Regulation of gene expression

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Regulation of gene expression

• Haixu Tang
• School of Informatics

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Genetic material are not lost
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Different Cell Types Synthesize Different Sets of
Proteins

• Many processes are common to all cells, and any
  two cells in a single organism therefore have
  many proteins in common.
• Some proteins are abundant in the specialized
  cells in which they function and cannot be
  detected elsewhere, even by sensitive tests.
  Hemoglobin, for example, can be detected only in
  red blood cells.
• Studies of the number of different mRNAs suggest
  that, at any one time, a typical human cell
  expresses approximately 10,000 20,000 of its
  approximately 30,000 genes
• Although the differences in mRNAs among
  specialized cell types are striking, they
  nonetheless underestimate the full range of
  differences

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Gene Expression is regulated in Response to
External Signals
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Switching devices for gene regulation

• Short stretches of DNA of defined sequence
  (cis-elements)
• gene regulatory proteins that recognize and bind
  to them (trans-factors)

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Base pairs in DNA can be recognized from their
edges
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DNA conformation changes after protein binding
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Table 7-1. Some Gene Regulatory Proteins and the
DNA Sequences That They Recognize
Bacteria lac repressor 5 AATTGTGAGCGGATAACAATT
CAP TGTGAGTTAGCTCACT
lambda repressor TATCACCGCCAGAGGTA
Yeast Gal4 CGGAGGACTGTCCTCCG
Mata2 CATGTAATT
Gcn4 ATGACTCAT
Drosophila Kruppel AACGGGTTAA
Bicoid GGGATTAGA
Mammals Sp1 GGGCGG
Oct-1 Pou domain ATGCAAAT
GATA-1 TGATAG
MyoD CAAATG
p53 GGGCAAGTCT
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DNA binding on the major groove
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The DNA-binding helix-turn-helix motif
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Some helix-turn-helix DNA-binding proteins
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lambda Cro protein
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Hemeodomain
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Zinc fingers
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DNA binding by a zinc finger protein
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A dimer of the zinc finger domain
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b sheets Can Also Recognize DNA
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Leucine Zipper
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Heterodomain of Leucine zipper
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Dimerization of HTH
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A heterodimer composed of two homeodomain
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DNA-protein interaction
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DNA recognition code
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Gel-mobility assay
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DNA affinity chromatography
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Tryptophan switch
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Switch on/off
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Switch on/off by tryptophan binding
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Dual control of the lac operon
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Enhancers from distance
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Binding of two proteins to separate sites on the
DNA double helix can greatly increase their
probability of interacting
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Protein interaction in gene switch
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Gene control region for a eukaryotic gene
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The modular structure of a gene activator protein
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Transcriptional synergy
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Repressor
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Assembled complex
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The nonuniform space distribution
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Switching gene expression by DNA inversion in
bacteria.
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Control of cell type in yeast
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Cassette model of yeast mating-type switching
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Speculative model for the heterochromatin
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A positive feedback loop
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Circadian clock
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Clustered genes coordinated by single protein
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Myogenic regulatory proteins in muscle
development
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ey gene in precursor cells of the leg
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X-inactivation
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DNA methylation patterns are faithfully inherited
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Genome imprinting
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CG island
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An explanation of CG island
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Post transcriptional regulation
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Alternative splicing
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Negative and positive control of alternative RNA
splicing
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Regulation of the site of RNA cleavage
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RNA editing in the mitochondria of trypanosomes
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Mechanism of A-to-I RNA editing in mammals
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Negative translational control
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The elF-2 cycle
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Translation initiation
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mRNA decay
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The competition between mRNA translation and mRNA
decay
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Two posttranslational controls mediated by iron
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Nonsense mRNA decay