David McQuarrie

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis by chemically caging acp3U. Excited to report this work lead by Vinnie @vinnieviruses.bsky.social and in collaboration with @vijayrathinam.bsky.social in @nature.com www.nature.com/articles/s41...

Photo of a hand cradling a shoot of the vine. Some leaves are elliptical, while others are 3-lobed. Photo by Scott Zona CCBYNC2.

Photo of a selection of isolated leaves. Some leaves are entire, some are lobed. Some leaves are large, some are small and narrow. Photo by Scott Zona CCBYNC2.

Passiflora suberosa exhibits heteroblasty (different-shaped leaves on the same plant). The 2nd photo shows leaves from a single plant. It’s part of the evolutionary arms race with butterflies. It may prevent gravid female butterflies from forming a search image. #Passifloraceae #Botany 🌾🧪🌱

Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects? By integrating a literature review with transcriptomic, proteomic, and phenotypic data from two model bacteria, Escherichia coli and Vibrio cholerae, …

Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects? 🦠 =>processes evolutionarily tuned to be sensitive to translation speed eg: motility, iron homeostasis, leader peptide attenuation (ex: trp). #rnasky #microsky www.sciencedirect.com/science/arti...

Neural anticipation of virtual infection triggers an immune response - Nature Neuroscience Serino et al. show that seeing an infectious avatar approach the body in virtual reality triggers an immune response, indicating that the brain prepares the body to fight infections even for perceived...

If this one holds up, it's a huge discovery.

www.nature.com/articles/s41...

Biochemical analysis of human eIF4E-DCP2 interaction: Implications for the relationship between translation initiation and decapping All eukaryotic mRNAs bear a 7-methylguanosine cap on their 5’ end. The 5’ cap enables mRNA translation by binding directly to eIF4E; which further recruits other factors and the 40S ribosome. Addition...

I nice little story from the lab: dx.plos.org/10.1371/jour...

A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans www.biorxiv.org/content/10.1...

Figure showing the experimental overview as a graphic. Remaining alt text taken from the figure caption in the paper: (A) we sampled flies from six wild orchard populations ranging from Homestead, FL, to Lancaster, MA, and established isofemale lines in the laboratory. (B) We returned to a focal orchard in Media, PA, at early- and late-season timepoints and collected flies to capture evolutionary patterns following winter and summer conditions. (C) We then seeded outdoor mesocosms (N = 9) with an outbred population originating from early-season collections in Media, PA, and sampled flies at the end of summer (mid-season) and fall (late-season) to determine if seasonal patterns are recapitulated in experimental populations controlled for migration, drift, and cryptic population structure. (D) Across each wild or experimental context, we sampled flies, established lines in the lab, completed common garden treatment to remove environmental effects, and scored females for abdominal pigmentation. We also conducted pooled DNA sequencing on additional flies sampled from each population to map genomic patterns for candidate pigmentation SNPs.

How predictably does complex trait adaptation proceed over space and time in wild populations?
doi.org/10.1093/evle...

Now in @evolletters.bsky.social by @skylerberardi.bsky.social, @paulrschmidt.bsky.social et al.

📷: Dr. Rush Dhillon

The histone core domain evolves at single-residue resolution to directly orchestrate transcription Nucleosomes are thought to be structural barriers to transcription, establishing a restrictive ground state that must be destabilized for gene express…

Happy to share our new paper out today in @cp-cellreports.bsky.social in collaboration with @tobiaswarnecke.bsky.social @akihisaosakabe.bsky.social about how evolution can do big things with small changes. www.sciencedirect.com/science/arti...

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals - Genome Biology Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypometh...

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process.
#plantscience
link.springer.com/article/10.1...?

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.

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)

Extracellular exosomal RNAs are glyco-modified - Nature Cell Biology Sharma, Jiao and colleagues report glycosylation of small RNAs within exosomes and propose a glycosylation-dependent mechanism for RNA targeting into exosomes, which may influence intercellular commun...

🍹Sharma, Jiao et al. report glycosylation of small RNAs within #exosomes and propose a glycosylation-dependent mechanism for #RNA targeting into exosomes, which may influence intercellular communication and RNA stability in the extracellular environment.
👉https://rdcu.be/eykKY
bit.ly/455vyuP

Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties Transposable elements are genetic parasites whose mobilization throughout the genome is a major source of deleterious mutations. However, some TE insertions are beneficial because they improve host fi...

