SheqLab

The Shechner lab in UW Pharmacology. We study Noncoding RNAs and cellular architecture. He/His/Him. All comments are my own. @ShechnerLab.bsky.social

[SheqLab @ShechnerLab]

It's my pleasure to present the next big preprint from SheqLab! An exciting application of our O-MAP platform that I hope will transform the study of nuclear architecture.

If you've ever wanted to dissect the subnuclear "neighborhood" around an individual locus, read on! (1/30)

[SheqLab @ShechnerLab]

There’s nothing *quite* like seeing two of my favorite labs collaborating on truly beautiful work. Congrats to all involved!!

[Furqan Fazal @FurqanMFazal]

Excited to share our collaborative work with the @TonyMustoe and @SuperSciJew labs, led by the fearless @RitwikaBose15.
In this study, we developed RAID-MAP, an approach to map RNA structure within biomolecular condensates in living cells.
https://t.co/zUeJTnnEMV

[SheqLab @ShechnerLab]

Good *gravy*, that’s beautiful! Congrats too all the authors!!

[Das Lab @RDasLab]

First AI-generated RNA with novel atomically ordered 3D fold! With @eternagame @StanfordBiochem @chaitjo @PossuHuangLab @UWproteindesign @ShujunHe0717 @navtejtoor @HHMIJanelia on bioRxiv https://t.co/rO8OVU1Avd

[SheqLab @ShechnerLab]

🤩🤩🤩

[Alice Ting @aliceyting]

Today we report single-cell APEX-seq (scAPEX-seq) — a new method for unbiased mapping of *subcellular* transcriptomes at single-cell resolution. This approach reveals cell states that are not detectable by standard scRNA-seq, and enabled us to identify regulators of CAR T function that improve solid tumor killing.

https://t.co/iAJUj6jBQ4

[SheqLab @ShechnerLab]

@pdhsu

[SheqLab @ShechnerLab]

AWESOME CONFERENCE ALERT!!

I had an absolute blast at the Fusion “Genome Regulation Through RNA” meeting back in 2024, and psyched to see its upcoming return! Let’s geek out about all things Chromatin and RNA together, in Cancun!

Talk abstract deadline: 10/17

Details👇

[SheqLab @ShechnerLab]

Nucleoli + AI = NucleolAI?

Seriously, this is awesome work! Congrats to all the authors!

[Anita Đonlić @anita_donlic]

I’m thrilled to share our preprint that uses deep learning to interrogate structure-function relationships in condensates! https://t.co/izhFI1ANXa In here, we ask: can AI read condensate biology from pictures alone? Turns out yes... see what we discover below! 🤖🧬🖼️ (1/10)

[SheqLab @ShechnerLab]

@guo_lab @jogleeson_ucsd @McKnightFdn @hyejung_won @SharmaLab_UCSC @Allan_HPool @ZucheroLab @EthanHughesLab Thanks, Junjie!!

[SheqLab @ShechnerLab]

*Huge* win for @genentech! Congrats, @DNAmyStrom!!

[Amy Strom @DNAmyStrom]

I'm thrilled to announce my next career step-- I’m joining Genentech as a Principal Scientist & Lab Head in Discovery Oncology!
I’ll be hunting new ways to target cancers using my background in disordered nuclear proteins.

[SheqLab @ShechnerLab]

@HsiehLab @BladderCancerUS Woohoo! Congrats, @HsiehLab!!

[SheqLab @ShechnerLab]

Amazing work, as always, from @Mayr_Christine’s lab. Congrats to all authors!!

[Christine Mayr @Mayr_Christine]

More than 2700 3′UTRs are highly conserved.

These 3′UTRs are essential components in mRNA templates, as their deletion decreases protein activity without changing protein abundance.

Highly conserved 3′UTRs help the folding of proteins with long IDRs.

https://t.co/b6hd4AlIoX

[SheqLab @ShechnerLab]

Awesome work from the Rouhanifard lab (as per usual 😊)

[Sara Rouhanifard @SRouhanifard]

New from the Rouhanifard Lab!
What if we could sort single cells based on whether a specific gene was actively being transcribed—and then ask what drives that burst?
Introducing: NuclampFISH

[SheqLab @ShechnerLab]

@stojic_lovorka @CellReports @FKHM Thanks, Lo!!

[SheqLab @ShechnerLab]

Hello RNA World! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @CellReports, @FKHM and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!

https://t.co/gVMCVbSRoS

[SheqLab @ShechnerLab]

@hyejung_won @CellReports @FKHM Yay! I hope you enjoy it, Hyejung, and thanks!!

[SheqLab @ShechnerLab]

@Doulatov_lab @ColumbiaPHY @columbiacancer Congrats, @Doulatov_lab!! I’m sad to see you go, but excited for what this next stage will bring!

[SheqLab @ShechnerLab]

@incaRNAtolab This is my everything.

[SheqLab @ShechnerLab]

@aliceyting Awesome! Great seeing this cool work out in the world. Congrats!!

[SheqLab @ShechnerLab]

🤩🤩🤩

[Rachael Kretsch @RachaelKretsch]

Check out our new study on water networks in high resolution cryo-EM RNA data! @chiulab @RDasLab

[SheqLab @ShechnerLab]

TOP FIVE METABOLIC PATHWAYS
…Based on whether they sound like the name of an old-school anime:

5. The Pentose-Phosphate Shunt

4. Peptidoglycan Degradation

3. Fatty Acid Beta-Oxidation

2. The Dark Reactions of the Calvin Cycle

1. Gluconeogenesis

[SheqLab @ShechnerLab]

Thank you so much for posting! And thanks to the inimitable @cellseywoodruff for the amazing writeup!!

[RNA-Seq Blog @RNASeqBlog]

#RNAsequencing helps map #RNA interactions with proteins and #DNA, revealing cellular processes and disease mechanisms. The O-MAP method by the @ShechnerLab enables precise RNA neighborhood mapping for deeper insights. - @UW https://t.co/qhR65PBJUt