Thrilled to share that our paper describing protein-dependent frameshifting is now out in Molecular Cell @cellpress.bsky.social. Huge congratulations to @jemmabetts.bsky.social for publishing the first research paper from her PhD 🧬🧪🥳 www.sciencedirect.com/science/arti... 1/8

A protein-dependent riboswitch activates ribosomal frameshifting in cardioviruses

Programmed −1 ribosomal frameshifting (PRF) is a translational control mechanism used by RNA viruses to regulate the relative abundance of proteins en…

sciencedirect.com

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Analog intrinsic recoding measures RNA dynamics without chemical conversion

Steady-state RNA abundance measurements mask the synthesis and decay rates that shape gene expression. Analog intrinsic recoding sequencing (AIR-seq) repurposes the base-pairing properties of N4-hydro...

biorxiv.org

So excited to share my first preprint of grad school! Check out this thread to learn more about a cool new technique we are using to learn more about hidden layers of RNA regulation! Thank you so much to my coauthors, mentors, and lab for helping us get this story up!

Stirling Churchman@stirlingchurchman.bsky.social · 3mo ago

RNA-seq tells us how much RNA is present in the cell. But to understand gene regulation, we need to easily measure the synthesis and decay rates driving this abundance. We introduce AIR-seq: analog intrinsic recoding sequencing. (1/6) www.biorxiv.org/content/10.6...

Excited to share our latest work! The oncogenic m5C writer NSUN2 achieves substrate specificity by recognizing RNA structure and conformational dynamics. RNA folding shapes methylation! Congratulations to the team! Thank you, colleagues and supporters! ttps://nature.com/articles/s41586-026-10582-9

Substrate selectivity of the human RNA m5C methyltransferase NSUN2 - Nature

NSUN2 is an enzyme that adds a small chemical mark to RNA molecules and uniquely selects its targets based on specific sequence patterns and structural features.

nature.com

1/9 New preprint from the Sternberg Lab in collaboration with the Nishimasu Lab! We uncover how the DRT3 antiphage immune system pairs two reverse transcriptases, one RNA-templated and one protein-templated, to build a double-stranded DNA effector. doi.org/10.64898/202...

If you want to know what 3′UTRs with long conserved sequence stretches do, check out our BioRxiv preprint doi.org/10.64898/202.... They form functional intermolecular 3′UTR-3′UTR interactions that enable co-folding of proteins to rapidly induce transcriptional programs.

(1/7) How does T. brucei achieve a 140-fold stoichiometric excess of VSG mRNA over upstream ESAGs from a single polycistronic unit? Our latest research in @natmicrobiol.nature.com reveals a mechanism of spatially regulated RNA decay to fine-tune expression of virulence genes

Some molecular machines, like ribosomes, can persist for long periods of time in cells. Could molecular aging of ribosomes shape how proteins are made? In our new preprint we track ribosomes as they age in cells and uncover unexpected effects on translation (1/10) www.biorxiv.org/content/10.6...

Preprint on the Stanford #RNA 3D folding Kaggle challenge is out. My scientific new year’s resolution is to brush up on template-based modeling. #gofai www.biorxiv.org/content/10.6...

Template-based RNA structure prediction advanced through a blind code competition

Automatically predicting RNA 3D structure from sequence remains an unsolved challenge in biology and biotechnology. Here, we describe a Kaggle code competition engaging over 1700 teams and 43 previous...

biorxiv.org

Rob Reiner made “the kinds of films that accompany people throughout their lives,” Alexandra Schwartz writes. “They are comfort watches in the best sense.” newyorkermag.visitlink.me/jCHRSD

Rob Reiner Made a New Kind of Fairy Tale

The director’s great achievement was placing real people, with real senses of humor, into the fantasies of mass culture.

newyorkermag.visitlink.me

🔬 #Trypanosomes process their large rRNA in a highly unusual way-by cutting it into six pieces. A new study from @schneian.bsky.social lab identified two essential proteins, TbLrRP1 and TbLrRP2, that drive this process. Read more: doi.org/10.1093/nar/... #NARBreakthrough #RibosomeBiogenesis

With many postdoc grants like the NSF PRFB, Ford Fellowship, and Hanna H. Gray fellowships disappearing, I am currently looking for grants that could fund incoming postdoctoral scholars. Here is a thread of some of them 🧵

Mamdani: "New York will remain a city of immigrants, a city built by immigrants, powered by immigrants, and as of tonight, led by an immigrant."

