Assessment of Selective mRNA Translation in Mammalian Cells by Polysome Profiling

The overall goal of the following experiment is to distinguish between highly and poorly translated mRNAs by the immobilization and separation of polyribosomes. This is achieved by first adding cyclo heide to cells to inhibit their ribosome, translocation and RNA translation. As a second step, lysates from the treated cells are loaded onto a sucrose gradient and ultracentrifuge to separate the stored polyribosomes according to their masses.

Next, the gradient is divided into equal fractions to separate the highly and poorly translated transcripts in the final step. R-T-Q-P-C-R is used to detect the presence of the mRNAs of interest within each fraction. Ultimately, ribosome profiling can be used to detect changes in the global as well as the specific translation of mRNA in response to distinct physiological and pathophysiological stresses.

PolyOne profiling can answer key questions in molecular and cell biology fields such as which mRNAs are selected, translated during S stress, and how this allows cells to adapt to these conditions. Demonstrating this procedure is mom Dar of a graduate student in the laboratory To use an automated gradient maker to prepare a sucrose gradient begin by turning the gradient maker on and level the plate that will hold the gradients when the plate is leveled. Click done.

Then to select the gradient program, open the grad menu and select list. Click on SW 41 and then scroll through the list until the 10 to 50%gradient 11 steps program is in view and press.Use. Next place an SW 41 conical ultracentrifuge tube into the marker block and use the provided fine tube marker to trace a line on the tube along the upper step of the block.

Place the tubes in a fitting rack on a stable surface, and then attach the two provided cannulas to two 10 milliliter syringes. Pipet warm distilled water containing RNAs in activation solution up and down a few times to wash the syringes. Then after removing all traces of the water, fill one of the syringes with 10%sucrose plus cyclo heide, and insert the cannula at the bottom of the ultracentrifuge tube.

Gently dispense the solution until it goes just past the mark made on the tube. Taking care to avoid bubbles. Then fill the other syringe with 50%sucrose plus cyclo heide, and clean any extra liquid off the tube with a wipe.

Use the cannula to gently insert the 50%sucrose solution into the tube stopping when the solution is level with the mark and then quickly and smoothly remove the cannula. The 10%sucrose solution should rise to form meniscus at the top of the tube. Next, tilt the ultracentrifuge tube slightly to displace any air bubbles and insert the cap using a micro pipette to remove any excess liquid in the cap’s reservoir.

Place the tubes on the gradient maker and then press the run button. Note that the plate will tilt at the specified angle. Pause for five seconds, and then the rotations to form the gradient will begin.

After about two minutes, the machine will beep indicating that the gradient formation is complete. Gently transfer the tubes to a rack and swiftly remove the caps in on upward movement to avoid disturbing the gradient. Then gently load equal a 260 units of previously prepared cell lysate onto each sucrose gradient, and spin the tubes for one and a half hours at 260, 343 times G and four degrees Celsius in an ultracentrifuge.

To set up the gradient fractionation system instrument begin by turning on the spectrophotometer. Next, pick the folder icon twice and then the return arrow twice to return to the home screen and to set the fraction collector to the PolyZone method to ensure the valve on the fraction collector is set to waste. Click on the arrow pointing to the trash bin icon and then place a 250 milliliter MIA flask containing distilled water under the waste collection tube.

Now select the following settings on the chart recorder the sensitivity dial to set lamp and optics the noise filter. Switch to 1.5 the peak separator dial to off the chart speed, dial to 30 centimeters per hour and the baseline and adjust dial on top of the spectrophotometer unit to max open. Then place the syringe and barrel in the pump and use the provided screws and Alan Key to tighten it into place.

Use the rev command at rapid speed to fill the syringe with chase solution. Then place the pump in the upright position and use the forward command to chase the air through the tubing. Next, install an ultracentrifuge tube filled with RNAs free water in the holder, and then pierce the tube with the cannula until the two black marks are visible.

The dispensing hole is between the two marks. Start the syringe pump on forward manual at 6.0 milliliters per minute. When the chase solution fills one third of the tube, switch to the speed to variable with a flow rate of 1.0 milliliters per minute.

Now turn the baseline adjust dial on the spectrophotometer until the voltage on the chart is at zero. Water will begin to exit from the waste tube into the el Mya flask. Then set the desired sensitivity to 1.0 au.

When the sensitivity has been adjusted, push the also baseline button and turn the recorder offset dial to adjust the baseline setting to the 10%mark on the chart recorder. Then once the stable baseline is achieved, turn the pump switch and the chart speed dial to off. Once the pump is off, switch it to the rev position to recover the chase solution until it reaches the first mark on the piercing cannula.

Then remove the centrifuge tube, disperse any bubbles in the cannula with a little chase solution, and clean up any residual water that may have leaked from the flow cell to fractionate the gradient. Next, install the centrifuge tube containing the sucrose gradient in the holder and pierce the tube with the cannula. Then place ten two milliliter micro centrifuge tubes into the fraction collector tray positions two to 11 and a waist tube into position one such that the caps do not protrude upwards.

Set the pump control dial to manual and the flow rate on the syringe pump to 6.0 milliliters per minute. Then press play on the fraction collector as soon as the arm reaches the first tube. Press the pause button to position the arm and to open the fraction dispensing valve.

Then use the forward command to start the pump and monitor the chart recorder pen. When the pen starts deflecting upwards, indicating that sample is passing through the flow cell, quickly replace the waste tube with tube number one. Then when the first drop is collected, quickly switch the commands to remote start, stop and variable 1.0 milliliters per minute and press play to allow the fraction collector interface to collect one milliliter fractions every minute.

Finally, after the blue chase solution enters the last tube, press stop. PolyZone profiling is a key technique for demonstrating the specific involvement of PD CD4 in IRAs mediated translation. For example, in this experiment, HEC 2 93 cells were transiently transfected to deplete the endogenous levels of PDC D four, and then subjected to PolyZone profile analysis.

Reducing the levels of PDC D four did not impair the global translation of the gene as judged by the lack of changes in the PolyZone profile. When comparing SI control and IPD CD four treated cells similarly polysome distribution of a non IRAs variant of XIAP was unchanged between the treated and untreated cells. In contrast, polysome distribution of the two IS harboring mRNAs XIAP and BCL XL was significantly altered.

In the absence of PD CD4, the distribution of these two mRNAs was shifted into heavy ribosomes. Since this is not accompanied by changes in the steady state levels of XIAP and BCL XL mRNA, these results demonstrate the enhanced translation of XIAP and BCL XL in cells with reduced PDC D four levels as further confirmed by Western blossoming. After watching this video, you should have a good understanding on how to measure mRNA translation by preparing Sucrose region and separating polysome by ultracentrifugation.