more regulating gene expression

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more regulating gene expression
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We looked at the mechanisms of gene expression,
now we will look at its regulation.
Combinations of 3 nucleotides code for each 1
amino acid in a protein.
3

• Gene Expression is controlled at all of these
  steps
• DNA packaging
• Transcription
• RNA processing and transport
• RNA degradation
• Translation
• Post-translational

Fig 15.1
Fig 16.1
4

• Gene Expression is controlled at all of these
  steps
• DNA packaging
• Transcription
• RNA processing and transport
• RNA degradation
• Translation
• Post-translational

Fig 15.1
Fig 16.1
5
Eukaryotic transcription must be activated by
binding of transcription factors
Fig 12.14
6
Mutations in the promoter show critical
nucleotides
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Fig 15.12
Enhancers are regulatory regions located some
distance away from the promoter
8
Proteins that help bend DNA can play an important
role in transcription
Fig 15.12
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Fig 15.12
DNA bends to bring different areas in to close
contact.
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How do eukaryotic cells jointly express several
proteins (without operons)?
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Promoter sequences where transcription factors
can bind activating multiple gene in response to
the environment
12
Fig 12.13
Promoters typically have several regulatory
sequences
13
Steroid response element
14
Fig 15.6

• Steroids bind to receptors/transcription factors
  inside cell
• get translocated to the nucleus
• bind to promoters andactivate transcription.

cytoplasm
15

• Gene Expression is controlled at all of these
  steps
• DNA packaging
• Transcription
• RNA processing and transport
• RNA degradation
• Translation
• Post-translational

Fig 15.1
Fig 16.1
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Fig 23.25
Alternate Splicing in Drosophila Sex Determination
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Fig 23.25
Alternate splicing leads to sex determination in
fruit flies
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• Mammalian mRNA Splice-Isoform Selection Is
  Tightly Controlled
• Jennifer L. Chisa and David T. Burke
• Genetics, Vol. 175 1079-1087, March 2007
• Regulation of gene expression is often in
  response to a changing environment.
• But how stable can alternative splicing be, and
  does it play a role in maintaining homeostasis?

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• Alternative splicing modifies at least half of
  all primary mRNA transcripts in mammals.
• More than one alternative splice isoform can be
  maintained concurrently in the steady state mRNA
  pool of a single tissue or cell type, and changes
  in the ratios of isoforms have been associated
  with physiological variation and susceptibility
  to disease.
• Splice isoforms with opposing functions can be
  generated for example, different isoforms of
  Bcl-x have pro-apoptotic and anti-apoptotic
  function.

Chisa, J. L. et al. Genetics 20071751079-1087
Fig. 1
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Alternatively spliced versions of different genes
were identified
Chisa, J. L. et al. Genetics 20071751079-1087
Fig. 1
21
variation in splice-isoform ratios is conserved
in two genetically diverse mouse populations
Black genetically heterogeneous population
UMHET3 Red a population of hybrid females
Chisa, J. L. et al. Genetics 20071751079-1087
Fig. 4
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In different individuals splice isoforms in
different tissues are conserved
Chisa, J. L. et al. Genetics 20071751079-1087
Fig. 5
23

• Conclusions
• Alternate splicing for some genes is tightly
  regulated between different individuals.
• Slight differences in alternative splicing may be
  indicative of abnormalities (disease).

24
mRNA transport is an important regulatory step
Molecular Biology of the Cell 4th ed. Alberts et
al. Fig 6.40 http//www.ncbi.nlm.nih.gov/books/bv
.fcgi?ridmboc4.TOCdepth2
25
mRNA can be localized to a specific parts of a
cell (from Drosophila embryo)
Molecular Biology of the Cell 4th ed. Alberts et
al. Fig 7.52 http//www.ncbi.nlm.nih.gov/books/bv
.fcgi?ridmboc4.TOCdepth2
26
At least 3 mechanisms are involved
Molecular Biology of the Cell 4th ed. Alberts et
al. Fig 7.98
Directed transport via cytoskeleton
Random diffusion and trapping
Degradation and local protection
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A processed mRNA ready for translation
5 untranslatedregion
3 untranslatedregion
Protects from degradation/ recognition for
ribosome
Protects from degradation/ transport to cytoplasm
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mRNA with 3 UTR properly localized
mRNA without 3 UTR improperly localized
Molecular Biology of the Cell 4th ed. Alberts et
al. Fig 7.99 http//www.ncbi.nlm.nih.gov/books/bv
.fcgi?ridmboc4.TOCdepth2
29

