Transcription and gene regulation

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Transcription and gene regulation

• sven.nelander_at_wlab.gu.se

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RNA in a mammalian cell

• Amount genes
• Protein-coding RNA 5 20000
• (mRNA)
• Non-coding RNA 95 lt1000
• (tRNA, rRNA, miRNA)

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mRNA expression levels
X axis organ (skin, heart, brain and so on) Y
axis mRNA expression level
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Rare and abundant transcripts
Tnnt2 TROPONIN T, CARDIAC MUSCLE
ISOFORM Actc1 ACTIN, ALPHA CARDIAC
Number of genes
Srf SERUM RESPONSE FACTOR
Transcripts per cell
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Expression patterns
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Co-expression
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How are transcript levels controlled?

• 1. Synthesis
• Changes in the chromatin
• Transcription
• 2. Decay
• Degradation by RNases

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Accessible and non-accessible chromatin
Quantitative chromatin profiling of the CD2
gene (Dorschner et al, Nature Methods)
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How is a gene made (in)accessible for
transcription?

• 1. Chemical modifications of histones
• Acetylation ? open configuration
• Deacetylation ? closed configuration
• 2. Chemical modification of the DNA
• Methylation ? no transcription

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RNA polymerase II

• The enzyme that makes protein-coding transcripts
• RNA pol II is non-specific in its pure form
• ANY DNA ? RNA COPY
• 40 basal transcription factors are needed to
  make RNApol II promoter-specific
• THE DNA OF A GENE ? RNA COPY
• 2000 transcription factors are needed to
  regulate the action of RNApol II
• THE DNA OF THE RIGHT GENE ? RNA COPY

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Transcription initiation
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Gene regulation

• We want to define
• The cis regulatory elements (CREs)
• The transcription factors that act on the CREs

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Studying gene regulation

• Traditional experiments
• Global experiments
• Computational methods

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Example 1 a traditional approach
Mack and Owens, Circ. Res. 84852, 1999
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Transcriptional Regulation of SMC Genes is
Dependent on Complex Combinatorial Interactions
of Many Cis Elements and Trans Factors
CArG B
GATA Factors
Myocardin
Myocardin
Myocardin
CRP2
CArG A
Pol II Complex
Int CArG
KLF5 KLF4 -
TBP
TCE
TATA
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Example 2 a modern experimental approach

• Which are the targets of transcription factor X?

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MyoD and myogenin targets in muscle development
(Blais et al, Genes Dev 2005)
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Example 3 a typical bioinformatic approach

• Which genes are targeted by factor X?
• 1. Identify genomic regions likely to contain
  regulators
• 2. Identify potential sites for factor X

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Two views on heart development !
SRF
TGIF/MEIS
MEF2
OTHERS
Cripps RM, Olson EM. Control of cardiac
development by an evolutionarily conserved
transcriptional network.Dev Biol. 2002 Jun
1246(1)14-28.
www.wlab.gu.se/lindahl/genebatteries
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Conclusions

• RNA levels are tightly regulated by transcription
  and degradation
• Transcription is a product of
• chromatin modifications
• cis regulatory elements
• transcription factors
• There is a number of experimental and
  computational methods

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Masters projects

• 1. EGFR pathway towards combinatorial treatment
  of solid tumours?
• 2. From stem cell to B cell
• 3. Evolution of Serum Response Factor regulation

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Previous students

• Erik Larsson
• Graduate student, Wallenberg Lab / GU
• Tanya Lobovkina
• Graduate student, Physical chemistry / Chalmers
• Nino Demetrashvili

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Reading tips

• About transcriptional regulation
• Genes and Signals by M Ptashne
• Genomic regulatory systems by E Davidson
• Some labs doing nice work
• Transcript exploration P Kapranov
• Chromatin R Young
• Nucleus biology P Silver
• Genome analysis D Haussler