Imaging mRNA modifications in situ

There are at least 170 known chemical modifications on RNA molecules in all organisms. Most of these modifications are on tRNAs, rRNAs and small RNAs. But over the past two decades, researchers found that eukaryotic mRNAs also carry some modifications, the most abundant being N⁶-methyladenosine (m6A). Most methods to date used various RNA sequencing technologies to detect such modifications or selectively sequence modified RNAs. But these lack spatial information on where these mRNAs reside.  In 2021, a m6A-Specific In Situ Hybridization Mediated Proximity Ligation Assay (m6AISH-PLA) was published. But it only recognizes modified mRNAs. ARPLA is a novel method that detects glycosylated RNAs, but not at single-molecule resolution. DART-FISH is a new in situ method that combines detection of m6A-modified and unmodified mRNAs at single-molecule resolution.

Re-opening the discussion on mRNA decay inside P-bodies

Processing bodies (P-bodies, PBs) are aggregates of mRNA degradation proteins, suggested 20 years ago to be sites of mRNA degradation. Later work provided evidence to the contrary, and the function of PBs remained controversial. A new pre-print from Bin Wu’s lab brings us back to this debate, with new evidence for a role in degradation. Bonus – how phototoxicity affects the outcome. (Note – updated with published paper).

Fixation of cells for imaging affects phase separation

An assumption in microscopy and other methods is that chemical fixation of the cells is fast enough not to affect the biological process we study. A new paper shows that fixation affects the appearance of phase-separated proteins.

Old conference live-tweet

Due to Twitter becoming a garbage can website, with prospect of collapsing, I’m copying here my previous conferences live-tweets.

I’ll do it gradually from last to first and I might edit it to look pretty later-on.

Troubles with mCherry

A group of researchers from Norway found that mCherry – and possibly other fluorescen proteins – has a shorter translated isoform in bacteria. This could affect localization and expression studies.

P-bodies and aging in yeast

A new preprint from Brian Zid’s lab shows accumulation of P-body-like aggregates in old yeast cells with a suggested pathological role in aging. I think some key experiments are missing. A short review.

Imaging of miRNA-mediated translational repression and mRNA decay at single molecule resolution

Three recent papers begin to explore the dynamics of miRNA translation repression and mRNA decay at the single-molecule resolution. One paper contradicts the others.