Matthew Taliaferro

How does one review his paper if he’s infallible?

New @prelights.bsky.social post ! I'm happy to highlight @jmtali.bsky.social lab latest preprint prelights.biologists.com/highlights/t...

We received notice that two F31s were terminated and submitted another F31 application two hours later. We keep on trucking, I guess.

Thanks Junjie!

Two updates with this project! First, this work is now published here: academic.oup.com/nar/article/...

Second, our software for identifying 8-oxoguanosine via RNAseq, PIGPEN, is now installable via bioconda: anaconda.org/bioconda/pig...

Bartolomeo Tagliaferro Sr. (1530-1601) - Find a... Born in Venice, Italy. Lived in various parishes in London until his death. Buried September 22, 1601, at St. Olave's Hart Street London. Married Joane Lanier/Lanyer on 1 JAN 1583 at St. Michaels, C...

Thanks Mike! I looked into this a while back, and I am a direct patrilineal descendant of this guy: www.findagrave.com/memorial/133.... Blacksmithing skills got lost somewhere along the way though.

TDP-43 directly inhibits RNA accumulation in neurites through modulation of RNA stability The subcellular localization of hundreds of RNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for the vast majority of these ...

www.biorxiv.org/content/10.1...

Thanks Manny!

TDP-43 directly inhibits RNA accumulation in neurites through modulation of RNA stability The subcellular localization of hundreds of RNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for the vast majority of these ...

www.biorxiv.org/content/10.1...

...the unnecessary loss of time, expertise, and money. In short, it is the opposite of increased efficiency.

...from the people in the lab doing the experiments to the staff that oversee compliance with regulations to ensure thoughtful stewardship of hard earned taxpayer money. Wild, unpredictable changes to the system result in turnover of these key personnel, resulting in...

Finally, one more comment given recent events. All this work, which may one day lead to cures for ALS, relies not just on federal funding, but on a *stable* funding system, including indirect costs. Those funds pay the salaries of people that are indispensable to this effort...

If we replace wildtype TDP-43 with an ALS mutant TDP-43, we again see that the same RNAs become aberrantly neurite-enriched. So this could be happening in ALS patient cells, but whether it makes contributions to patient phenotypes is another question for another day.

Does any of this have anything to do with ALS? Maybe. We see the same RNA localization defects happening in primary mouse motor neurons and human iPS-derived motor neurons upon TDP-43 loss.

260mers that drove TDP-43-dependent localization and were bound by TDP-43 in vitro also showed TDP-43-dependent changes in stability, directly linking all three processes. All of these qualities were eliminated if TDP-43 motifs in the 260mers were eliminated.

OK, so *how* is TDP-43 doing this? TDP-43 negatively regulates RNA stability and recent work has linked RNA localization and stability. So is this what's going on? To test this we measured the stability of the same ~10k reporters with and without TDP-43 using SLAM-seq.

Sure enough, 260mers that have TDP-43-dependent localization activity are directly bound by TDP-43, and mutation of TDP-43 motifs within them abrogates both binding and activity.

OK so we have 260mers that have TDP-43-dependent RNA localization activity. But are they actually bound by TDP-43? To test this, we measured the TDP-43 affinity for the exact same ~10k 260mer RNAs in vitro, allowing us to directly relate binding to activity.

So what distinguishes these bound/active motifs from unbound/inactive motifs? Secondary structure. Bound motifs are significantly more single-stranded. We can predict whether or not a TDP-43 motif regulates RNA localization simply by looking at its secondary structure character.

Only some TDP-43 motifs are actually occupied by TDP-43 in cells, and only those motifs made RNAs TDP-43-sensitive. Further, mutation of those motifs abolished activity, while mutation of other non-occupied motifs had no effect.

We found specific pieces of UTRs that were sufficient to make the localization of reporters sensitive to TDP-43. Interestingly, these often overlapped perfectly with known TDP-43 CLIP sites. Their activity was also abolished by mutated TDP-43 motifs within them.

To answer that, we used an MPRA where we chopped up those UTRs into ~10k 260mer RNA sequences. We then incorporated each of those into a reporter and tested the localization of those reporters with and without TDP-43.

Further, the 3' UTRs of the 3 exemplar RNAs were sufficient to make the localization of a reporter RNA similarly dependent upon TDP-43. But what about these UTRs wast10
making them TDP-43-sensitive?

TDP-43 binds GU-rich kmers. 3' UTRs of RNAs that became more neurite-enriched upon TDP-43 loss were very strongly enriched in these motifs as well as CLIP-defined TDP-43 binding sites, suggesting that they are being directly regulated by TDP-43.

Interestingly, many RNAs became *more* neurite-enriched without TDP-43. This is exemplified by 3 RNAs, Diras1, Ksr2, and Wasf3. Although the total cellular level of these RNAs stays ~ the same, in neurites they go up 20-fold without TDP-43.

Interestingly, many RNAs became *more* neurite-enriched without TDP-43. This is exemplified by 3 RNAs, Diras1, Ksr2, and Wasf3. Although the total cellular level of these RNAs stays ~ the same, in neurites they go up 20-fold without TDP-43.

To ask how TDP-43 regulates RNA localization, we then analyzed neurite enrichments changed with and without dox-inducible loss of cellular TDP-43.

We used a compartmentalized culture system to separate cell bodies and neurites. By profiling the RNA content of each fraction using RNAseq, we learn the relative abundance of each RNA in neurites vs. soma.

First, I must note that all this work was NIH funded. We are very grateful for all taxpayer money and strive to be good stewards of it. The recent actions taken by the govt threaten progress toward cures of countless diseases and the livelihoods of countless talented people.

TDP-43 directly inhibits RNA accumulation in neurites through modulation of RNA stability The subcellular localization of hundreds of RNAs to neuronal projections allows neurons to efficiently and rapidly react to spatially restricted external cues. However, for the vast majority of these ...

This has been the work of many people, most notably Charlie Moffatt and Ankita Arora with help from the labs of Daniel Dominguez and Holger Russ. www.biorxiv.org/content/10.1...