Genes, Genomes, and Gene Expression

1
Genes, Genomes, and Gene Expression

• Debra T. Burhans, Ph.D.
• Director, Bioinformatics Program
• Canisius College
• burhansd_at_canisius.edu
• Bioinformatics Workshop for TeachersUniversity
  at Buffalo
• August 15-19, 2005

2
Outline

• A closer look at genes and genomes
• Gene expression
• Summary
• Textbook reference (Mount) Chapters 9,11,13

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A closer look at genes and genomes
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Genomics and genes

• Nova Cracking the Code of Life video
  Instructions for a Human Being http//www.pbs.org/
  wgbh/nova/genome/program.html
• UCSC Genomics http//genome.ucsc.edu/
• Gramene http//www.gramene.org
• NCBI Mapview http//www.ncbi.nlm.nih.gov/mapview/
• The best way to learn about genomes is to look at
  them in varying levels of detail
• Gene structures are revealed in genome browsers
  along with various types of evidence for their
  existence
• Many genes have been confirmed by experimentation
  but others remain putative based on what we know
  about other genes and their features

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Genome annotation

• Once a genome has been sequenced the work of
  annotating the sequence begins
• Annotation involves identifying features along
  the sequence, including genes, regulatory
  regions, and other features of interest
• Once features are identified their function can
  be studies
• Feature and functional annotation is an ongoing
  process that takes place after a genome has been
  sequenced
• Example Apollo, a genome annotation tool

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Gene Expression
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Gene Expression

• We say that a gene is expressed when it is being
  transcribed
• Evidence for gene expression is the mRNA in the
  cell
• Gene expression patterns are spatially and
  temporally mediated
• This means that in different tissues and at
  different times, for example, during development,
  there are different expression patterns
• Gene expression in diseased cells differs from
  that in healthy cells
• Genes that are expressed together may encode
  proteins that are part of the same biochemical
  pathway

8
Measuring gene expression

• Microarrays are a technology that was developed
  to measure gene expression patterns
• There are several different types of microarrays
• Two common types are
• cDNA spotted arrays
• Affymetrix arrays (oligonucleotide short nucl
  sequence)
• cDNA arrays are custom designed and made, in
  Buffalo there is a cDNA array facility at Roswell
  Park Cancer Institute
• Affymetrix is a company that manufactures gene
  chips for use in the laboratory, Roswell also has
  an Affymetrix facility

9
Spotted cDNA Microarray chips

• Microarray animation creating a spotted cDNA
  array
• http//www.bio.davidson.edu/courses/genomics/chip
  /chip.html
• Another animation highlighting different parts of
  the process
• http//darwin.bio.uci.edu/faculty/wagner/array2.
  html
• A third animation showing actual footage of a
  robot arm spotting arrays http//www.hhmi.org/bioi
  nteractive/

10
cDNA tissue array

• This spotted array show gene expression in
  different tissues, the image gives you a general
  idea of how these arrays look on a slide (from
  http//www.tissue-array.com/ver3/)

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Glass slides for cDNA microarrays

• This is another view of glass slide microarrays
  in a holder for a microarray reader (from
  http//www.vp-scientific.com/glass_slide_microarra
  yer.htm)

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cDNA microarray technology
lab_vol/P21/p21microarray.htm
13
Affymetrix chips
from www.affymetrix.com
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Affymetrix technology

• Affymetrix educator resources http//affymetrix.co
  m/corporate/outreach/educator.affx

Photolithography (from www.affymetrix.com)
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Affymetrix technology
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Oligonucleotide arrangement on GeneChip

• http//cnx.rice.edu/content/m12388/latest/

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Experiments with Affy chips

• A typical experiment with an oligonucleotide
  chip preparation of sample for GeneChip arrays.
  Messenger RNA (mRNA) is extracted from the cell
  and converted to cDNA. It then undergoes
  amplification and labeling step before
  fragmentation and hybridization to 25-mer oligos
  on the surface to the chip. After washing of
  unhybridized material, the chip is scanned in a
  confocal laser scanner and the image analyzed by
  computer. (www.affymetrix.com)

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Microarray results
Results from comparing gene expression in
patients with ALL with patients with AML Golub
et al, Science, found on the following web
site http//www.genetics.ucla.edu/labs/horvath/Bi
ostat278/GolubLanderSciencePaper.ppt
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Differential gene expression in cancers

• Gene expression patterns in different can cers
  from http//gg.bu.edu/microarray/