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more regulating gene expression
Combinations of 3 nucleotides code for each 1 amino acid in a protein.
We looked at the mechanisms of gene expression, now we will look at its regulation.
Fig 16.1
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
Gene Expression is controlled at all of these steps:•DNA packaging•Transcription•RNA processing and transport•RNA degradation•Translation•Post-translational
Fig 15.1
Eukaryotic transcription must be activated by binding of transcription factors Fig 12.14
Mutations in the promoter show critical nucleotides
Enhancers are regulatory regions located some distance away from the promoter
Fig 15.12
Proteins that help bend DNA can play an important role in transcription
Fig 15.12
DNA bends to bring different areas in to close contact.
Fig 15.12
How do eukaryotic cells jointly express several proteins (without operons)?
Promoter sequences where transcription factors can bind activating multiple gene in response to the environment
Promoters typically have several regulatory sequences
Fig 12.13
Steroid response element
•Steroids bind to receptors/transcription factors inside cell
•get translocated to the nucleus
•bind to promoters andactivate transcription.
cytoplasm
Fig 15.6
Fig 16.1
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 23.25
Alternate Splicing in Drosophila Sex Determination
Alternate splicing leads to sex determination in fruit flies
Fig 23.25
Mammalian mRNA Splice-Isoform Selection Is Tightly ControlledJennifer L. Chisa and David T. BurkeGenetics, 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?
•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 2007;175:1079-1087 Fig. 1
Chisa, J. L. et al. Genetics 2007;175:1079-1087 Fig. 1
Alternatively spliced versions of different genes were identified
Chisa, J. L. et al. Genetics 2007;175:1079-1087 Fig. 4
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 2007;175:1079-1087 Fig. 5
In different individuals splice isoforms in different tissues are conserved
Conclusions:
•Alternate splicing for some genes is tightly regulated between different individuals.
•Slight differences in alternative splicing may be indicative of abnormalities (disease).
Molecular Biology of the Cell 4th ed. Alberts et al. Fig 6.40http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2
mRNA transport is an important regulatory step
Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.52http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2
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 7.98
At least 3 mechanisms are involved:
Directed transport via cytoskeleton
Random diffusion and trapping
Degradation and local protection
A processed mRNA ready for translation
Protects from degradation/ recognition for ribosome
Protects from degradation/ transport to cytoplasm
5’ untranslatedregion
3’ untranslatedregion
Molecular Biology of the Cell 4th ed. Alberts et al. Fig 7.99http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.TOC&depth=2
mRNA with 3’ UTR properly localized
mRNA without 3’ UTR improperly localized
Fig 16.1
Gene Expression is controlled at all of these steps:•DNA packaging•Transcription•RNA processing and transport•RNA degradation•Translation•Post-translational
Fig 15.1
Seeds germinated underground begin growing in darkness then emerge into light and begin photosynthesis
energy from seed
energy from sun
The level of this mRNA increases after plants are exposed to light.
•How might the cell accomplish this?
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
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?
Fig 16.1
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 15.25
Regulation of iron assimilation in mammals:Regulating of Translation
Fig 15.26Ferritin is regulated at translation
C. elegans is commonly used to study development
C. elegans development
C. elegans mutants with cells that do not develop properly.
C. elegans mutants with cells that do not develop properly.
The product of these genes was found to be RNA?
Cell vol. 116,281-297 2004
MicroRNAs (miRNA) are ~22nt RNAs that play important regulatory roles
How do microRNAs control gene expression?
miRNA expressed
miRNA processed to ~22nt RNA
Mature miRNA
Fig 15.23 and
A processed mRNA ready for translation:microRNAs inhibit translation by binding to the 3’ end of mRNA
microRNA bind to 3’-UTR
5’-UTR3’-UTR
miRNA expressed
miRNA processed to ~22nt RNA
Mature miRNA
the 3’ end with attached microRNA interacts with the 5’ end, blocking translation
Fig 15.23 and
miRNAs can lead to methylation of DNA that
leads to inhibition of transcription
microRNAs primarily target gene products that function during development
Tbl 1
PNAS vol. 101 #1 pg 360-365, 2004
tissue specific expression of mouse microRNA
Silencing RNAs (siRNA) are artificially induced dsRNA
Fig 15.21
siRNA with exact matches to the target mRNA causes degradation of the mRNA
microRNA siRNA
Translation inhibited mRNA degraded
Fig 16.1
Gene Expression is controlled at all of these steps:•DNA packaging•Transcription•RNA processing and transport•RNA degradation•Translation•Post-translational
Phosphorylation and dephosphorylation of proteins can change activity
Ubiquitinization targets proteins for degradation
All protein interactions in an organism compose the interactome
Some proteins function in the cytoplasm; others need to be transported to various organelles.
How can proteins be delivered to their appropriate destinations?
Fig 13.23
Proteins are directed to their destinations via signals in the amino acid sequence
Protein Destinations: secretion or membrane
• Signal sequences target proteins for secretion
Translation of secreted proteins
Translation of membrane bound proteins
Translation of secreted or membrane bound proteins
This step determines secretion or membrane bound.
Protein Destinations: nucleus Signal anywhere in protein, Translation in cytoplasm,Signal not removed
Protein Destinations: mitochondria or chloroplast
Signal translated first, Translation in cytoplasm, Signal removed
Protein Destinations: signals in protein determine destination
Tbl 13.8
Development: differentiating cells to become an organism