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Matthew Taliaferro @jmtali.bsky.social · May 9

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

Reposted by Matthew Taliaferro

Felipe del Valle Batalla @fadelvalle.bsky.social · Apr 10

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

TDP-43 directly inhibits RNA accumulation in neurites through modulation of RNA stability - preLights

An intriguing twist! TDP-43 (linked to ALS) keeps RNAs out of neuronal projections by making them unstable preventing RNA buildup in neurites

prelights.biologists.com

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Matthew Taliaferro @jmtali.bsky.social · Apr 2

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

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Matthew Taliaferro @jmtali.bsky.social · Mar 21

Thanks Junjie!

Matthew Taliaferro @jmtali.bsky.social · Mar 21

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...

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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...

www.findagrave.com

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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

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

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

Thanks Manny!

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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

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

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

...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...

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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...

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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?

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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Matthew Taliaferro @jmtali.bsky.social · Mar 3

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.

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