David McQuarrie
@davidmcquarrie.bsky.social
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
Pinned
RNA modifications
Join the conversation
go.bsky.app
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
Let me know if you’d like to be added or know someone who should be.
go.bsky.app/E7zXGSF
#RNAmodifications
Reposted by David McQuarrie
RNA stability enhancers for durable base-modified mRNA therapeutics go.nature.com/4opTAsV
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.
go.nature.com
November 7, 2025 at 5:06 PM
RNA stability enhancers for durable base-modified mRNA therapeutics go.nature.com/4opTAsV
Reposted by David McQuarrie
m⁵C-Rol-LAMP, a simple qPCR-based assay, quantifies m⁵C RNA methylation at single nucleotides and uncovers stress-regulated rRNA modification in bacteria. #LMU_muenchen #lifescimunich #RNA #CRC1309 bit.ly/43AWnr4
November 20, 2025 at 1:54 PM
m⁵C-Rol-LAMP, a simple qPCR-based assay, quantifies m⁵C RNA methylation at single nucleotides and uncovers stress-regulated rRNA modification in bacteria. #LMU_muenchen #lifescimunich #RNA #CRC1309 bit.ly/43AWnr4
Reposted by David McQuarrie
Programmable initiation of mRNA translation by trans-RNA - @cornelluniversity.bsky.social @iecb.bsky.social go.nature.com/3K7SEdO
Programmable initiation of mRNA translation by trans-RNA - Nature Biotechnology
Translation can be initiated from a specific start codon using trans-RNA.
go.nature.com
November 21, 2025 at 2:44 PM
Programmable initiation of mRNA translation by trans-RNA - @cornelluniversity.bsky.social @iecb.bsky.social go.nature.com/3K7SEdO
Reposted by David McQuarrie
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by David McQuarrie
A new fossil fungus discovered in Scotland shows evidence of plants and fungi sharing nutrients to survive on land.
The fossil, more than 400 million years old, offers hints about the origin of one of the greatest partnerships in the history of life on Earth.
www.nhm.ac.uk/discover/new...
The fossil, more than 400 million years old, offers hints about the origin of one of the greatest partnerships in the history of life on Earth.
www.nhm.ac.uk/discover/new...
Ancient fossil reveals how plants and fungi first developed on land | Natural History Museum
A new fossil fungus discovered in Scotland shows evidence of plants and fungi sharing nutrients to survive on land.
www.nhm.ac.uk
November 20, 2025 at 3:35 PM
A new fossil fungus discovered in Scotland shows evidence of plants and fungi sharing nutrients to survive on land.
The fossil, more than 400 million years old, offers hints about the origin of one of the greatest partnerships in the history of life on Earth.
www.nhm.ac.uk/discover/new...
The fossil, more than 400 million years old, offers hints about the origin of one of the greatest partnerships in the history of life on Earth.
www.nhm.ac.uk/discover/new...
Reposted by David McQuarrie
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis | Science www.science.org/doi/10.1126/...
Very nice work from Holger Puchta & colleagues
Very nice work from Holger Puchta & colleagues
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis
The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...
www.science.org
November 20, 2025 at 8:47 PM
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis | Science www.science.org/doi/10.1126/...
Very nice work from Holger Puchta & colleagues
Very nice work from Holger Puchta & colleagues
Reposted by David McQuarrie
Looking for a PhD in RNA biology? The deadline is approaching fast! This is a great opportunity to do a PhD together with an industry partner fully funded by @nrpdtp.bsky.social BBSRC Case studentship.
New BBSRC funded PhD opportunity in my group with Inspiralis Ltd and @conradn.bsky.social. If you are interested in RNA - protein interactions and RNA modifications check the details below for how to apply. @nrpdtp.bsky.social @biouea.bsky.social @earlhaminst.bsky.social tinyurl.com/bdzvn4dr
How do RNA molecules shape genome regulation in the nervous system? (AKAY_U26CASE) | Doctoral Training Partnership
This PhD project will investigate how RNA modifications influence the activity of topoisomerase I (TOP1), a crucial enzyme that regulates DNA supercoiling during replication and transcription. Using C...
biodtp.norwichresearchpark.ac.uk
November 20, 2025 at 8:05 AM
Looking for a PhD in RNA biology? The deadline is approaching fast! This is a great opportunity to do a PhD together with an industry partner fully funded by @nrpdtp.bsky.social BBSRC Case studentship.
