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Markus Hafner

@markushafnerrna.bsky.social
1.2K followers 966 following 12 posts

Posttranscriptional Gene Regulation @NIH, proud father, 🇩🇪🇺🇸🇭🇷 - any opinions strictly my own.

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Markus Hafner @markushafnerrna.bsky.social · 27/08/2026
Become our colleague at NIAMS! We’re looking for a new tenure-track investigator. NIH is an exceptional place to start a lab: fantastic colleagues across every discipline, outstanding core facilities, stable funding, and the freedom to develop a research program limited only by your imagination.
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Journal of Clinical Investigation @jci.org · 20/08/2026
Inhibiting growth of the most common and deadly primary brain tumor: doi.org/10.1172/JCI1... Roger Abounader, Markus Hafner @markushafnerrna.bsky.social & team developed new approaches to identify and deliver master regulatory miRNAs that inhibit the growth of glioblastoma in mice.
doi.org
JCI - Discovery and therapeutic delivery of microRNAs targeting deregulated glioblastoma pathways inhibits tumor growth in mice
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Igor Ulitsky @igorulitsky.bsky.social · 15/05/2026
Now out @natbiotech.nature.com ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones.
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Robin Allshire 🇮🇪 🇪🇺✊🏿 ⬆️ Zak’s favourite nucleosome: K9me @allshire-lab.bsky.social · 09/04/2026
Very upsetting to hear the sad news of Greg Hannon’s passing. I always enjoyed our far too few conversations we had over the years. He had an interesting and insightful perspective on any science being discussed. He will be missed. www.cruk.cam.ac.uk/news/in-memo...
cruk.cam.ac.uk
In Memoriam: Professor Greg Hannon (1964–2026) - Cancer Research UK Cambridge Institute
Greg was already a world-renowned scientist when appointed Director, and for the community, he was a visionary leader, a cherished mentor, and a singular force of nature whose influence shaped the research landscape.
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David Bartel's Lab @bartellab.bsky.social · 30/03/2026
Our work investigating mRNA 3' UTRs that trigger target-directed miRNA degradation is now published! genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
mRNA 3′ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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RNA Society @rnasociety.bsky.social · 27/03/2026
Poster abstracts and early bird registrations for the 31st Annual Meeting of the RNA Society are due by March 31st! RNA 2026 website: rnasociety.org/conferences/ #RNA26
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Junior RNA scientists @jrrnascientists.bsky.social · 27/03/2026
Heads up all Junior RNA Scientists - March 31st is the deadline for poster abstract submission and early bird registration for the 2026 Annual RNA Society Meeting in Montreal! Don't miss out, we have an exciting panel and fun events planned!
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eric lai @lucksmith.bsky.social · 22/03/2026
current location. IYKYK !!! #RNA
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David Bartel's Lab @bartellab.bsky.social · 19/03/2026
Our work on the E3 ligase mechanism of target-directed microRNA degradation is now published! Amazing collaboration with Brenda Schulman’s lab led by @jakobfarnung.bsky.social and @elenaslo.bsky.social, with special thanks to @wyppeter.bsky.social, Lianne Blodgett, and Daniel Lin! tinyurl.com/Z8TDMD
tinyurl.com
The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation - Nature
Target-directed microRNA degradation is driven by the atypical ZSWIM8–CUL3 E3 ubiquitin ligase that uses a two-RNA-factor authentication mechanism to specifically recognize AGO–miRNA–trigger...
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Josh Mendell @mendell-lab.bsky.social · 14/10/2025
Colliding ribosomes are potent signals of cellular stress. But do cells use ‘programmed’ ribosome collisions to regulate gene expression? I’m excited to present a new story from my lab led by Frederick Rehfeld(@fred-rehfeld.bsky.social) which revealed that the answer is YES! Read on to find out how👇
biorxiv.org
Oxidative stress sensing by the translation elongation machinery promotes production of detoxifying selenoproteins
Selenocysteine, incorporated into polypeptides at recoded termination codons, plays an essential role in redox biology. Using GPX1 and GPX4, selenoenzymes that mitigate oxidative stress, as reporters,...
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Eugene Valkov @eugenevalkov.bsky.social · 03/10/2025
👀
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Markus Hafner @markushafnerrna.bsky.social · 27/09/2025
Such a form of “multifactor auyhorization” of course protects posttranscriptional regulatory pathways from aberrant expression of individual components - as we observed in the case of DND1/NANOS3: their ectopic expression sends any cell into cell-cycle arrest.
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Markus Hafner @markushafnerrna.bsky.social · 27/09/2025
The specific motif built up by these two RBPs cannot be identified by studying each of them in isolation, so one important question we would like to raise is: How many RBPs form heteromultimeric complexes with specificity other than the sum of the individual RBPs?
