Does gene order matter?

1
Does gene order matter?

• Cis-regulatory elements, proteins, and messengers
  are integrated into biological circuits.
• Does gene location in the genome affect the
  circuit?
• Genome evolution gene order does matter thats
  why we observe synteny

2
Gene order in T7

• T7 produces 59 proteins from 56 genesonly 33
  have known function
• T7 infection is unique, first 850 bp are
  inserted, transcription begins, then the
  remainder is pulled in
• E. coli polymerase pulls the first 15 of genomic
  DNA into the cell at 45 bp/sec through
  transcription at 5 promoters what a cool
  molecular machine

3
Gene 1

• T7 RNA polymerase
• Uses 17 different promoters in the remaining 85
  of genome
• Pulls at a rate of 200 bp per second.
• What happens if Gene 1 is moved elsewhere on the
  genome?

4
In silico analysis

• http//model.mit.edu/cgi-bin/t7web/t7v2.5
• Measured optimal time for phage-induced lysis for
  72 distinct T7 genomes
• Some genotypes were better than others
• T7 is suboptimal? Wheres the data?

5
Experiments

• Three phage genome constructs were generated and
  tested at positions 1.7, 3.8 and 12 (controls had
  random DNA inserted at these positions or a late
  promoter inserted early in genome)
• Little agreement between predicted and
  experimental data

6
Systems biology

• Watson School of Biological Sciences at CSH
• The systems approach defines all of th
  eelements in a system and then studies how each
  behaves in relation to the others as the system
  is functioning. Ultimately the systems approach
  requires mathematical model which will both
  describe the nature of the system and its systems
  properties.

7
Systems Biology Superstars

• Integration of multiple -omes
• Metabolomics
• Proteomics
• Genomics
• Looking at individual silos of genomics,
  proteomics, or metabolomics is akin to using a
  laser pointer in a dark office to describe its
  contents

8
Galactose metabolism in yeast as an example

• Define all genes in the genome and the subset of
  genes, proteins and other molecules constituting
  the galactose pathway..build a model
• Perturb each pathway component using genetics or
  environmental challenges
• Utilize microarrays and ICAT to collect gene
  expression data
• Refine model

9
Functional genomics

• Grew wild type and deletion strains and assessed
  gene expression via microarrays
• Used Northerns as controls
• How reliable are microarrays?

10
Proteomics

• http//occawlonline.pearsoned.com/bookbind/pubbook
  s/bc_mcampbell_genomics_1/medialib/method/ICAT/ICA
  T.html
• Measured 289 proteins using ICAT, only 30
  observed differences 15 of which showed no
  change in RNA levels, post-transcriptional control

11
Going system

• http//depts.washington.edu/sfields/
• Ideker uses Fields protein interaction data to
  identify 997 mRNA and 15 proteins whose
  expression is altered by galactose
• Discovery questions 7-9 in Chapter 9
• I relent on the writing Typically, if good data
  conflict with your model, trust your data