Markus Hafner
markushafnerrna.bsky.social
Markus Hafner
@markushafnerrna.bsky.social
Posttranscriptional Gene Regulation @NIH, proud father, 🇩🇪🇺🇸🇭🇷 - any opinions strictly my own.
Reposted by Markus Hafner
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,...
www.biorxiv.org
October 14, 2025 at 10:28 PM
Reposted by Markus Hafner
👀
October 3, 2025 at 12:08 AM
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.
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?
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.
September 27, 2025 at 3:53 PM
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?
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.
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.
September 27, 2025 at 3:50 PM
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.
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 ...
www.biorxiv.org
September 27, 2025 at 3:43 PM
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 ...
www.biorxiv.org
September 27, 2025 at 3:39 PM
Reposted by Markus Hafner
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
July 25, 2025 at 1:37 PM
Reposted by Markus Hafner
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...
www.nature.com
July 13, 2025 at 3:59 AM
Reposted by Markus Hafner
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,...
www.science.org
June 27, 2025 at 8:39 AM
Reposted by Markus Hafner
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
May 29, 2025 at 3:55 PM
Reposted by Markus Hafner
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
May 27, 2025 at 11:04 AM
Reposted by Markus Hafner
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...
www.cell.com
May 6, 2025 at 9:02 AM
Reposted by Markus Hafner
The whole-genome sequences of herding dogs reveal how selection has sculpted the unique behavioral traits
www.science.org/doi/10.1126/...
April 30, 2025 at 9:06 PM
Reposted by Markus Hafner
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...
April 28, 2025 at 9:21 PM
Reposted by Markus Hafner
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...
www.nature.com
April 10, 2025 at 9:59 PM
Reposted by Markus Hafner
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....
April 25, 2025 at 10:42 AM
Reposted by Markus Hafner
April 25, 2025 at 10:40 AM
Reposted by Markus Hafner
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.
www.nature.com
April 24, 2025 at 2:06 PM
Reposted by Markus Hafner
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
April 16, 2025 at 10:47 AM
Reposted by Markus Hafner
Highly sensitive method captures rare RNAs in blood to search for disease www.nature.com/articles/d41...
@nature.com
www.nature.com/articles/s41...
April 16, 2025 at 4:44 PM