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Markus Hafner @markushafnerrna.bsky.social · 27/09/2025
This work was spearheaded by Masataka Suzawa in my (NIAMS) and Chen Qiu in Traci Hall’s lab (NIEHS IRP) and initiated together with Masashi Yamaji’s group at Cincinnati Children’s. Wonderful collaboration with @eugenevalkov.bsky.social and Vittorio Sartorelli.
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Markus Hafner @markushafnerrna.bsky.social · 27/09/2025
www.biorxiv.org/content/10.1... Delighted to share the story of two germline RBPs - one with little (DND1) and one with no (NANOS3) intrinsic sequence-specificity - that together build a continuous RNA binding surface recognizing a 7-mer (AUGAAUU) in target mRNA 3’UTRs, leading to deadenylation.
biorxiv.org
The DND1-NANOS3 complex shapes the primordial germ cell transcriptome via a heptanucleotide sequence in mRNA 3'UTRs
The RNA-binding proteins DND1 and NANOS3 are essential for primordial germ cell survival. Their co-immunoprecipitation and overlapping loss-of-function phenotypes suggest joint function, yet how they ...
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Evelina Tutucci @anilevetu.bsky.social · 31/08/2025
#RNAbiology #RNAlocalization #LocalizedTransaltion www.cell.com/cell/fulltex...
cell.com
Proximity-specific ribosome profiling reveals the logic of localized mitochondrial translation
Development of LOV-domain-controlled ligase for translation localization (LOCL-TL), an optogenetic approach for monitoring translation with codon resolution at any defined subcellular location under p...
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Vikram Agarwal @vagar.bsky.social · 25/07/2025
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
url.de.m.mimecastprotect.com
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.
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Markus Landthaler @landthalerm.bsky.social · 22/07/2025
www.cell.com/cell/fulltex...
cell.com
SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress
SPIDR, a massively multiplexed method that simultaneously maps dozens of RNA-binding proteins to their RNA targets at single-nucleotide resolution, uncovers new RNA-protein interactions and provides c...
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Eugene Valkov @eugenevalkov.bsky.social · 13/07/2025
Happy to share the latest work on a bacterial protein that inhibits human mRNA decay machinery, in collaboration with @smlea.bsky.social #RNAsky www.nature.com/articles/s41... Intracellular pathogen effector reprograms host gene expression by inhibiting mRNA decay | Nature Communications
nature.com
Intracellular pathogen effector reprograms host gene expression by inhibiting mRNA decay - Nature Communications
Intracellular pathogens hijack host gene expression to subvert cellular processes. Here, the authors show that Legionella pneumophila’s PieF effector inhibits the human CCR4-NOT deadenylation machiner...
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Kevin Mitchell @wiringthebrain.bsky.social · 27/06/2025
Predicting expression-altering promoter mutations with deep learning www.science.org/doi/10.1126/... - well this looks useful!
science.org
Predicting expression-altering promoter mutations with deep learning
Only a minority of patients with rare genetic diseases are currently diagnosed by exome sequencing, suggesting that additional unrecognized pathogenic variants may reside in non-coding sequence. Here,...
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Phil Holliger @philholliger.bsky.social · 29/05/2025
New paper from my group rdcu.be/eoaRr "Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme" in Nature Chemistry — great collaboration with attwaterlab.uk.
rdcu.be
Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme
Nature Chemistry - Models of abiotic RNA replication suffer from inherent product inhibition arising from the high stability of RNA duplexes. Now, it has been shown that RNA trinucleotide...
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Anita Corbett @acorbe2.bsky.social · 27/05/2025
Excited to finally be heading to RNA 2025 in San Diego! Have worked with amazing colleagues to co-organize this meeting so I can’t wait to see all the exciting science and connect with colleagues! @rnabiologist.bsky.social @kkarbstein.bsky.social
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Liam Faller @liamfaller.bsky.social · 06/05/2025
Very interesting work from Samie Jaffrey's lab: m6A promotes ribosome collisions, with big effects on RNA stability. #RNASky www.cell.com/cell/fulltex...
cell.com
m6A alters ribosome dynamics to initiate mRNA degradation
m6A is a potent inducer of ribosome stalling and collisions that trigger YTHDF-mediated mRNA degradation, a process that highlights the ribosome as a critical sensor linking translation dynamics to m6...
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Waggoner Lab @labwaggoner.bsky.social · 30/04/2025
The whole-genome sequences of herding dogs reveal how selection has sculpted the unique behavioral traits www.science.org/doi/10.1126/...
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Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · 28/04/2025
Congratulations to MSK’s Dr. Stefanie Gerstberger for receiving the @theaacr.bsky.social Women in Cancer Research Scholar Award! 🎉 #AACR25 Learn more about her fascinating work investigating #phenotypic plasticity & chemo resistance in colorectal cancer here: www.abstractsonline.com/pp8/#!/20273...
