Transcript Chapter 18
CHAPTER 18 LECTURE SLIDES Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Whole Genome Sequencing • The ultimate physical map is the base-pair sequence of the entire genome • Automation of this process increased the rate of sequence generation • Genome sequencing is one case in which technology drove the science, rather than the other way around 2 • Sequencers provide accurate sequences for DNA segments up to 800 bp long • To reduce errors, 5–10 copies of a genome are sequenced and compared • Vectors used to clone large pieces of DNA – Yeast artificial chromosomes (YACs) – Bacterial artificial chromosomes (BACs) 3 The Human Genome Project • Originated in 1990 by the International Human Genome Sequencing Consortium – Goal of this publicly funded effort was to use a cloneby-clone approach to sequence the human genome • Craig Venter formed a private company and entered the “race” in May, 1998 – Using shotgun-sequencing • In 2001, both groups published a draft sequence • Gaps in sequence still being filled • Still being revised 4 The Human Genome Project In 2004, the “finished” sequence was published as the reference sequence (REF-SEQ) in databases -3.2 gigabasepairs -1 Gb = 1 billion basepairs -Contains a 400-fold reduction in gaps -Error rate = 1 per 100,000 bases 5 Characterizing Genomes The Human Genome Project found fewer genes than expected -Initial estimate was 100,000 genes -Number now appears to be about 25,000! In general, eukaryotic genomes are larger and have more genes than those of prokaryotes -However, the complexity of an organism is not necessarily related to its gene number 6 Characterizing Genomes 7 Finding Genes Genes are identified by open reading frames -An ORF begins with a start codon and contains no stop codon for a distance long enough to encode a protein Sequence annotation -The addition of information, such as ORFs, to the basic sequence information 8 Noncoding DNA in Eukaryotes Each cell in our bodies has about 6 feet of DNA stuffed into it -However, less than one inch is devoted to genes! Six major types of noncoding human DNA have been described 9 Noncoding DNA in Eukaryotes Noncoding DNA within genes -Protein-encoding exons are embedded within much larger noncoding introns Structural DNA -Called constitutive heterochromatin -Localized to centromeres and telomeres Simple sequence repeats (SSRs) -One- to six-nucleotide sequences repeated 10 thousands of times Noncoding DNA in Eukaryotes Segmental duplications -Consist of 10,000 to 300,000 bp that have duplicated and moved Pseudogenes -Inactive genes 11 Noncoding DNA in Eukaryotes Transposable elements (transposons) -Mobile genetic elements -Four types: -Long interspersed elements (LINEs) -Short interspersed elements (SINEs) -Long terminal repeats (LTRs) -Dead transposons 12 Noncoding DNA in Eukaryotes 13 Expressed Sequence Tags ESTs can identify genes that are expressed -They are generated by sequencing the ends of randomly selected -But how can 25,000 human genes encode three to four times as many proteins? -Alternative splicing yields different proteins with different functions 14 Alternative Splicing 15 Variation in the Human Genome Single-nucleotide polymorphisms (SNPs) are sites where individuals differ by only one nucleotide -Must be found in at least 1% of population 16 Genomics Functional genomics is the study of the function of genes and their products DNA microarrays (“gene chips”) enable the analysis of gene expression at the whole-genome level -DNA fragments are deposited on a slide -Probed with labeled mRNA from different sources -Active/inactive genes are identified 17 18 19 Genomics 20 Genomics 21 Genomics 22 Genomics 23 Proteomics Proteomics is the study of the proteome -All the proteins encoded by the genome The transcriptome consists of all the RNA that is present in a cell or tissue 24 Applications of Genomics Genome science is also a source of ethical challenges and dilemmas -Gene patents -Should the sequence/use of genes be freely available or can it be patented? -Privacy concerns -Could one be discriminated against because their SNP profile indicates susceptibility to a disease? 25