Manolis Maragkakis
@manolis-maragkakis.bsky.social
Stadtman Principal Investigator @NIH / NIA. Computational Genomics, RNA, Aging, Stress Response, Senescence. Posts are my own.
Pinned
RNAkinet identifies nascent RNA by predicting 5EU metabolically labeled #RNA from raw #nanopore electrical signal. Should allow association of RNA metabolism dynamics with isoform usage, poly(A) tails and native RNA mods. academic.oup.com/nargab/artic...
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
#RNAsky
June 9, 2025 at 4:37 PM
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
#RNAsky
Reposted by Manolis Maragkakis
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...
@kevinrhine.bsky.social
www.nature.com/articles/s41...
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.
www.nature.com
June 6, 2025 at 5:10 PM
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...
@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
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
June 4, 2025 at 5:30 PM
🚨 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
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
Reposted by Manolis Maragkakis
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...
www.nature.com/articles/s41...
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...
www.nature.com
June 3, 2025 at 8:29 PM
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...
www.nature.com/articles/s41...
Reposted by Manolis Maragkakis
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
April 29, 2025 at 8:31 PM
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...
www.biorxiv.org/content/10.1...
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.
April 10, 2025 at 4:09 PM
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.
Reposted by Manolis Maragkakis
Online Now: A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance Online now:
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.
dlvr.it
April 10, 2025 at 11:32 AM
Online Now: A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance Online now:
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
#RNAsky
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…
www.sciencedirect.com
April 10, 2025 at 12:28 AM
Wonderful collaboration with Payel Sen's group. Spatial transcriptomics reveal #inflammation origins in the white matter of the #aging mouse #brain
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...
www.nature.com
April 8, 2025 at 6:26 PM
Wonderful collaboration with Payel Sen's group. Spatial transcriptomics reveal #inflammation origins in the white matter of the #aging mouse #brain
Reposted by Manolis Maragkakis
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/...
Great work from @ferhatalkan.bsky.social, Edwin Kyei-Baffour, and Qi Chang Lin!
royalsocietypublishing.org/doi/10.1098/...
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...
royalsocietypublishing.org
March 6, 2025 at 12:37 PM
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/...
Great work from @ferhatalkan.bsky.social, Edwin Kyei-Baffour, and Qi Chang Lin!
royalsocietypublishing.org/doi/10.1098/...
Reposted by Manolis Maragkakis
Latest work from our next door neighbors! #RNAsky #RNAbiology
Online Now: The integrated stress response regulates 18S nonfunctional rRNA decay in mammals
The integrated stress response regulates 18S nonfunctional rRNA decay in mammals
To maintain translational fidelity, cells degrade decoding-incompetent ribosomes through the 18S nonfunctional rRNA decay (NRD) pathway. Coria et al. demonstrate that the concerted actions of GCN2, RNF10, and RIOK3 lead to a block in translation…
dlvr.it
February 12, 2025 at 10:49 PM
Latest work from our next door neighbors! #RNAsky #RNAbiology
Reposted by Manolis Maragkakis
Here's Twitter's descent since 2022
February 6, 2025 at 9:16 AM
Here's Twitter's descent since 2022
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
🤔 useful to further reduce translational load during #ISR?
#RNAbiology
December 21, 2024 at 1:36 AM
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
🤔 useful to further reduce translational load during #ISR?
#RNAbiology
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
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...
us02web.zoom.us
December 17, 2024 at 8:25 PM
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
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
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.
www.cell.com
December 12, 2024 at 2:30 PM
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
Reposted by Manolis Maragkakis
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
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
December 11, 2024 at 3:00 PM
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
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
Reposted by Manolis Maragkakis
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...
December 11, 2024 at 9:35 PM
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...
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
#genomics #bioinformatics
December 11, 2024 at 5:36 AM
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
#genomics #bioinformatics
Reposted by Manolis Maragkakis
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....
December 7, 2024 at 12:42 PM
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....
Reposted by Manolis Maragkakis
🎄🧪 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
Check the app here 👉 pagoba.shinyapps.io/strain_explo...
#AcademicSky
#Science
pagoba.shinyapps.io
December 7, 2024 at 10:05 AM
🎄🧪 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
Check the app here 👉 pagoba.shinyapps.io/strain_explo...
#AcademicSky
#Science
G3BP1 promotes intermolecular RNA-RNA interactions during #RNA condensation
#RNAsky
www.cell.com/molecular-ce...
#RNAsky
www.cell.com/molecular-ce...
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.
www.cell.com
December 5, 2024 at 3:05 AM
G3BP1 promotes intermolecular RNA-RNA interactions during #RNA condensation
#RNAsky
www.cell.com/molecular-ce...
#RNAsky
www.cell.com/molecular-ce...
Reposted by Manolis Maragkakis
A chimeric peptide promotes immune surveillance of senescent cells in injury, fibrosis, tumorigenesis and aging
www.nature.com/articles/s43...
www.nature.com/articles/s43...
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...
www.nature.com
December 5, 2024 at 12:41 AM
A chimeric peptide promotes immune surveillance of senescent cells in injury, fibrosis, tumorigenesis and aging
www.nature.com/articles/s43...
www.nature.com/articles/s43...
Reposted by Manolis Maragkakis
Tracking transcription–translation coupling in real time
doi.org/10.1038/s415...
doi.org/10.1038/s415...
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...
doi.org
December 4, 2024 at 9:14 PM
Tracking transcription–translation coupling in real time
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted by Manolis Maragkakis
#paperalert!
In our new study, we ask the question: Can we predict RNA stability across conditions and protocols, based solely on experimental and/or computationally predicted RNA binding protein target sites?
Read the paper to find out !
www.biorxiv.org/content/10.1...
In our new study, we ask the question: Can we predict RNA stability across conditions and protocols, based solely on experimental and/or computationally predicted RNA binding protein target sites?
Read the paper to find out !
www.biorxiv.org/content/10.1...
Cell-type specific prediction of RNA stability from RNA-protein interactions
RNA-binding proteins (RBPs) are important contributors to post-transcriptional regulatory processes. The combinatorial action of expressed RBPs and non-coding factors bound to the same transcript dete...
www.biorxiv.org
December 4, 2024 at 12:52 PM
Reposted by Manolis Maragkakis
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...
www.nature.com/articles/s41...
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...
www.nature.com
December 3, 2024 at 12:31 AM
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...
www.nature.com/articles/s41...