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