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Prajna Hebbar @prajnahebbar.bsky.social · 10/04/2025
Our primate T2T paper came out in Nature yesterday! It was a huge effort and I'm so grateful that I got the opportunity to work with this amazing group of scientists over the first two years of my PhD! www.nature.com/articles/s41...
nature.com
Complete sequencing of ape genomes - Nature
Complete sequences of chromosomes telomere-to-telomere from chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan and siamang provide a comprehensive and valuable resource for future evol...
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The EMBO Journal @embojournal.org · 25/04/2025
Rbm24a dictates mRNA recruitment for germ granule assembly in zebrafish Yizhuang Zhang et al show that loss of maternal Rbm24a causes complete degradation of germ granules and disappearance of primordial germ cells www.embopress.org/doi/full/10....
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Eugene Valkov @eugenevalkov.bsky.social · 25/04/2025
#RNAsky #RNAbiology
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immunoboys @immunoboys.bsky.social · 24/04/2025
Asada et al 2025 "The integrated stress response pathway controls cytokine production in tissue-resident memory CD4+ T cells" @natureportfolio.nature.com www.nature.com/articles/s41...
nature.com
The integrated stress response pathway controls cytokine production in tissue-resident memory CD4+ T cells - Nature Immunology
Panzer and colleagues show that the integrated stress response pathway regulates cytokine translation in CD4+ TRM cells during homeostasis and inflammation.
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Nature Reviews Genetics @natrevgenet.nature.com · 18/04/2025
ICYMI: New online! The regulation and function of post-transcriptional RNA splicing
nature.com
The regulation and function of post-transcriptional RNA splicing
Nature Reviews Genetics, Published online: 11 April 2025; doi:10.1038/s41576-025-00836-zPost-transcriptional splicing has emerged as a key layer of gene expression regulation but is challenging to differentiate from co-transcriptional splicing. The authors review methodologies to detect post-transcriptional splicing, the mechanisms controlling splicing timing and how the temporal regulation of splicing affects gene expression.
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Di Jiang @dijiang319.bsky.social · 17/04/2025
🧬@science.org Structural basis for nucleolin recognition of MYC promoter G-quadruplex | Science www.science.org/doi/10.1126/... @cancer-inst-purdue.bsky.social danzhou-yang.com #DNA #StructuralBiology
science.org
Structural basis for nucleolin recognition of MYC promoter G-quadruplex
The MYC oncogene promoter G-quadruplex (MycG4) regulates transcription and is a prevalent G4 locus in immortal cells. Nucleolin, a major MycG4-binding protein, exhibits greater affinity for MycG4 than...
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Anders H. Lund @andershlund.bsky.social · 16/04/2025
I am happy to share the latest paper from the lab. We detail a tripartite cell-free translation system based on the separation of mRNAs, ribosomes and ribosome-depleted cytoplasmic lysate from human cells, allowing for flexible reconstitution of translation reaction. #RNA #Ribosome
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Nikos Kouvelas @nickkouvelas.bsky.social · 17/04/2025
#RNA #RNASky
nature.com
Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines - Nature
Upon intramuscular administration, COVID-19 mRNA vaccines are primarily taken up by macrophages, in which the cellular machinery extends their poly(A) tails, thereby increasing mRNA stability and tran...
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Waggoner Lab @labwaggoner.bsky.social · 16/04/2025
Highly sensitive method captures rare RNAs in blood to search for disease www.nature.com/articles/d41... @nature.com www.nature.com/articles/s41...
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Cell - a Cell Press journal @cp-cell.bsky.social · 14/04/2025
Now online! Integrator loss leads to dsRNA formation that triggers the integrated stress response
dlvr.it
Integrator loss leads to dsRNA formation that triggers the integrated stress response
Integrator (INT) prevents the escape of immature RNAPII to ensure full-length mRNA production. INT deficiency causes defects in RNAPII maturation that lead to premature termination, accumulation of immunogenic dsRNA, and activation of the integrated stress response (ISR) observed in patient cells.
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Christine Mordstein @cmordstein.bsky.social · 05/04/2025
A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance: Molecular Cell www.cell.com/molecular-ce... #RNAsky #RNAbiology #RNAdecay
cell.com
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 ex...
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WeRateDogs @weratedogs.com · 07/04/2025
This is Ripley. He was nervous about taking the stairs. May have panicked a bit. 12/10
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Kurianlab @kurianlab.bsky.social · 06/04/2025
www.science.org/doi/10.1126/...
science.org
Exogenous RNA surveillance by proton-sensing TRIM25
Exogenous messenger RNAs (mRNAs) require cellular machinery for delivery and translation but also encounter inhibitory factors. To investigate their regulation, we performed genome-wide CRISPR screens...
