Manolis Maragkakis

Excited to share our work with @markrcookson.bsky.social and Payel Sen labs. We combine #SingleCell and #Nanopore sequencing to profile #RNA isoforms from young to geriatric mouse brains. We uncover #aging changes in transcription, processing, and splicing that also impact coding potential.

#RNAsky

Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress - Nature Neuroscience Rhine et al. find that neuronal aging leads to widespread dysregulation of RNA biology, including mislocalization of splicing proteins like TDP-43, chronic cellular stress and reduced resiliency.

Neuronal aging leads to widespread dysregulation of RNA biology, including mislocalization of splicing proteins like TDP-43, chronic cellular stress, and reduced resiliency

@kevinrhine.bsky.social

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

🚨 We’re looking for a curious mind to join our lab at the NIH!
Passionate about #RNA biology, #MachineLearning, and the #genomics of #aging?

Interested in a postdoc or a PhD research visit at NIH? Let’s connect.
📩 DM or email for details!

#Bioinformatics #AI #ComputationalBiology

Programmable RNA acetylation with CRISPR–Cas13 - Nature Chemical Biology Yu et al. developed a programmable RNA acetylation system using dCas13–eNAT10 to specifically install N4-acetylcytidine on target RNAs in cells and in vivo, enabling functional studies of RNA acetylat...

A programmable RNA acetylation system using dCas13-eNAT10 is developed to install N4-acetylcytidine on target RNAs in cells and in vivo, enabling functional studies of RNA acetylation and revealing the unique role of RNA acetylation in transcript localization

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

Single-molecule multimodal timing of in vivo mRNA synthesis mRNA synthesis requires extensive pre-mRNA maturation, the organisation of which remains unclear. Here, we directly sequence pre-mRNA without metabolic labelling or amplification to resolve transcript...

The timeline of co-transcriptional #mRNA processing and #modification may have to be revised: cleavage, termination, and #m6A deposition may occur earlier than most #splicing! Potential textbook changing study in bioRxiv by edueyras.bsky.social & Rippei Hayashi labs!
www.biorxiv.org/content/10.1...

Yeah almost all pop up when I allow the word mRNA. Also cleaning up some myself. Hopefully it doesn't get too much out of hand.

It is based on regular expressions, not tags, so anything (with some filters :) ) with the word RNA in some context will make it to the feed. If signal to noise ratio gets lower, then stricter filters may be needed.

I've built an #RNA feed for personal use to capture RNA biology posts across the entire network. Some arbitrary filters used to hopefully increase signal to noise ratio but otherwise not moderated. Feel free to follow if you find useful.

A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance Soles et al. demonstrate that the combination of a 5′ splice site and a poly(A) junction constitutes a nuclear RNA degradation code that targets RNAs for degradation by the PAXT adaptor and the RNA exosome. This study provides fundamental insight into how the RNA exosome specifically recognizes misprocessed RNAs.

Online Now: A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance Online now:

An RNA condensate model for the origin of life The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA Wor…

An interesting perspective and framework: #RNA condensates-not individual RNAs-may have acted as replicative units in early life. RNAs in condensate recruit similar RNAs, then the condensate divides once it reaches a critical size.

#RNAsky

Spatial transcriptomics of the aging mouse brain reveals origins of inflammation in the white matter - Nature Communications This study profiles the spatial transcriptomic landscape of mouse brain coronal sections across three age groups and both sexes. Here, authors show a strong female-biased pro-inflammatory gene signatu...

Wonderful collaboration with Payel Sen's group. Spatial transcriptomics reveal #inflammation origins in the white matter of the #aging mouse #brain

High-throughput approaches for the identification of ribosome heterogeneity | Philosophical Transactions of the Royal Society B: Biological Sciences Recent advances in the fields of RNA translation and ribosome biology have demonstrated the heterogeneous nature of ribosomes. This manifests not only across different cellular contexts but also withi...

New review from the lab looking at high throughput methods of identifying ribosome heterogeneity.
Great work from @ferhatalkan.bsky.social, Edwin Kyei-Baffour, and Qi Chang Lin!
royalsocietypublishing.org/doi/10.1098/...

Latest work from our next door neighbors! #RNAsky #RNAbiology

2022-2025 X Twitter mention data

Here's Twitter's descent since 2022

Thanks Eugene!

Our paper out in eLife. Full-length direct RNA #nanopore sequencing uncovers 5' #RNA shortening upon cellular #stress that depends on ✅ stress-granules and #XRN1 but ❌ not poly(A) or cap removal elifesciences.org/articles/96284

🤔 useful to further reduce translational load during #ISR?

