The RNA society meeting is big. With over 150 talks and almost 700 posters, there’s a lot of new stuff to learn. This was my first RNA society meeting and I decided from the beginning to take it easy. That is why I did not live tweet like I usually do.
Instead, I thought of writing a summery blog post.
A recent bioRxiv pre-print publication from Christine Holt’s lab suggests that ribosomes may be remodeled in axons by locally translated ribosomal proteins. This is surprising because we know that ribosomes are assembled in the nucleolus. Well, I have some concerns about a few of the experiments depicted there.
Single molecule FISH is currently the best method to get accurate measurements of mRNA levels at single molecule, single cell level in cell culture or tissue slices with a spatial resolution of ~200 nanometer (or less). One of the drawbacks of this method is the deterioration of the fluorescent signal (bleaching) of the organic dyes that are used to label the probes. Andrew Smith’s lab from University of Illinois now show how FISH can work with quantum dots instead of organic dyes. This provides better fluorophore stability and also the possibility to have more colors with less overlap of the emission spectra.
One of the greatest breakthroughs of the past decade was the development of the next generation sequencing. Sequencing of DNA of course. It is relatively easy to sequence DNA – the polymerase is doing it for you – simply add fluorescently labeled nucleotides. For RNA sequencing, we simply convert it into DNA. We now even have a method for in situ sequencing of RNA. But proteins pose a challenge. Now, maybe, this challenge can be overcome with a new-old method to sequence peptides.
I co-authored a Correspondence pre-print article that puts into question the Smartflare technology. SmartFlares (the commercial name of NanoFlares) are gold nanoparticles covered in oligos specific to a certain mRNA of interest (aka spherical nucleic acids). Supposedly, cells internalize these particles and, once the mRNA hybridize to the oligo, a complementary fluorecently labeled oligo is being unquenched and “flares”, indicating the presence of said mRNA. In this post I want to briefly mention the main topics of our pre-print, and expand on some points. I encourage readers to comment here or on Pubpeer on our article.
Previously, on the story of MS2 labeling of mRNA in yeast: Roy Parker published a short letter to the editor, indicating that the MS2 system might cause accumulation of 3′ fragments. We wrote a response, showing that it is not always the case for endogenously expressed mRNAs, but it is exaggerated when over-expressed (Part 1)*. Later, Karsten Weis’s group confirmed Parker’s initial observation but their report still had some questions unanswered, and no solution to the problem; I was unhappy (Part 2). Now, Evelina Tutucci and Maria Vera together with Jeet Biswas (all from Rob Singer’s lab) seem to have resolved the issue and solved the problem, with the development of the MBS version 6. Continue reading
Posted in FISH, Gene expression, Journal club, MS2-like systems, stress response
Tagged mRNA decay, mRNA localization, MS2, quantitative microscopy, Singer lab, single molecule, yeast
My paper was recently published. I suggest that you read it before reading this post (it is an open access paper). In this paper we show that full-length mRNA molecules can be transferred between mammalian cells through membrane nanotube-like extensions that connect the cells.
Posted in Cell-Cell communication, epi, FISH, Gene expression, membranes, MS2-like systems, Transport & Trafficking
Tagged HHMI Janelia, Mammalian cell, membrane nanotubes, mRNA localization, MS2, my pics, personal experience, Singer lab, single molecule