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Astrid Haase @astridhaase.bsky.social · 04/04/2025
Thank you for organizing this wonderful symposium and bringing us all together to discuss what we love most: the many amazing mechanisms in RNA biology! @vidigaljoana.bsky.social @drjz.bsky.social
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Josh Mendell @mendell-lab.bsky.social · 03/04/2025
It's difficult to focus on science with everything going on, but I still enjoy hearing about other people's work here, so I want to continue sharing ours. Congrats to postdoc Jong-Sun Lee for his outstanding work published in @cp-molcell.bsky.social! Details in thread👇 www.cell.com/molecular-ce...
cell.com
An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation
Cancer cells frequently enhance ribosome production to support rapid growth. Here, Lee et al. demonstrate that an isoform of lncRNA CRNDE containing an ultraconserved element (CRNDEUCE) promotes 60S r...
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Joana Vidigal @vidigaljoana.bsky.social · 03/04/2025
In the midst of everything it feels particularly appropriate to highlight all the amazing #RNA research taking place at #NIH! Follow this thread to join us for our biannual #RNASymposium, this year featuring intramural research superstars!
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Justin Blumenstiel @bdelloid.bsky.social · 27/03/2025
Some good doggos in this figure. Canine genome-wide association study identifies DENND1B as an obesity gene in dogs and humans | Science www.science.org/doi/10.1126/...
A funny figure of polygenic scores for dog obesity, with a lab, two retrievers and a derpy lil pug.
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Ryan Flynn @raflynn5.bsky.social · 26/03/2025
A nearly 9 year effort to design and implement new CLIP-based technologies to define multimeric protein assemblies on RNA. Enables ‘watching’ of RNP assemblies inside living cells Special congrats to Luca Ducoli, Brian Zarnegar, and Paul Khavari @nature.com www.nature.com/articles/s41...
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eric lai @lucksmith.bsky.social · 25/03/2025
i'm starved for good news these days. and some of the best news is hearing of former trainee successes. our old postdoc just wrote to say their ms was accepted at Nature, yes *the* Nature! i know some feel we shouldn't care about prestige signaling, but whatever. this is awesome news, go Lai lab!!!
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Golnaz Vahedi @vahedilab.bsky.social · 19/03/2025
Congrats to Atishay and Carlos for their review article on the epigenetics regulation of T cells: www.nature.com/articles/s41...
nature.com
The epigenetic landscape of fate decisions in T cells - Nature Immunology
Vahedi and colleagues review the mechanisms shaping the epigenetic landscape of CD4+ and CD8+ T cells during development and differentiation.
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Jordan Meier @doc-jlmeier.bsky.social · 20/03/2025
Excited to share this one! We developed an in vivo model for specific manipulation of transfer RNA acetylation and found it serves as a sentinel modification whose loss causes ribosome stalling and stress signaling. Implications for a genetic disorder and cancer. www.science.org/doi/10.1126/...
science.org
Transfer RNA acetylation regulates in vivo mammalian stress signaling
An ancient tRNA modification is used by mammalian cells to coordinate protein translation and adaptive signaling.
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Aaron and the Hoskins Lab at UW Madison @uwmadisonrna.bsky.social · 19/03/2025
Cool new paper on nuclear import/export from the Musser lab at Texas A&M. I happened to catch this on a poster at the #BPS2025 @biophysicalsoc.bsky.social meeting and it was a highlight! www.nature.com/articles/s41...
nature.com
Overlapping nuclear import and export paths unveiled by two-colour MINFLUX - Nature
High spatiotemporal precision tracking using 3D MINFLUX shows that nuclear import and export occur in overlapping regions of the central pore, providing insight into transport across the nuclear pore ...
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Kurianlab @kurianlab.bsky.social · 15/03/2025
www.nature.com/articles/s41... ☝🏽
nature.com
Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts - Nature Communications
Ribosome profiling faces issues with rRNA contamination and measurements of ribosome numbers on transcripts. Here, the authors develop Ribo-FilterOut and Ribo-Calibration, methods which can be used to...
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Astrid Haase @astridhaase.bsky.social · 14/03/2025
Happy pi (RNA) day!
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Carmelo Ferrai @carmeloferrai.bsky.social · 13/03/2025
Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag Nadiya Khyzha ∙ Kami Ahmad∙ Steven Henikoff www.cell.com/molecular-ce...
cell.com
Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag
Khyzha et al. developed SLAM-RT&Tag, a kinetic labeling strategy for profiling RNA dynamics within nuclear compartments. Applied to Polycomb domains and nuclear speckles, they identified compartment-s...
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