• Gene Expression is controlled at all of these
  steps
• DNA packaging
• Transcription
• RNA processing and transport
• RNA degradation
• Translation
• Post-translational

Fig 15.1
Fig 16.1
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Seeds germinated underground begin growing in
darkness then emerge into light and begin
photosynthesis
energy from seed
energy from sun
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The level of this mRNA increases after plants are
exposed to light.

• How might the cell accomplish this?

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The level of this mRNA increases after plants are
exposed to light.

• How might the cell accomplish this?Increased
  transcription and/or decreased mRNA degradation

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Northern blot analysis The level of this mRNA
increases after plants are exposed to light.

• How might the cell accomplish this?
• Does this necessarily lead to increased protein
  production?

34

• Gene Expression is controlled at all of these
  steps
• DNA packaging
• Transcription
• RNA processing and transport
• RNA degradation
• Translation
• Post-translational

Fig 15.1
Fig 16.1
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Fig 15.25
Regulation of iron assimilation in
mammals Regulating of Translation
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Fig 15.26
Ferritin is regulated at translation
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C. elegans is commonly used to study development
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C. elegans development
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C. elegans mutants with cells that do not develop
properly.
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C. elegans mutants with cells that do not develop
properly. The product of these genes was found
to be RNA?
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MicroRNAs (miRNA) are 22nt RNAs that play
important regulatory roles
Cell vol. 116, 281-297 2004
42
miRNA expressed
How do microRNAs control gene expression?
miRNA processed to 22nt RNA
Mature miRNA
Fig 15.23 and
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A processed mRNA ready for translation microRNAs
inhibit translation by binding to the 3 end of
mRNA
microRNA bind to 3-UTR
5-UTR
3-UTR
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miRNA expressed
the 3 end with attached microRNA interacts with
the 5 end, blocking translation
miRNA processed to 22nt RNA
Mature miRNA
Fig 15.23 and
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miRNAs can lead to methylation of DNA that leads
to inhibition of transcription
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microRNAs primarily target gene products that
function during development
Tbl 1
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tissue specific expression of mouse microRNA
PNAS vol. 101 1 pg 360-365, 2004
48
Silencing RNAs (siRNA) are artificially induced
dsRNA
Fig 15.21
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siRNA with exact matches to the target mRNA
causes degradation of the mRNA
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microRNA
siRNA
mRNA degraded
Translation inhibited
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• Gene Expression is controlled at all of these
  steps
• DNA packaging
• Transcription
• RNA processing and transport
• RNA degradation
• Translation
• Post-translational

Fig 16.1
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Phosphorylation and dephosphorylation of proteins
can change activity
53
Ubiquitinization targets proteins for degradation
54
All protein interactions in an organism compose
the interactome
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Some proteins function in the cytoplasm others
need to be transported to various organelles.
56
How can proteins be delivered to their
appropriate destinations?
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Fig 13.23
Proteins are directed to their destinations via
signals in the amino acid sequence
58
Protein Destinations secretion or membrane
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• Signal sequences target proteins for secretion

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Translation of secreted proteins
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Translation of membrane bound proteins
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Translation of secreted or membrane bound proteins
This step determines secretion or membrane bound.
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Protein Destinations nucleus
Signal anywhere in protein, Translation in
cytoplasm, Signal not removed
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Protein Destinations mitochondria or chloroplast
Signal translated first, Translation in
cytoplasm, Signal removed
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Protein Destinations signals in protein
determine destination
Tbl 13.8
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Development differentiating cells to become an
organism
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