and on humans “We have ten times as many microbial cells in our body as human ones, and though they are tiny, that still means that a 200-pound man is carrying two to six pounds of microbes, mostly bacteria.” Type of bacteria Body location Nature June 14, 2012 Genomic projects are usually large-scale, collaborative efforts Human Microbiome Project Consortium Nature 486:407, 2012

  5. “PERSONAL GENOMICS” - sequence analysis of the genomes of individuals News release March 17, 2010 Glenn Close has had her genome mapped by Illumina, one of the companies that is leading the race in whole-genome sequencing. Glenn Close Close said that she decided to take the test, which costs $48,000 to “move science forward”. How much would you pay to have your genome sequenced? Nature (June 24, 2010) poll of 1000 life scientists

  6. PERSONALIZED CANCER GENOMICS - sequence analysis of DNA from cancer cells New York Times, July 7, 2012: “In Treatment for Leukemia, Glimpses of the Future” “Lukas Wartman, a leukemia doctor and researcher, developed the disease himself. As he faced death, his colleagues sequenced his cancer genome. The result was a totally unexpected treatment.” “They fully sequenced the genes of both his cancer cells and healthy cells for comparison, and at the same time analyzed his RNA, a close chemical cousin to DNA, for clues to what his genes were doing.” “And they found a culprit - a normal gene that was in overdrive, churning out huge amounts of a protein that appeared to be spurring the cancer’s growth.” “Even better, there was a promising new drug [kidney cancer one] that might shut down the malfunctioning gene.” “Dr. Wartman became the first person ever to take it for leukemia. And now, against all odds, his cancer is in remission and has been since last fall.”

  7. PHARMACOGENOMICS - study of how human genetic makeup influences drug response Designer drugs & personalized medicine “PERSONAL GENOMICS” - sequence analysis of the genomes of individuals “Careers & recruitment in Pharmacogenomics” Nature 436:746, 2005

  8. Pharmacogenetics & pharmacogenomics are relatively new fields “Although frequently used interchangeably, pharmacogenetics is often considered the study of drug response in relation to specific genes, whereas pharmacogenomics is the study of drug response in relation to the genome” [analyzing many genes simultaneously] . Scott Genet. Med 13:987, 2011

  9. expression no expression EPIGENOMICS - genome-wide study of impact of chromatin structure on gene regulation - heritable effects of DNA methylation, histone modification... DNA methylation (brown circles) • Genetically identical mice but different DNA methylation states (eg. in regulatory region of brown-coat-colour agouti gene) • Diet of pregnant mother can shift distribution of coat colour in littermates Jirtle Nature Rev Genet 8:253, 2007 Feinberg, Nature 447: 433, 2007

  10. METABOLOMICS - high-throughput study of metabolites (lipids, carbohydrates, amino acids… ) in cell or tissue see Fig. 6.22

  11. EVOLUTIONARY GENOMICS - study of genome evolution and consequences “A Deep Catalog of Human Genetic Variation” … through genomic sequencing of different human populations Nature October 28, 2010 When did resistance to malaria arise in humans? or lactose tolerance….? Vitti et al. Trends Genet 28:137, 2012

  12. HUMAN GENOME SEQUENCE Watson & Crick 50th anniversary of discovery of double helix (2003) “Sequence and expression analysis of gaps in human chromosome 20” (Nucl Acids Res, in press 2012) - draft sequence Feb. 2001 (some gaps & sequence ambiguities) Oct. 2004 - “ finished” euchromatic sequence

  13. How large is the human genome? in base pairs (bp) or ______ billion bp or _________ Mbp Mega: 106 2001 papers in Nature & Science or __________ kb kilo: 103 Formally it should be kbp (since DNA is double-stranded), but often abbreviated to kb Whose DNA was used to obtain “the human genome” sequence? How many genes are present in the human genome?

  14. Trend of human gene number counts (& human genome-related milestones) These numbers are for protein-coding genes “Currently, a total of 7,053 small RNAs are annotated by GENCODE” Nature 489:105, Sept.6, 2012 Pertea & Salzberg Genome Biol 11:206, 2010

  15. SOME SEQUENCED GENOMES (see Tables 7.4 & 8.3) (protein-coding) 2001 draft human genome: Francis Collins (International Consortium) & Craig Venter (TIGR private company)

  16. How many genomes have been completely sequenced? September 2000 = September 2001 = September 2002 = September 2003 = September 2004 = September 2005 = September 2006 = September 2007 = September 2008 = September 2009 = September 2010 = September 2011 = 43 70 100 156 218 294 422 635 843 1078 1486 2972 (First year of BPS program) September 2012 = From GOLD - Genomes OnLine Database www.genomesonline.org/ Eukaryotic, Bacterial & Archaebacterial Metagenome projects also listed Alaskan soil, New York air, human intestine...

  17. Are genome sequence papers still receiving a lot of attention? Nature December 8, 2005 Nature October 27, 2011 Nature May 31, 2012 International consortium

  18. HUMAN NUCLEAR CHROMOSOMES In somatic cells (diploid) = 46 chromosomes 2 copies of 22 autosomes and 2 sex chromosomes XY in males, XX in females In gametes (egg, sperm) = 23 chromosomes 1 copy of 22 autosomes plus 1 sex chromosome Fig.7.5 “The nuclear genome … is divided into 24 linear chromosomes…” p.4

  19. “The nuclear genome comprises approximately 3,200,000,000 nucleotides of DNA...” p.4 They really mean bp (base pairs) not nucleotides here... So do not multiply this number by 2 when expressing as bp In the genomics field, the DNA units are often “abbreviated” as: Mb (Megabases) instead of Mbp kb (kilobases) instead of kbp but it’s implicitly understood that it refers to double-stranded DNA Also, note that genome sizes are expressed as haploid state So do not multiply the number by 2 (or 4 or 6...) when stating “genome sizes” for diploid (or tetraploid or hexaploid...) organisms However, if referring to the amount of DNA in a human somatic cell, the numerical value would be:

  20. Where is DNA located in humans? Mitochondrial genome (many copies/organelle & many mitochondria/cell) - maternally inherited Fig.8.11 - mitochondrial genes are essential for energy production (respiration) Nuclear genome Fig. 1.1

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