The overall goal of this optimized single molecule RNA in situ hybridization, or smFISH, is to detect and quantify individual RNA molecules on a per cell basis during the vegetative growth and meiosis of budding yeast. This method reveals cell to cell variability in gene expression on subcellular RNA localization and is therefore a powerful technique to study gene regulation. Asides from the unique information that can be revealed by smFISH, the main advantage of the technique is that once optimized, it's robust and highly reproducible.
A meiotic culture will be used for the demonstration of this protocol. To fix the culture in 3%formaldehyde, add 1840 microliters of the culture to 160 microliters of 37%formaldehyde in a two milliliter microcentrifuge tube. Invert about five times to mix.
Place the tube on a roller drum at room temperature for 20 minutes. After 20 minutes, continue fixing at four degrees Celsius with rotation overnight. On the following day, prepare for the digestion by first thawing 200 millimolar vanadyl ribonucleoside complexes, or VRC, at 65 degrees Celsius for at least 10 minutes.
To prepare the digestion master mix, first pipette 2125 microliters of buffer B into a 15 milliliter tube. Then vortex the warm VRC for five seconds to fully resuspend it and add 200 microliters of VRC to the 15 milliliter tube. The mix should appear light brownish green in color.
Centrifuge the meiotic sample at 21, 000 x g for one and a half minutes at room temperature. Aspirate the supernatant carefully, placing the vacuum tip on the opposite side of the pellet to avoid disturbing the pellet. Resuspend the cells in one and a half milliliters of cold buffer B by pipetting up and down to mix.
Centrifuge at 21, 000 x g for one and a half minutes. Remove the bulk of the liquid by vacuum aspiration, leaving behind about 100 microliters. Resuspend the cells in one and a half milliliters of cold buffer B.Centrifuge the samples, remove the liquid, and resuspend the cells in one and a half milliliters of cold buffer B again.
Centrifuge at 21, 000 x g for one and a half minutes. Aspirate the liquid completely by pipetting. Resuspend the cells in 425 microliters of digestion master mix and vortex briefly.
Add five microliters of zymolyase to the tube and vortex for two to three seconds to mix. Place the tube on a roller drum and digest at 30 degrees Celsius for 15 to 30 minutes. After 15 minutes, check the cells by microscopy every five minutes and stop the digestion when about 80%of the cells appear non-transparent and non-refractive.
Centrifuge the tube at 376 x g for three minutes. Remove the supernatant completely. Gently resuspend the cells with one milliliter of buffer B by pipetting up and down one to two times to mix.
Centrifuge the tube and remove the buffer. Gently resuspend the cells in one milliliter of 70%ethanol and incubate at room temperature for three and half to four hours. To begin the hybridization procedure, centrifuge the tube of cells at 376 x g for three minutes.
Remove 500 microliters of the 70%ethanol from the tube. Gently pipette up and down to resuspend the remaining cells and transfer the cells to a low adhesion tube. Transferring the sample to a low adhesion tube is critical for preventing excess cell loss during the subsequent formamide washes.
Centrifuge the low adhesion tube and remove all the ethanol. Add one milliliter of 10%formamide wash buffer to the tube and gently pipette up and down two to three times to resuspend the cells. Allow the cells to set at room temperature for about 20 minutes while preparing the hybridization solutions, as described in the text protocol.
Centrifuge the sample and remove the supernatant into hazardous waste. Add at least 50 microliters of each hybridization solution to the tube and flick the tube to mix. Incubate at 30 degrees Celsius on a roller drum for at least 16 hours in the dark.
When the hybridization is complete, place the tube of cells into a foil covered box to protect from light. Centrifuge the sample at 376 x g for three minutes. Remove the supernatant into hazardous waste by pipetting.
Resuspend the sample in one milliliter of 10%formamide wash buffer by gently pipetting up and down two to three times. Place the tube of cells back into a foil covered box to protect from light and incubate at 30 degrees Celsius for 30 minutes. After 30 minutes, centrifuge the sample.
Remove the supernatant to hazardous waste by pipetting, leaving about 50 microliters. Resuspend the sample in one milliliter of DAPI solution by gently pipetting up and down two to three times. Once again, place the tube of cells into the foil covered box and incubate at 30 degrees Celsius for 30 minutes.
Centrifuge the sample and remove the supernatant completely by pipetting. For samples that will not be imaged immediately, resuspend the pellet in 50 microliters of GLOX buffer without enzymes. Pipette up and down three to four times to mix.
Keep in the foil covered box at four degrees Celsius until ready to image. For samples being imaged immediately, add 15 to 20 microliters of GLOX buffer with enzymes. Pipette five microliters onto a cover slip and put the cover slip on a slide.
Place a laboratory wipe on top of the slide where the cover slip is placed. Gently press on the wipe to set the slide. Place the slide into a box covered by aluminum foil for transfer to the microscope room.
This protocol was used to examine the expression of the NDC80 gene, which expresses two mRNA isoforms. The long undecoded transcript isoform has a 400 base pairs five prime extension in comparison to the short isoform. Two sets of probes were designed.
The CF 590 set binds to the unique five prime region of the long isoform, and the Q 670 set binds to the common region of both isoforms. Under optimized conditions, distinct smFISH spots were clearly identified for both probe sets. The two probe sets were used to study NDC80 expression during vegetative growth and meiosis.
In vegetative cells, robust signal from the Q 670 probe set was detected, but not from the CF 590 probe set. In contrast, robust signal from both probe sets was detected in meiotic prophase, and the majority of the spots had co-localized signal. Northern blot analysis confirmed that the long isoform was expressed specifically in meiosis.
Vegetative cells were found to have a median of five short isoform transcripts per cell, whereas in meiotic prophase cells, the median significantly dropped to four transcripts per cell. In meiotic prophase, the median number of long isoform transcripts per cell was 21 and 100%of the cells expressed the transcript. Once mastered, this technique can be done in 72 hours if it is performed properly.
While attempting this procedure, it's important to first optimize the digestion duration and a concentration of smFISH probes required to achieve the optimal signal to noise ratio. In addition, remember to add VRC during digestion and overnight hybridization to prevent nuclease activity. With this development, this technique paved the way for researchers to explore dynamic gene regulation and subcellular RNA localization.
After watching this video, you should have a good understanding of how to perform single molecular RNA FISH in budding yeast meiosis.
