David McQuarrie

Spligation enables programmable chimeric RNA generation in living cells
doi.org/10.64898/202...

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs https://www.biorxiv.org/content/10.64898/2026.03.05.709866v1

Regulatory paradigm of Dscam1 stochastic alternative splicing through conserved long-range RNA structures Abstract. Pancrustacean Dscam1 genes encode 2 000–120 000 distinct isoforms via mutually exclusive splicing; however, the underlying regulatory mechanisms

academic.oup.com/nar/article/...

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We are excited to share our new preprint: iCLIP3 — an improved protocol for transcriptome-wide mapping of protein–RNA interactions at single-nucleotide resolution.

Out now! In collaboration with Leifu Chang, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems!

Links to the published articles:
tinyurl.com/55kpavet
tinyurl.com/sk6djwx3

Previous thread for the preprint:
bsky.app/profile/did:...

Interstep compatibility of a model for the prebiotic synthesis of RNA consistent with Hadean natural history | PNAS Models for prebiotic syntheses often have many steps, each separately validated by laboratory experiments. The challenge then asks whether these st...

RNA from scratch.. 💫 Interstep compatibility of a model for the prebiotic synthesis of RNA consistent with Hadean natural history | PNAS
www.pnas.org/doi/10.1073/...

After 5 years of developing, a new preprint from the lab - introducing our workflow for comparative insect connectomics, aimed at democratizing connectomics. @erc.europa.eu @lundvision.bsky.social @biologylu.bsky.social Read it here: www.biorxiv.org/content/10.6...

23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures https://www.biorxiv.org/content/10.64898/2026.03.01.708810v1

Gene body methylation buffers noise in gene expression in plants Abstract. Non-genetic variability in gene expression is an inevitable consequence of the stochastic nature of processes driving transcription and translati

Hot off the press, our latest publication on the functional role of gene body methylation (gBM).

academic.oup.com/nar/article/...

Work spearheaded by Jakub Zastapilo with help from @robynemm.bsky.social and Liudmila Mikheeva and co-led by Marco Catoni and @ubechtold.bsky.social 1/3

Hmmmm. “Mars Potato Cultivation: Analysis, Challenges, Sustainable Scientific Conceptions”

#plantscience #astrobiology

pubmed.ncbi.nlm.nih.gov/41752916/

Paralog interference contributes to the preservation of genetic redundancy Duplicated self-interacting proteins can interact and interfere with each other’s function. Cisneros, Mattenberger, et al. show that selection against interfering loss-of-function alleles extends the ...

New paper alert: Paralog interference contributes to the preservation of genetic redundancy www.cell.com/current-biol...

We wrote a piece on how easy it is to write gene regulatory sequences. - Turns out, it isn't that easy even though we know a lot about cis-regulation.

huge credit to @carldeboer.bsky.social to seeing this through so our thoughts aren't lost. I promise, it's a worthwhile read!

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...

🤩💪 Out now! 3D regulatory hubs in sex determination

With @mamartirenom.bsky.social & Capel labs, led by @imotagom.bsky.social & @jrotwitguez.bsky.social

1️⃣ METALoci – explore #3DGenome 🧬
2️⃣ Non-coding region controlling Fgf9 🧩
3️⃣ Meis genes = new key players 🌟

👉 rdcu.be/e5sm2

1/n Bluetorial 👇

Have you ever wondered 🤔... Does phenotypic variance respond to environmental perturbation? Does it have a genetic basis? Are mean and variance regulating loci exposed to different selection pressures? These and more questions are explored in our new preprint 🔥

www.biorxiv.org/content/10.6...

LINE-L1, HIV, Ty3 retrotransposons in insects.
several of these genomes are > 40% adenosine!

What is the molecular origin & evolutionary pressure resulting in A-rich genomes of retrotransposons & some retroviruses?

it must be so hardwired that hosts exploit this bias for genome defense

any ideas?

Two-panel figure linking piRNA production to uridine. Left: distributions of piRNA biogenesis efficiency for CDS and 3′UTR tiles grouped into efficiency bins (log scale). Right: violin plots showing uridine content (%) in the analysis window for each efficiency bin; higher-efficiency bins have higher U content, indicating U-rich sequence associates with stronger piRNA output.

We discovered that Yb acts as a U-content sensor. It selectively channels uridine-rich transcripts to piRNA biogenesis, effectively initiating their phased processing into piRNAs. (6/19)

🎉Proud to present our latest paper, out now in Nature Communications: www.nature.com/articles/s41...

RNA Binding Proteins (RBPs) are often full of intrinsically disordered regions (IDRs), but what these regions do during RNA recognition is often unclear. 1/10
#RNA #IDR #RBP

Pseudouridine selects RNAs for extracellular transport RNAs move through the extracellular space to transmit information between cells, including mammalian neurons, yet how specific RNAs are channeled into these extracellular routes is unknown. Using geno...

RNAs outside of cells?! How did they get there?

(Thread coming soon 👀)

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

Single-round evolution of RNA aptamers with GRAPE-LM - Nature Biotechnology Combining generative AI and one round of wet lab evolution generates high-affinity RNA aptamers.

Single-round evolution of RNA aptamers with GRAPE-LM go.nature.com/4bFDI22

Happy to share scHiCAR, an ultra-high throughout (millions of cells), low cost (5 cents/cell including NGS), and trimodal platform for integrated single-cell level analysis of mRNA, open chromatin, and 5-kb resolution looping with ground-truth data the same individual cell.

Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5′ (blue) to 3′ (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org 🧪 plos.io/4aoOQiX

Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes Cells down-regulate protein synthesis when stressed to conserve energy and shift resources toward repair. We found that in some mammalian cells, including neurons, stress also resulted in the formatio...

Out now in @science.org
Ribosomal RNA expansion segments mediate the oligomerization of inactive animal ribosomes | Science www.science.org/doi/10.1126/...

Selection of U-rich sequences reminds me of A-rich selection by the HUSH complex to silence sense transposons (I beleieve in non germ line cells). This also reminds me of how introns (at least in vertebrates) tend to be U-rich and exons A-rich (but short). www.tandfonline.com/doi/10.1080/...

A Naïve RNA Sampling Core Enables Adaptive piRNA Specificity Against Transposable Elements https://www.biorxiv.org/content/10.64898/2026.02.07.704324v1

Advances in CLIP-derived methods have enabled high-resolution mapping of individual RNA binding protein-RNA interactions as well as RNA binding protein-associated RNA–RNA interactions #RNA #CLIP @evannostrandlab.bsky.social bit.ly/4bYjAsg

A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variabil...

🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇

Chromosomal Rearrangements and Transposable Elements in Locally Adapted Island Drosophila Abstract. Chromosomal rearrangements, particularly those mediated by transposable elements (TEs), can drive adaptive evolution by creating chimeric genes,

Turner et al. investigated the role of chromosomal rearrangements during habitat shifts in two locally adapted populations of Drosophila from the island of São Tomè; findings suggest that rearrangements may act as a source of innovation.

🔗 doi.org/10.1093/gbe/evaf236

#genome #evolution #drosophila

Programmable and Switchable RNA Scaffolds for Synthetic Condensate Engineering in Mammalian Cells https://www.biorxiv.org/content/10.64898/2026.02.14.705909v1

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.

How does the piRNA pathway solve the self vs. non-self problem? 🧬

Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)