Lecture 18: Genomics

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Lecture 18Genomics
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Outline

• Genomics in general
• DNA sequencing method
• Human Genome Project
• What to learn from HGP
• Bioinformatics
• predicting Open Reading Frame
• comparing two sequences ---gt information

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Genomics in general

• originated from the journal name mid 1980s
• gene mapping, molecular cloning, large-scale DNA
  sequencing and
• computational analysis
• large-scale and high-throughput study on
  genes or
• genomes using molecular biology
• ------gt system biology (more advanced form of
  genomics)
• structural versus functional genomics
• organization and evolution of genomics
  (Comparative genomics)

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What to learn from Genomics

• Analyzing organisms using genome sequences
• Genomics can provide many unknown functional
  aspects of any given gene
• for example, gene locations and surrounding
  genes ----gt
• affect function of another gene
• Comparing genome sequence derived from different
  species
• similarities and differences at DNA sequence
  levels between species
• evolution patterns of individual genes can
  provide insightful hints regarding genes
• functions
• genes that are involved in fundamental functions
  of organisms
• (YY1)
• versus
• genes that are involved in species-specific
  functions
• (olfactory receptor genes and vomeronasal organ
  receptor genes)

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DNA sequencing methods

• Chain termination method (Sanger et al., 1977)
• enzymatic method with polymerase substrate
  inhibitors
• dideoxynucleotides (ddA, ddG, ddC, ddT)
• - requires primer and single-stranded template
  DNAs
• Chemical degradation Method (Maxam and Gilbert,
  1977)
• chemical degradation method
• sequence-specific cutting with chemicals
• require double-stranded DNAs
• The Sanger method is widely used now mainly due
  to the easiness,
• automation capability and non-toxicity.

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The chain termination method

• require polymerase (T4)
• dNTPs with ddNTPs (101 ratio)
• template DNAs
• primers
• each DNA sample requires
• 4 different chain terminaton rxns
• (ddA, ddG, ddC, ddT)

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The chain termination method
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The chain termination method

• four different rxn mixtures are separated
• in different lanes of sequencing gels
• detection by autoradiogram
• the primer is labeled with isotopes

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The chain termination method

• New method for detecting
• automated sequencing
• with fluroscence-labled ddNTP

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Sequencing of long DNAs

• the current sequencing method
• can sequence up to 500 bp in length
• to sequence one large DNA
• chromosomes (1x108 bp in length),
• you need to prepare a a large number
• of clones wth different inserted DNA
• up to million clones
• a huge effort for sequencing human
• genome ------gt Human Genome Project!

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Human Genome Project

• sequencing the entire human genome (3x109 base
  pair long)
• started mid 1980s by a group of scientist
• the working draft-stage human genome
• sequence was published 2000
• spent about 3 billions dollars (?)
• the original sequencing strategy
• was top-to-bottom approach

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Human Genome Project
URL---gt file//localhost/Volumes/digital_content_m
anager/digital_content/animations_library/genome.h
tm
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Trivia question 1 for HGP How much of human
body is DNA?

• Molecular weight (M.W.) of Human Genome
• 660 grams per base x 3x109 bases 2.0 x 1012
  grams
• 1 avogadros number 6 x 1023
• 2.0 x 1012 / 6 x 1023 3.3 x 10-12 grams 3.3
  picograms
• Human body 1013 cells
• 3.3 x 10-12 x 1013 x 2 66 grams
• 66 grams / 66 kilograms 0.1
• 0.1 of our body is DNA

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Trivia question 2 for HGP How long is human
genomic DNA?

• As a string of DNA
• 0.34 nm per base 3.4 x 10-10 meters
• 3.4 x 10-10 x 3 x 109 1.02 meters
• As a written sequence book
• one page of books 3000 letters
• one book 1000 pages 3,000,000 letters 3 x
  106 letters
• 3 x109 bases (letters) / 3 x 106 letters 1000
  books
• Human genome is equivalent to 1,000 books
• Can we read through and analyze these important
  books with our naked eyes?
• computer help --------gt bioinformatics!

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Notes for the final exam and others
The homework for this week ------gt Chapter 9
2, 11, 12, 13, 14, 15 Final grades 3 sets of
exams Review session for the final exam ----gt
discussion session in the next week No homework
for the next week