David McQuarrie
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davidmcquarrie.bsky.social
David McQuarrie
@davidmcquarrie.bsky.social
1.4K followers 450 following 41 posts
Postdoc in the Jaffrey lab at @WeillCornell.bsky.social @CornellUniversity.bsky.social former PhD in the Soller lab interested in RNA-binding proteins and RNA modifications; #RNA #RNAmodifications #Genetics 🧫🪰 #MolecularBiology #Evolution
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davidmcquarrie.bsky.social
David McQuarrie @davidmcquarrie.bsky.social · Nov 21
Hi #RNAsky, I've made a much needed #RNA modifications starter pack!
Let me know if you’d like to be added or know someone who should be.
go.bsky.app/E7zXGSF
#RNAmodifications
RNA modifications
Join the conversation
go.bsky.app
Reposted by David McQuarrie
natbiotech.nature.com
Fine-scale chromatin mapping uncovers principles of cis-regulatory element interactions. #NBThighlight www.cell.com/cell/fulltex...
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Li et al. apply base-pair resolution Micro Capture-C ultra to map chromatin contacts between individual motifs within cis-regulatory elements and reveal a unified model of biophysically mediated enhan...
www.cell.com
November 10, 2025 at 8:58 AM
Reposted by David McQuarrie
biorxivpreprint.bsky.social
Control of gene output by intron RNA structure https://www.biorxiv.org/content/10.1101/2025.11.08.687378v1
November 10, 2025 at 3:46 AM
Reposted by David McQuarrie
kurianlab.bsky.social
www.nature.com/articles/s41...
RNA stability enhancers for durable base-modified mRNA therapeutics - Nature Biotechnology
A systematic screen identifies RNA elements that enhance the stability and translation of base-modified mRNA.
www.nature.com
November 10, 2025 at 5:17 AM
Reposted by David McQuarrie
pierrebaduel.bsky.social
Happy to share the results of a long-haul post-doc project, now online @science.org, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below!
doi.org/10.1126/scie...
Transposable elements are vectors of recurrent transgenerational epigenetic inheritance
DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...
doi.org
September 18, 2025 at 6:35 PM
Reposted by David McQuarrie
natbiotech.nature.com
KATMAP infers splicing factor activity and regulatory targets from knockdown data - @daspliceisright.bsky.social go.nature.com/47ycrMJ
KATMAP infers splicing factor activity and regulatory targets from knockdown data - Nature Biotechnology
A biophysical model uses knockdown or overexpression data to infer splicing factor activity.
go.nature.com
November 4, 2025 at 3:13 PM
Reposted by David McQuarrie
haoyin.bsky.social
Epitranscriptomics #PhaseSeparation

m6A-modified #EnhancerRNA & YTHDC1-BRD4 assemble transcriptional condensate

MINT-seq detects >3-fold more m6A peaks than MeRIP-seq

Stringtie annotate eRNAs & promoter upstream antisense RNAs, 24% & 48% are m6A+ (MCF7)

#MolCell 2021
www.cell.com/molecular-ce...
October 19, 2025 at 7:12 PM
Reposted by David McQuarrie
biorxiv-molbio.bsky.social
FTO depletion does not alter m6A stoichiometry in AML mRNA: a reassessment using direct RNA nanopore sequencing https://www.biorxiv.org/content/10.1101/2025.10.22.681652v1
October 23, 2025 at 3:22 PM
Reposted by David McQuarrie
jsantoyo.bsky.social
Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing. #DirectRNAseq #Sequencing #RNAmodifications @nanoporetech.com
www.biorxiv.org/content/10.1...
November 6, 2025 at 11:30 AM
Reposted by David McQuarrie
biorxiv-molbio.bsky.social
The mammalian rapid tRNA decay pathway is critical for N⁷-methylguanosine-hypomodified tRNA degradation under physiological conditions https://www.biorxiv.org/content/10.1101/2025.11.05.686800v1
November 6, 2025 at 5:18 AM
Reposted by David McQuarrie
natbiotech.nature.com
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - @distefanolab.bsky.social @brumbaugh-lab.bsky.social go.nature.com/3X215du
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - Nature Biotechnology
Stem cell differentiation is controlled by manipulating RNA condensates.
go.nature.com
October 28, 2025 at 6:50 PM
Reposted by David McQuarrie
natplants.nature.com
New OA Article: "RNA m6A regulates the transcription and heterochromatin state of retrotransposons in Arabidopsis" rdcu.be/eM95H

