Comm meeting 03

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Is Gene Position Adaptively Favored?
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Why do we care?

• Genomic clusters of genes
• Yeast
• 98 of genes in metabolic pathways cluster (Lee
  Sonnhammer)
• 25 of cell-cycle dependent genes are directly
  adjacent (Cho et al.)
• Drosophila
• 20 of genes in co-expression clusters (Spellman
  et al.)

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Why do we care?

• Genomic clusters of genes
• Arabidopsis
• 43 of genes in metabolic pathways cluster (Lee
  Sonnhammer)
• Blocks of neighboring genes co-express (Williams
  Bowles)
• Clusters up to 20 genes, 100kb
• Evolutionary process?

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Idea to test

• Gene clusters occur due to evolutionary processes
• Look for evidence of selection on clusters

5
Method

• Plot co-expression vs recombination rate for each
  gene, compare to selection models

Co-expression / Co-expression
Recombination rate
Chromosomal position
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Hill-Robertson Effect

• Reduction in the efficacy of selection
• In regions of low recombination, mutations are
  linked
• This limits the effective population size for
  region
• Mutations more likely to be fixed in small
  populations

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The test

• Selection
• Relatively neutral - clusters scattered
• Positive - skew toward high recombination
• Negative - skew toward low recomb regions

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Method

• Plot co-expression vs recombination rate for each
  gene, compare to selection models

Recombination rate
Chromosomal position
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Recombination rate

• Estimated for 17.8k genes by Jianhua Hu

cM (genetic dist)
Chromosome position
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Recombination rate
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Method

• Plot co-expression vs recombination rate for each
  gene, compare to selection models

Co-expression / Co-expression
Chromosomal position
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Expression Data

• NASC Expression data
• Affymetrix arrays of Arabidopsis genes
• 22,700 genes
• 59 datasets, 534 arrays
• AtGenExpress data
• gt500 datasets, 1300 arrays

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Co-expression measurement

• Measures of co-expression
• R Pearson / Spearman correlation
• Linear relationship between points (scaled)
• Demonstrate positive or negative correlation
  (-1..1)
• Euclidean distance
• Distance between two points
• Demonstrates correlation (0..1)
• Calculate for neighboring genes

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Other factors

• Factors to consider
• Tandem duplicates likely to co-express
• Array conditions

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Method

• Plot co-expression vs recombination rate for each
  gene, compare to selection models

Co-expression / Co-expression
Recombination rate
Chromosomal position
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Regional transcription

• Mechanisms
• Matrix attachment sites
• Change chromatin loops (3D structure)
• Insulators, Boundary elements

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