Markus Hafner
@markushafnerrna.bsky.social
Posttranscriptional Gene Regulation @NIH, proud father, 🇩🇪🇺🇸🇭🇷 - any opinions strictly my own.
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.
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.
JCI - Discovery and therapeutic delivery of microRNAs targeting deregulated glioblastoma pathways inhibits tumor growth in mice
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doi.org
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.
Igor Ulitsky@igorulitsky.bsky.social · 11mo agoA preprint‼️that's bound to ruffle some 🪶 "Widespread DNA off-targeting confounds studies of RNA chromatin occupancy" led by our Micah Goldrich and Louis Delhaye from Pieter Mestdagh in Ghent. TL;DR we show that many of lncRNA chromatin occupancy obtained are flawed www.biorxiv.org/content/10.1...
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...
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.
cruk.cam.ac.uk
Our work investigating mRNA 3' UTRs that trigger target-directed miRNA degradation is now published! genesdev.cshlp.org/content/earl...
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
genesdev.cshlp.org
David Bartel's Lab@bartellab.bsky.social · 11mo agoCheck out the latest work from our lab, led by Daniel Lin and Lara Elcavage: www.biorxiv.org/content/10.1... (1/3)
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
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!
RNA Society@rnasociety.bsky.social · 6mo agoPoster 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
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
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...
tinyurl.com
David Bartel's Lab@bartellab.bsky.social · 9mo agoWe are thrilled to share our latest work uncovering the mechanistic basis of target-directed microRNA degradation (TDMD). This work was driven by @jakobfarnung.bsky.social and @elenaslo.bsky.social in a fantastic collaboration with Brenda Schulman's lab. tinyurl.com/E3TDMD (1/5)
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👇
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,...
biorxiv.org
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.
Markus Hafner@markushafnerrna.bsky.social · last yr.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?
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?
Markus Hafner@markushafnerrna.bsky.social · last yr.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.
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.
Markus Hafner@markushafnerrna.bsky.social · last yr.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.
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.
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 ...
biorxiv.org
#RNAbiology #RNAlocalization #LocalizedTransaltion www.cell.com/cell/fulltex...
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...
cell.com
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
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.
url.de.m.mimecastprotect.com
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
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...
nature.com
Predicting expression-altering promoter mutations with deep learning www.science.org/doi/10.1126/... - well this looks useful!
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,...
science.org
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.
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...
rdcu.be
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
Very interesting work from Samie Jaffrey's lab: m6A promotes ribosome collisions, with big effects on RNA stability. #RNASky www.cell.com/cell/fulltex...
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...
cell.com
The whole-genome sequences of herding dogs reveal how selection has sculpted the unique behavioral traits www.science.org/doi/10.1126/...
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...
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...
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...
nature.com
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....
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...
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.
nature.com
ICYMI: New online! The regulation and function of post-transcriptional RNA splicing
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.
nature.com