m6A is recognized by nuclear readers CPSF30-L and ECT12, which associate with SUVH4/5/6 and ATXR5/6 to enhance histone methylation...
October 28, 2025 at 7:10 PM
Reposted by David McQuarrie
lucksmith.bsky.social
🪰 folks! I spoke to the Transmitter about FlyBase. As noted at flybase.org, bridge $ ran out and many staff were laid off.

Good news is stopgap contributions will keep core FlyBase operations active. But community support remains essential. Please donate @FlyBase and share! 1/2

tinyurl.com/FlyBase
FlyBase secures funding for year, but future still uncertain
The FlyBase team’s fundraising efforts have proven successful in the short term, but restoration of its federal grant remains uncertain.
tinyurl.com
October 29, 2025 at 12:31 PM
Reposted by David McQuarrie
yukihaba.bsky.social
How does life evolve to adapt to modern cities?

Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation.

🧵(1/n)
@science.org
www.science.org/doi/10.1126/science.ady4515
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
www.science.org
October 25, 2025 at 4:46 AM
Reposted by David McQuarrie
bryangitschlag.bsky.social
NEW PAPER! Some kinds of genetic mutations are more likely to arise than others. Such "biases" in mutation vary between species.

Analyzing data from 14 species, we show that this variation explains species differences in the genetics of adaptation!

(1/3)

www.biorxiv.org/content/10.1...
Graph showing a positive correlation between "bias in adaptive outcome" on the vertical axis and "mutation bias" on the horizontal axis, with 14 data points representing 14 respective species, with a line of best fit equal to a slope of 0.82 on the log-scale axes. Each data point contains horizontal and vertical error bars to illustrate the uncertainty in both the mutational and adaptive data. The 95% confidence interval of the slope is shown in parentheses (0.44 to 1.24), based on 10,000 simulated data sets, where the simulated data sets are based on statistical resampling of the empirical data (i.e. "bootstrap" data sets). Regression lines based on these bootstrap data sets are shown as light gray lines. The type of bias reported here refers to the ratio of transitions versus transversions, where transitions are a DNA mutation that preserves the basic structure of the DNA base (i.e. a purine-to-purine or pyrimidine-to-pyrimidine mutation), and transversions are mutations that alter the structure of the DNA base at a particular site (i.e. replacing a purine with a pyrimidine or vice versa). In other words, this graph shows that transitions contribute more toward adaptive evolution in species where transitions arise at a higher rate.
September 8, 2025 at 7:38 PM
Reposted by David McQuarrie
sedonamurphy.bsky.social
Here, we show that the unique regulatory landscape of ecDNA enables an ancient LINE to resurrect and act as an enhancer of Myc. This was so fun with @katerinakraft.bsky.social and @mattjones.bsky.social and others. www.nature.com/articles/s41...
Enhancer activation from transposable elements in extrachromosomal DNA - Nature Cell Biology
Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They show that EIE 14 integrat...
www.nature.com
October 21, 2025 at 9:43 AM
Reposted by David McQuarrie
timothyfuqua.bsky.social
Forgot to add the graphical abstract :)
Diagram illustrating promoter architecture and factors influencing mutational robustness. Top panel: The promoter sequence is shown with a -35 box (orange, labeled “TTG...”) and a -10 box (purple, labeled “TATA...”), separated by 17 ± 1 bp. Sequence logos above each box indicate conserved nucleotides. Bottom panel: Titled “Mutational robustness influenced by:”, it shows four numbered factors: Strength – represented by an upward diagonal arrow. Box position – two colored bars (orange and purple) aligned on numbered positions (1–6), with a dashed box highlighting overlapping regions. Box overlap – orange and purple boxes partially overlapping. Spacer length – orange and purple boxes separated by a double-headed arrow labeled “17 bp.”
October 23, 2025 at 11:19 AM
Reposted by David McQuarrie
alperakay.bsky.social
This is a super interesting paper by @conradlab.bsky.social lab on METTL16. They separate METTL16 function on U6 and MAT2A allowing more accurate analysis. Their results cast serious doubt on hundreds of papers claiming METTL16 methylates vast number of mRNAs. www.cell.com/cell-reports...
The catalytic efficiency of METTL16 affects cellular processes by governing the intracellular S-adenosylmethionine setpoint
Flaherty et al. demonstrate that the catalytic efficiency of METTL16 regulates expression of MAT2A to determine the intracellular SAM setpoint. Their data indicate that this is required for several SA...
www.cell.com
October 21, 2025 at 1:38 PM
Reposted by David McQuarrie
matthiassoller.bsky.social
Last of the trilogy about core promoter evolution thanks to @davidmcquarrie.bsky.social
academic.oup.com/genetics/adv...
Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related Drosophila species
Abstract. Seminal fluid proteins (Sfps) are essential for reproductive success and evolve fast on average, possibly driven by post-copulatory sexual select
academic.oup.com
October 20, 2025 at 7:04 AM
Reposted by David McQuarrie
biorxiv-evobio.bsky.social
Transposable elements drive much of naturally occurring genetic lethality in Drosophila melanogaster https://www.biorxiv.org/content/10.1101/2025.10.16.682755v1
October 16, 2025 at 7:32 PM
Reposted by David McQuarrie
p-santamaria.bsky.social
Good ! These results indicate that regulatory evolution, rather than genome background variation, drives Acp expression changes and promotes their rapid evolution.