Reposted by David McQuarrie
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by David McQuarrie
Single-nucleotide resolution mapping of m6A of zebrafish mRNAs in early embryonic development links m6A modifications to the maternal-to-zygotic transition https://www.biorxiv.org/content/10.1101/2025.11.19.688951v1
November 19, 2025 at 4:33 PM
Single-nucleotide resolution mapping of m6A of zebrafish mRNAs in early embryonic development links m6A modifications to the maternal-to-zygotic transition https://www.biorxiv.org/content/10.1101/2025.11.19.688951v1
Reposted by David McQuarrie
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Reposted by David McQuarrie
🦣🧬🦣🤯💥We are pleased to share our new paper about ancient RNA expression profiles from the Woolly Mammoth, now published in Cell @cellpress.bsky.social
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
November 14, 2025 at 4:08 PM
🦣🧬🦣🤯💥We are pleased to share our new paper about ancient RNA expression profiles from the Woolly Mammoth, now published in Cell @cellpress.bsky.social
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
www.cell.com/cell/fulltex...
If you want to know more, read the 🧵 below:
Reposted by David McQuarrie
🚨 New preprint alert!
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
Environmental fluctuations influence heritable phenotypes through complex molecular mechanisms. In zebrafish (Danio rerio), the interplay between temperature variation, transposable element (TE) activ...
www.biorxiv.org
November 16, 2025 at 10:18 AM
🚨 New preprint alert!
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Our latest work from @immler.bsky.social lab 🐟🧬
Sex-specific responses of small RNAs and transposable elements to thermal stress in zebrafish germ cells
#TESky #TE #piRNA #miRNA #zebrafish #DanioDigest
🔗 Read here www.biorxiv.org/content/10.1...
A thread 🧵...
Reposted by David McQuarrie
www.biorxiv.org/content/10.1... @rohitpappu68.bsky.social and Jim Shorter latest banger just dropped
Nuclear-import receptors remodel the dilute phase to suppress phase transitions of RNA-binding proteins with prion-like domains.
RNA-binding proteins (RBPs) with prion-like domains, including FUS, hnRNPA1, and hnRNPA2, assemble into functional, metastable condensates that organize ribostasis, but can also transition into self-t...
www.biorxiv.org
November 16, 2025 at 2:11 AM
www.biorxiv.org/content/10.1... @rohitpappu68.bsky.social and Jim Shorter latest banger just dropped
Reposted by David McQuarrie
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
Fine-scale chromatin mapping uncovers principles of cis-regulatory element interactions. #NBThighlight www.cell.com/cell/fulltex...
Reposted by David McQuarrie
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
Control of gene output by intron RNA structure https://www.biorxiv.org/content/10.1101/2025.11.08.687378v1
Reposted by David McQuarrie
Reposted by David McQuarrie
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...
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
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...
doi.org/10.1126/scie...
Reposted by David McQuarrie
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
KATMAP infers splicing factor activity and regulatory targets from knockdown data - @daspliceisright.bsky.social go.nature.com/47ycrMJ
Reposted by David McQuarrie
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...
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
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...
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...
Reposted by David McQuarrie
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
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
Reposted by David McQuarrie
Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing. #DirectRNAseq #Sequencing #RNAmodifications @nanoporetech.com
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 6, 2025 at 11:30 AM
Establishing benchmarks for quantitative mapping of m6A by Nanopore Direct RNA Sequencing. #DirectRNAseq #Sequencing #RNAmodifications @nanoporetech.com
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by David McQuarrie
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
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
Reposted by David McQuarrie
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
Selective RNA sequestration in biomolecular condensates directs cell fate transitions - @distefanolab.bsky.social @brumbaugh-lab.bsky.social go.nature.com/3X215du
Reposted by David McQuarrie
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...
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
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...
m6A is recognized by nuclear readers CPSF30-L and ECT12, which associate with SUVH4/5/6 and ATXR5/6 to enhance histone methylation...
Reposted by David McQuarrie
🪰 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
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
🪰 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
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