6/10 We found that DRT10 synthesizes tandem-repeat cDNAs through a mechanism strikingly reminiscent of DNA repeat addition by telomerase. But does this similarity represent convergent evolution or shared ancestry?

Today is only the beginning. Our time has come, New York. Our time is now.

Today is only the beginning.

YouTube video by Zohran Mamdani for NYC

youtube.com

Excited to announce the YAK lab's first paper and the discovery of the FIRST human cellular PRF signal to give access to two overlapping open reading frames (science.org/doi/10.1126/...)! Before we dive in, the story actually begins in a Nature from 11 years ago

cshperspectives.cshlp.org/content/earl... Review alert! In our latest review, we dissect the mechanistic structural and kinetic principles that govern -1 ribosome frameshifting and discuss how different flavours arise from distinct molecular pathways, yet converge on shared mechanistic features.

Collective homeostasis of condensation-prone proteins via their mRNAs | Nature share.google/zkKumKefL83G...

Collective homeostasis of condensation-prone proteins via their mRNAs - Nature

The authors discover a homeostatic process termed interstasis, in which an increased concentration of proteins within RNA–protein condensates induces the sequestration of their own mRNAs.

share.google

NSF today released instructions for the next round of applicants to its Graduate Research Fellowship Program. A key group—second-year Ph.D. students—is no longer eligible, and students who are still able to apply will face an unusually narrow timeframe. https://scim.ag/3KlQkQk

‘Completely shattered.’ Changes to NSF’s graduate student fellowship spur outcry

The announcement comes months later than usual, leaving many would-be applicants stranded

science.org

Please consider signing this letter in support of the NSF graduate fellowship program. It is an important program for training scientists, particularly for disciplines that are not well-supported by research grants.

Jason “Obstacle to Progress” Williams@jasonwilliamsny.bsky.social · last yr.

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment. The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP jasonjwilliamsny.github.io/grfp2025/

Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment. The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP jasonjwilliamsny.github.io/grfp2025/

In a first, a gene therapy seems to slow Huntington disease | Science | AAAS www.science.org/content/arti... 🧪

In a first, a gene therapy seems to slow Huntington disease

Small study suggests uniQure drug could be first successful treatment for devastating brain disorder

science.org

Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)

HuD controls widespread RNA stability to drive neuronal activity-dependent responses

Neuronal activity shapes brain development and refines synaptic connectivity in part through dynamic changes in gene expression. While activity-regulated transcriptional programs have been extensively...

biorxiv.org

Been thinking about creating a collection of good protein structure figures, as inspiration for my own work. #1 www.nature.com/articles/s41...

Our study from the Steckelberg lab is out now in @narjournal.bsky.social !! We dove into a new nuclease-blocking viral #RNA structure important for viral infection, which provided evidence of similar structure-based strategies across diverse viral families. academic.oup.com/nar/article/...

A conserved viral RNA fold enables nuclease resistance across kingdoms of life

Abstract. Viral exoribonuclease-resistant RNA (xrRNA) structures block cellular nucleases to produce subgenomic viral RNAs during infection. High sequence

academic.oup.com

I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in @natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)

Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis - Nature Biotechnology

Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.

nature.com

New paper: More than 2700 human 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. www.biorxiv.org/content/10.1...

“Musk’s casualties are not only in Washington but all over the world, in refugee camps and scientific labs whose funding was abruptly cut off, in national parks you can’t get into this summer, and in communities across the country where polluters will no longer be prosecuted.”

The New Yorker@newyorker.com · last yr.

Elon Musk promised to slash the U.S. budget. But his actions may cost the government as much as $135 billion in this fiscal year alone, according to recent estimates.

Identified in the 1970s, the precise molecular function of the alternative initiation factor eIF2A has remained unclear. Here, we map its interactome and uncover a surprising role in ribosome-associated quality control (RQC) upon ribosome stalling. 1/x www.biorxiv.org/content/10.1...

The alternative initiation factor eIF2A regulates 40S subunit turnover in ribosome-associated quality control

The noncanonical translation initiation factor eIF2A plays critical roles in diverse cellular processes, including the integrated stress response, neurodegeneration and tumorigenesis. However, the pre...

biorxiv.org