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Human cell mRNA decay Pulse-Chase assay:

Pulse-Chase mRNA decay assay in HeLa Tet-off cells:

 

This protocol is for four time-points in 12-well plates. Scale up or down as needed.

 

Day 1: Plate cells:

Split one or more 10-cm plate(s) with 80-100% confluent HeLa Tet-off cells to a final volume of 10-11 ml. Make sure to break up cell clusters to ensure single cells.

Dilute freshly split cell suspension 1:12 or 1:15 (depending on % confluency) in DMEM/10% FBS in a 50 ml conical in a total volume equal to or more than the number of wells to be plated (for e.g. make about 50 ml for 48 wells -12  experiments of 4 time-points).

Plate 1 ml per well in 12-well plates.

Incubate over night.

 

Day 2: Transfections

Using Mirus TransIT HeLaMonster (check manufacturers protocols if using other reagents)

Cells should be 40-60% confluent - not more.

 

For each of four wells:

1) Add a total of 4.5 g plasmid to an eppendorf tube:

For B-globin reporters use:

45 ng pcBwtGAP3 UAC (internal control mRNA)

0.9 g pPC or pcTET2 B-globin reporter

3.6 g of other plasmid(s) - such as protein expressing or empty vectors

 

Optional: If using same reporters in all experiments, make a larger mix of internal control and B-globin reporter. For e.g., for 12 experiments, mix

45 ng x 12.5 of pcBwtGAP3 UAC (internal control mRNA)

0.9 g x 12.5 of pPC or pcTET2 B-globin reporter

Then, divide the mix into 12.5 equal parts and pipet into separate eppendorfs.

 

2) Mix 225 l O-MEM with 13.5 l TransIT HeLa reagent

            Add 0.225 l of 1 mg/ml Tetracycline (in EtOH).

(a final concentration of 50 ng/ml Tet ensures no expression from the TET-driven promoter)

            Incubate 5-20 mins at RT

 

3) Mix 5 l HeLaMonster reagent with 45 l ddw. Store on ice.

(Important: Thaw HeLaMonster reagent just before use, keep on ice and return to freezer immediately).

 

Optional: Bigger mixes can be made by multiplying O-MEM, TransIT reagent and Tetracycline volumes (Step 2) or HeLaMonster and ddw volumes (Step 3) by the number of experiments (+0.5). 

 

4) Add 225 l O-MEM/TransIT HeLa mix to the plasmid mix.

            Incubate 5-20 mins at RT

 

5) To each 2.0-cm well of HeLa Tet-off cells:

            Add 50 l of O-MEM/TransIT/Plasmid mix.

 

6) To each 2.0-cm well of HeLa Tet-off cells:

Add 10 l of diluted HeLaMonster reagent.

 

Place plates in incubator.

 

Day 4: Pulse-Chase assay.

 

1) Pulse transcription (Early morning):

Start transcription from Tet-promoter:

Wash wells carefully (!) with 1 ml PBS.

Add 1 ml DMEM/10% FBS.

Incubate 6 hours

 

2) Chase:

Stop transcription (the complete stop will take 20 mins):

To each well, add 10 l of O-MEM/100 g/ml Tetracycline

Place back in incubator.

 

3) Time points:

Take the first time point 20-30 mins after addition of tetracycline (t=0).

For each time point:

Wash cells with 1 ml PBS.

Add 0.5 ml Trizol. Pipet up and down until non-viscous.

Transfer to pre-labeled eppendorf tube.

Store in  -20 C.

 

Day 5: RNA preps:

 

To each tube with 0.5 ml Trizol:

Add 100 l Chloroform.

Mix by shaking for 30 sec or more.

Leave at RT, 10 min.

Spin 12,000 rpm, 10 min.

Transfer 250 l supernatant to new tube. Avoid interphase!!

Add 0.7 volumes of isopropanol (175 l). Mix and leave at RT, 10 min.

Spin 12,000 g (not faster!), 4C, 10 min.

Remove supernatant carefully.

Wash carefully with 0.5 ml of 70% EtOH. Spin at 7,500 g for 5 min, 4C.

Air dry.

Dissolve in 10 l formamide load buffer.

 

Run 5 l on a Northern Gel.