Adaptive P-element insertions in a long non-coding RNA are associated with unique silencing properties

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

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa Abstract. Transfer RNA (tRNA) modifications have emerged as critical post-transcriptional regulators of gene expression affecting diverse biological and di

tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa 🦠👏High-throughput tRNA epitranscriptome profiling using mass spec on P. aeruginosa transposon insertion library and links with metabolic networks #microsky #rnasky doi.org/10.1093/nar/...

#rnasky #microsky

Excited to share one of the first papers to link #lncRNA #structure to its function in #cancer!

We mapped the structure of a tumor-suppressive DRAIC lncRNA and identified a 36-nucleotide hairpin as necessary and sufficient for its #anti-oncogenic function.

www.sciencedirect.com/science/arti...

Predicting the translation efficiency of messenger RNA in mammalian cells Nature Biotechnology - A deep convolutional neural network model predicts the influence of the full-length mRNA sequence on translation efficiency.

Very excited that our most significant work, a collaboration w/ Dr. Can Cenik at UT Austin on translational gene regulation, was finally published in Nature Biotechnology in a dual set of studies:

Paper 1 -- an AI model trained to predict translation rates from mRNA sequences: rdcu.be/exN1l

U-rich elements drive pervasive cryptic splicing in 3’ UTR massively parallel reporter assays - Nature Communications Massively parallel reporter assays (MPRAs) are powerful technologies for measuring the impact of non-coding sequences on gene expression. Here, the authors demonstrate that MPRA reporters often underg...

Our collaboration with Tony Mustoe's lab us out today. MPRA libraries and possible cryptic splicing in MPRA reporters, or reporters in general. The additional novelty here is that such events are controlled or influenced by AU-rich sequences.

www.nature.com/articles/s41...

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function go.nature.com/4mc1SmQ

Wow. Scientists have edited mosquito DNA to prevent the spread of malaria to humans "while supporting essential physiological functions... and negligible fitness costs" to the mosquito population.

Potentially ending the mosquito-born spread of malaria to humans.

www.nature.com/articles/s41...

Super excited to release a huge evolution project on the works for many years:

Evolution experiments synchronized across climates to understand rapid adaptation

Preprint: doi.org/10.1101/2025...
All data available: www.grene-net.org/data

#MOILAB
@ucberkeleyofficial.bsky.social
@hhmi.org

🧵👇

Genomes from historical Drosophila melanogaster specimens illuminate adaptive and demographic changes across more than 200 years of evolution Genomes from 25 museum specimens of Drosophila melanogaster (some more than 200 years old) reveal that small populations occupying northern Europe gave way to well-connected fly populations across the...

For those at #SMBE2025, here's the cool @plosbiology.org Drosophila "museomics" paper name-checked by @philipphummer.bsky.social at the start of his talk on TE spread in global D. melanogaster populations: journals.plos.org/plosbiology/...

RMBase v3.0: decode the landscape, mechanisms & functions of RNA modifications
The Encyclopedia of RNA Epitranscriptome

More than m6A
"73 RNA modifications of 62 species"

bioinformaticsscience.cn/rmbase/

@narjournal.bsky.social 2024
academic.oup.com/nar/article/...

A new protein-dependent riboswitch activates ribosomal frameshifting Programmed -1 ribosomal frameshifting (PRF) is a ubiquitous translational control mechanism in RNA viruses, allowing them to change the relative abundance of proteins encoded in different reading fram...

New preprint alert! 🚨👇 I'm delighted to share the latest research from @jemmabetts.bsky.social
in our group: ‘A new protein-dependent riboswitch activates ribosomal frameshifting’. Huge congratulations to Jemma for the first manuscript of her PhD! ✨

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

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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...

m6A in the coding sequence: linking deposition, translation, and decay N6-methyladenosine (m6A) is the most abundant internal modification in mRNA and plays a crucial role in regulating mRNA turnover. This review explores the characteristics of m6A sites in the coding se...

🚨Check out our brand new review on m6a in the CDS!🚨

m6A in the coding sequence: linking deposition, translation, and decay: Trends in Genetics www.cell.com/trends/genet...