BCHS 4397 – Gene Regulation 8/22/19 1

1. Tissue-specific transcription

a. *Signaling pathway ‘A’ activates transcription, signaling pathway ‘B’ (further

down) represses*

b. Chromatin remodeling to allow or dis-allow accessibility of binding proteins

i. Chromatin doesn’t exist in bacteria

ii. When chromatin binds onto DNA, it inhibits RNA from attaching

c. Specific combinations of proteins could be required for activation or repression

d. These proteins could require specific protein: protein interactions to activate or

repress

e. Interactions could require post-translational modifications or ligand binding

f. Such “conditional” responses allow modulation in response to external cues

i. Activation or repression of signaling events (growth factors, cell-cell

contact, presence of hormone)

g. Same principles apply to other sites of regulation: the combined outcome of

multiple “inputs” ultimately determine:

i. Transcription regulation

ii. Splicing regulation

iii. mRNA translation regulation

iv. mRNA stability

v. Protein stability

vi. Protein modification

h. Mechanisms of Regulation
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i. Basic Questions about what causes a change in the activity of a

regulatory factor:

1. Does the steady state level change?

2. Is there a change in intracellular localization?

3. Is there a change in post-translational modification?

4. Is a ligand required for activity?

5. Is (are) there a protein binding partner(s) required for activity?

i. Take rabbit protein and make it into antibodies (IgG)

i. Cell extraction -> PAGE

2. Rate of Accumulation of RNA and protein depends on both the rates of synthesis and

degradation

a. dC/dt = T-DCT where T = rate of synthesis, D = rate of degradation or ln2/t/0.5

and CT = the concentration at any given time

b. The phenotype of cells and their corresponding level of a given mRNA and

protein may be influenced as much by their intrinsic stability as on their rates of

transcription.

3. Scenario #1: You see a 5x increase in steady state levels of protein z based on western

blot analysis

a. Most common: transcription, mRNA stability, translation efficiency protein

stability

b. Also consider: nuclear -> cytoplasmic mRNA

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c. If you measure by fluorescence there are 1000 – 10,000 levels of magnitude (no

clue what this means)

4. Scenario #2: No increase in steady state levels of protein Z but have 5x increase in

ACTIVITY

a. Change in nuclear: cytoplasmic distribution

b. Post-translational modification

5. Interactomes: Complete set of molecular interactions that occur inside a specific cell

Lec 2:

1. Slide 3, you use URADINE to build RNA with NTPs

2. Adenylation – refresh yourself on this. *triggers breakdown? Or is that uridylation? *

3.