#RNAbiology

Welcome! You are invited to join a webinar: RNA Collaborative - NCI RNA Biology Initiative. After registering, you will receive a confirmation email about joining the webinar. Featuring: “Genome-Scale Exon Deletion Screens Reveal Exons Critical for Cell Fitness and Gene Expression” Thomas Gonatopoulos-Pournatzis, PhD NIH Stadtman Investigator, Functional Transcriptomics S...

If you want to hear me rant about #RNA, #stress, #aging, #senescence come join me at the RNA collaborative seminar tomorrow Wed 4pm (EST) #RNAsociety #RNAsky #RNAbiology

Circular RNAs trigger nonsense-mediated mRNA decay Boo and Shin et al. uncover that the EJC deposited onto circRNAs after back-splicing is spatially located near the 3′ UTR of mRNA through circRNA-mRNA interaction. The EJC on circRNA triggers NMD of the mRNA. Mechanistic studies reveal the roles of circNMD in apoptosis and its therapeutic potential for mRNA downregulation.

circRNAs as tools for gene silencing, similar to microRNA-mediated gene silencing. Do we also need circRNA target prediction software? Circular RNAs trigger nonsense-mediated mRNA decay: Molecular Cell

SERVICE UPDATE

We normally don't ask you to "share like and subscribe" but please distribute this.

You are now able to delete the link after it embeds on your post so you can get those precious extra characters, and we will catch your post mentioning research.

#AcademicSky #Medsky #HigherEd

Our latest work is out in Nature today! Using smFRET, we directly visualized recruitment of the eIF4F complex to the 5' cap of eukaryotic mRNAs and formation of an activated mRNA. Our findings reveal new and surprising roles for each eIF4F component. 1/3 www.nature.com/articles/s41...

Thanks. 👀 seems I'm the most permanent staff. Coming from snakemake, maybe time to dive into nextflow as well 😅

Yes I do use snakemake regularly but that's only because I found it a bit easier for my workflow several years back. Mostly HPC.

Not looking to start a debate on #nextflow vs. #snakemake, but curious about their ease of adoption in a typical lab setting with ~4-year PhD/postdoc turnover. How do you feel newcomers adapt to each? Would you recommend one for easier onboarding? Feedback appreciated!
#genomics #bioinformatics

How can physics define universal laws for computation, from cells and chips to brains? In this @pnas.org Perspective, led by @sfiscience.bsky.social David Wolpert and Jan Korbel, they suggest how Stochastic Thermodynamics can provide the proper framework pnas.org/doi/epub/10....

🎄🧪 Racing to submit your manuscript before the holidays? Check out our ShinyApp for editorial insights on publishers & journals—submission-to-acceptance times and more! Based on data from: doi.org/10.1162/qss_...

Check the app here 👉 pagoba.shinyapps.io/strain_explo...

#AcademicSky
#Science

G3BP1 promotes intermolecular RNA-RNA interactions during RNA condensation Parker et al. demonstrate that some proteins responsible for organizing ribonucleoprotein granules can chaperone intermolecular RNA-RNA interactions in addition to their role in scaffolding. These findings cement RNA-RNA interaction networks as a key component of granules, highlighting the need to further explore the regulation of RNA dynamics within granules.

G3BP1 promotes intermolecular RNA-RNA interactions during #RNA condensation
#RNAsky

www.cell.com/molecular-ce...

A chimeric peptide promotes immune surveillance of senescent cells in injury, fibrosis, tumorigenesis and aging - Nature Aging Ming, Yang, Huang et al. design a chimeric matchmaker peptide, which targets a senescent cell-specific surface marker and modifies the cell surface with polyglutamic acid. This promotes interactions w...

A chimeric peptide promotes immune surveillance of senescent cells in injury, fibrosis, tumorigenesis and aging

www.nature.com/articles/s43...

Tracking transcription–translation coupling in real time - Nature Single-molecule fluorescence microscopy experiments with a recombinant Escherichia coli transcription–translation system provides insights into the coordination of the transcription and translation ma...

Tracking transcription–translation coupling in real time
doi.org/10.1038/s415...

#RNAsky #RNAbiology

A modular platform for bioluminescent RNA tracking - Nature Communications Studying RNA dynamics in vivo often relies on fluorogenic approaches, but these can be hampered by factors such as limited sensitivity and sample autofluorescence. Here, the authors describe an ultras...

Cool new work from Jenn Prescher and coworkers @ucirvine.bsky.social, “RNA lantern” technology for bioluminescence imaging of RNA transcripts

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