Genes

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Genes
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Outline

• Genes definitions
• Molecular genetics - methodology
• Genome Content
• Molecular structure of mRNA-coding genes
• Genetics
• Gene regulation
• Genetics
• Molecular biology
• Arrays
• Issues
• Genetic and misexpression approaches

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Gene Definitions

• Gene
• Molecular definition stretch of DNA that
  encodes
• Functional RNAs - tRNA, rRNA
• Functional proteins - mRNA
• All sequences necessary for proper function
  (genetic) includes regulatory elements and
  transcription unit
• Generally excludes other types of genomic
  sequences
• Centromeres, telomeres, origins of DNA
  replication, transposons
• Genetic definition element required for proper
  organismal function

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Molecular Genetics

• Genetics mutant phenotype
• Molecular Biology gene sequence,
  expression-arrays
• Biochemistry activities, interactions
• Cell biology structure, dynamics

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Genomic Content

• Calf Thymus DNA sheared to a size of 300 bp,
  denatured, and reannealed
• 3 classes
• Highly repetitive 10 DNA - anneals very
  rapidly
• Middle repetitive 30 DNA - C0t1/2 0.04
• Non-repetitive (unique) 60 DNA - C0t1/2 4000

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Highly Repetitive Simple Sequence DNA

• Clusters of tandemly-linked 5-10 bp repeats
• Can have gt 106 copies/genome
• Not transcribed

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Intermediately Repetitive DNA Mobile Elements
Unique DNA
Repeat

• Repetitive elements interspersed among unique DNA
• Most are transposons mobile DNA
• Many are no longer able to transpose
• Dispersed throughout the genome
• Different classes
• Transpose as DNA or RNA intermediates

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Unique DNA-Coding Sequence Genes

• Slow kinetic class corresponds mainly to
  protein-coding genes
• Average gene size (transcribed region
  only)/organism
• E. coli 1.2 kb
• Yeast 1.7 kb
• Drosophila 11.3 kb
• Human 27.0 kb
• As complexity increases, so does gene size

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Overview of Gene Expression-1
Regulatory region
Transcription unit
DNA gt ACGT
RNA gt ACGU
Nucleus
Transport to cytoplasm
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Overview of Gene Expression-2
aa1 methionine
Protein - myoglobin
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DNA and Clones

• Genomic or chromosomal DNA genomic clones
  (exons, introns, spacer, etc.)
• Transcription unit entire region of gene
  transcribed (exons introns)
• mRNA cDNA clones (exonic sequences)
• ESTs expressed sequence tags
• Oligonucleotides small stretches of DNA (20-50
  nt)

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Human Genome Project Gene Number

• Size 3,200 Mb
• Predicted gene number
• Celera 39,114
• Public consortium 29,691
• Refseq (known genes) 11,015
• Non-identity
• 64 novel genes dont overlap
• gt 80 novel genes expressed
• Indicates they are real
• Estimate 50,000 genes
• Estimate 64 kb/gene
• Transcribed region 27 kb
• Spacer DNA 37 kb
• Repeats control elements
• Human large number of transcripts/gene
• exist because of alternative splicing

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Completed Genomic Sequencing Projects

• Human disease genes
• Drosophila model system for animal development
  and gene control
• Strength - genetics
• Nematode - model system for development and
  behavior
• Strength - genetics
• Fly and human more related than worm-human
• Arabidopsis weed model plant genetic system
• Crop plants rice, maize
• Yeast typical eukaryotic cell
• E. coli
• Many pathogenic bacteria - disease

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Genome Projects in Progress

• Multiple Humans SNPs disease genes and
  predispositions
• Mouse model system to study human/mammalian
  gene function
• Strength knockout mutants
• Zebrafish - model vertebrate genetic system
• Strength large-scale genetic screens
• Crop plants poplar, apple, tomato pests
• Additional Drosophila species
• Identify gene control regions

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Drosophila

• Drosophila genome 180 Mb
• Sequenced 120 Mb euchromatic region
• 60 Mb heterochromatic region unsequenced (few
  genes)
• Annotation 13,601 predicted genes
• Genie predicts ORFs/exons
• Compare to Expressed Sequence
• Tags (ESTs-cDNAs)
• Blast searches sequence identity
• to known genes

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Complications of Gene Prediction by Computer
Cranky Example

• RT-PCR of embryonic RNA
• 33 kb

EST-LP05454-3'
Exons
EST-LP05454-5'
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7
8
9
5
3
4
2
1
CG14554
Genie
CG12561 1-3
CG14552 1-4
CG14553 1-3
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Drosophila Gene Functions

• 14,113 predicted transcripts with different
  coding sequences
• Biochemical function
  Process
• 2,081 Transcription factors 2,274
  Metabolism
• 2,422 Enzymes 530
  Cell communication
• 665 Transporters 486
  Development
• 622 Signal transduction 201
  Physiology
• 303 Structural proteins 118
  Sensation behavior
• 216 Cell adhesion 8,884
  Unknown
• 7,576 Unknown

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