pubmed.ncbi.nlm.nih.gov/41108154/
Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related Drosophila species - PubMed
Seminal fluid proteins (Sfps) are essential for reproductive success and evolve fast on average, possibly driven by post-copulatory sexual selection (PCSS) originating from sperm competition and crypt...
pubmed.ncbi.nlm.nih.gov
October 19, 2025 at 7:10 AM
Reposted by David McQuarrie
zeynepbaharoglu.bsky.social
New species from space 🦠💫Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station www.nature.com/articles/s41...
Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station - Scientific Reports
Scientific Reports - Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station
www.nature.com
October 18, 2025 at 12:52 PM
Reposted by David McQuarrie
fly-broadcast.bsky.social
Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related Drosophila species
#Drosophila
Rapid promoter evolution of male accessory gland genes is accompanied by divergent expression in closely related Drosophila species #Drosophila
PubMed link
pubmed.ncbi.nlm.nih.gov
October 18, 2025 at 5:23 PM
Reposted by David McQuarrie
danielibrahim.bsky.social
What is a promoter? And how does it work?

We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters

www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 3:06 PM
Reposted by David McQuarrie
perrimonlab.bsky.social
New paper: A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome
Kim, Huang, Johnson, Yaron-Barir, Keven Wang, Cantley, Hu, Perrimon
bioRxiv 2025.10.10.681672; doi: doi.org/10.1101/2025...
A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome
Protein kinases orchestrate cellular processes through phosphorylation, yet the structural basis for their specific binding partner interactions remains largely unmapped. Here, we present a structure-...
doi.org
October 12, 2025 at 8:51 PM
Reposted by David McQuarrie
anafiszbein.bsky.social
Thrilled to share our work on transcription initiation and termination being spatially coordinated out today in Science! www.science.org/doi/10.1126/...
mRNA initiation and termination are spatially coordinated
Transcriptional initiation and termination decisions drive messenger RNA (mRNA) isoform diversity but the relationship between them remains poorly understood. By systematically profiling joint usage o...
www.science.org
October 10, 2025 at 6:14 PM