Team:MIT/Experiments/Promoters/Experiment-Details-for-Cascades
Note: THIS INFORMATION NOW LIVES ON THE PROOF OF CONCEPT PAGE.
DO NOT LINK TO HERE.
Robust parts and genetic devices should not only behave as expected in isolation. Rather, they must also behave well when cascaded together with other parts and genetic devices.
In order to create emergent functions and logic structure from our individuals parts and devices, we cascaded them together in larger 4 to 5 transcriptional unit circuits. We created both estrogen inducible promoter - repressor cascades in order to create "estrogen low" sensing logic, as well as estrogen inducible promoter - recombinase cascades in order to create "estrogen high" latches. Our attempts with experimenting with these cascades and getting them to function as expected met with only limited success. Some of this can be attributed to natural limitations encountered with creating larger genetic circuits, such as metabolic costs.
Estrogen Sensitive Promoters in Repressor Cascades
Our Genetic Circuit for Repressor Cascade Characterization
Figure . Our estrogen sensitive promoters respond to increases in E2 levels by producing more of the repressor. The repressors then bind to binding sites in a promoter upstream of fluorescent reporter eYFP. The constitutively active trans-activator Gal4-VP16 sets a large basal eYFP expression when there is no repressor, so that a measurable drop in signal can be observed when repressors are active. Constituvely active hEF1a mKate serves as a transfection marker by which we bin our data.
Repressor Cascades in ISH
The first cell line in which we deployed our genetic circuit was ISH, the endometrial epithelial cell line. We had expected eYFP expression to decrease after induction of our promoter - repressor cascades with E2. However, we were unable to resolve a clear fold difference between the uninduced and induced population in any of the pERE#n and TAL14, BM3R1 cascades. This is probably an artifact of poor transfection in the ISH cell line for this experiment (less than 2 percent transfected after cationic lipid transfection), which leads to erratic jumps in the data after binning by constitutive marker. In the future, we may want to try other modes of transfection for ISH to improve the transfection efficiency.
Figure . Results from pERE#n - repressor cascades pairing pERE3, pERE5, pERE6 and TAL14, BM3R1 transfected into MCF7. Blue contours represent the cell population that was left uninduced, green contours represent the cell population that was induced with 5 nM E2.
Repressor Cascades in MCF7
We hypothesized that we were unable to resolve a clear fold difference in our pERE#n - repressor cascades transfected into ISH because of the limited functionality of our promoters in the ISH cell line. So, we proceeded to transfect our cells into the MCF7 cell line where we had observed up to a 11 fold difference in the activity of some of our promoters.
Figure . Results from pERE#n - repressor cascades pairing pERE3, pERE5, pERE6 and TAL14, BM3R1 transfected into MCF7. Blue contours represent the cell population that was left uninduced, green contours represent the cell population that was induced with 5 nM E2.
Similarly, we had expected eYFP expression to decrease after induction of our promoter - repressor cascades with E2. However, we were still unable to resolve a clear fold difference between the uninduced and induced population in any of the pERE#n and TAL14, BM3R1 cascades. Given more time, we would like to explore whether transfecting our entire circuit on one plasmid instead of five separate plasmids would lead to better results.
Estrogen Sensitive Promoters in Recombinase Cascade
We also tested activation of recombinase TP901 under estrogen responsive promoters pERE5 and pERE6 in the MCF7 cell line. Upon activation of TP901, the inverted eYFP gene flanked by recombinase recognition sites is flipped to the correct orientation and expresses fluorescence.
We have previously demonstrated activation of TP901 under the inducible promoter EGSH, which is activated by transactivator VgEcR along with estrogen analog PonA. Despite high levels of TP901 basal expression, we observed a clear difference in activation between the induced and uninduced wells. We expected to see similar results in this experiment with TP901 under estrogen inducible promoters.
In order to test this cascade, we transfected MCF7 cells with pERE5: TP901 or pERE6: TP901, the inverted eYFP - recombinase site plasmid, and constitutively active BFP as a transfection marker. We induced half the wells with 5.0 nM E2 in order to compare on vs. off states of the promoter.
Unfortunately, we had poor transfection efficiency in this experiment, and thus the results are inconclusive. The data showed no clear fold difference between the induced and uninduced populations. We would like to try this experiment again in the future to get better results.
