Excited to share our newest work! We asked whether RNA molecules need to be in a specific place in the cell to do their job. We found that a single RNA must reach the midbody, the structure that pinches two dividing cells apart, for cell division to finish efficiently. 🧵⬇️
Amazing insight from David Brow @bmolchem.bsky.social on potential mechanisms of U6 snRNA dysfunction in retinitis pigmentosa! Plus a potential therapeutic strategy based on some classic nucleic acid biochemistry experiments and competing RNA structures. rnajournal.cshlp.org/content/earl...
Past studies suggest potential therapies for newly discovered retinitis pigmentosa mutations in U6 and U4 snRNAs
A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
rnajournal.cshlp.org
Check out our new preprint www.biorxiv.org/content/10.6...)! Most human mRNAs recruit ribosomes by cap-dependent initiation (CDI). But during viral infection & cell stress, CDI gets inhibited. So how do mRNAs keep translating? Viruses use IRESes, but do human genes? (1/5) #RNA #virology #IRES
biorxiv.org
Happy to announce publication of a collaboration between my group, Neelam Sen's lab and Alan Hinnebusch at NAR combining FACS-uORF (MPRA) and Ribo-seq to clarify how Ded1 enhances mRNA translation. Great team effort! academic.oup.com/nar/article/...
Suppression of upstream ORF translation is not a widespread mechanism of translational stimulation by yeast helicase Ded1
Abstract. Ded1 is an essential DEAD-box helicase in yeast that broadly stimulates translation initiation and is critical for messenger RNAs (mRNAs) with st
academic.oup.com
Hey, wouldja look at that! An incredible one man show from Pablo Bora, an amazing postdoc...we used Steven Floor's beautiful REMORA approach (fusing RNA base editors to RBPs, allowing RBP cargo to be identified by edits) to explore RBP-RNA binding in mouse embryos doi: doi.org/10.64898/202...
Probing RNA-protein interactions in the early mouse embryo
The union of two germ cells to form a zygote, and subsequent early embryo development, are marked by radical remodeling of virtually every major class of biomolecules as the specialized germline states give way to the rapid and active growth that marks early development. In recent years, advances in ultra-low input genome-wide methods have enabled systematic analyses of mRNA abundance, and of chromatin organization, throughout early development in a variety of model systems. Here, we extend these efforts to the study of RNA binding protein (RBP) function in early mouse embryos, adapting REMORA 1 -- based on fusing an RNA-editing enzyme to an RBP of interest -- for use in early embryos. We benchmark our approach for several well-studied RBPs, successfully recovering expected features of their RNA cargos, and assayed the RNA cargos for 17 RBPs of interest for early gene regulation. Analysis of changes in mRNA metabolism following knockdowns of the RBPs surveyed here allowed us to identify direct regulatory functions for a subset of RBPs in the early mammalian embryo, including an unanticipated role for the RNA export adaptor Alyref in control of 3 prime polyadenylation sites. Together, our data provide a proof of concept resource for systematically exploring RBP functions in mammalian embryogenesis. ### Competing Interest Statement The authors have declared no competing interest. Eunice Kennedy Shriver National Institute of Child Health and Human Development, https://ror.org/04byxyr05, NIHR01HD099816
doi.org
Major new work by the #TransCODE Consortium out today in @nature.com. Read all about our efforts to shed light onto the forgotten areas of the human proteome. #Microproteins #Peptideins #DarkProteome This was a huge global collaboration, in part funded via #NIH www.nature.com/articles/s41... 1/
Expanding the human proteome with microproteins and peptideins - Nature
A large-scale proteomics analysis of the dark proteome by the TransCODE Consortium reveals many translated non-canonical open reading frames to encode microproteins and peptideins.
nature.com
Massive and important positive news... #NSF #GRFP awards are out. 2,599 awards! + 1,440 Honorable Mentions. A significant boost from last year. Congratulations to the winners (and HM-s)! & many thanks to the reviewers & program officers who made this possible. www.research.gov/grfp/Awardee...
Delighted to share our discoveries about one of the brain's neurotransmitter systems: www.biorxiv.org/content/10.6... Together with colleagues at the @alleninstitute.org, we have learned a lot about a tiny cluster of neurons in the brainstem locus coeruleus (LC) that releases norepinephrine (NE). 1
biorxiv.org
Point of View: An easy way to improve lab meetings doi.org/10.7554/eLif... I'm really happy to see this one out @elife.bsky.social. Awesome Cara Glynn and I describe and reflect on a year-long, low-cost practice that transformed our group meetings. #researchculture #ECR #labmeetings
Point of View: An easy way to improve lab meetings
Sharing positive and negative experiences at lab meetings can make a career in science a little less hard, a little more pleasant, and a little more human.
doi.org
This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...
Protein language models reveal evolutionary constraints on synonymous codon choice
Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...
biorxiv.org
Excited to share our @natprot.nature.com paper on using RNA proximity labeling to map subcellular RNA transcriptomes. We’ve been working in this area for a while and wanted to create a resource paper to guide the uninitiated reader. rdcu.be/fblvI
APEX-seq maps transcriptome-wide subcellular RNA localization in living cells
Nature Protocols - This Protocol describes the transcriptome-wide labeling of RNAs in a particular subcellular compartment using proximity biotinylation by localized APEX2 enzyme and subsequent...
rdcu.be
Check out our new preprint on IRES studies (www.biorxiv.org/content/10.6...). We show a recently proposed IRES “toolbox” results in mRNA annotation errors and false-positive IRES activities. We provide an alternative set of robust approaches. (1/4)
Awesome representation from @uwmadscience.bsky.social at the @asbmb.bsky.social #ASBMB2026 meeting in DC! #ScienceServesUsAll
We are delighted to announce our next RNA Society Member Spotlight! www.rnasociety.org/joel-mcmanus... Dr. Joel McManus @mcmanuslabrna.bsky.social is an Associate Professor of Biological Sciences at Carnegie Mellon University in Pittsburgh, USA.
Another record month for bioRxiv - and further evidence the pandemic spike+dip was just that and growth continues. Thanks to all involved and that includes 🫵
These are amazing stories. Lucy Shapiro is one of my scientific heroes, Steve McKnight has made such fundamental contributions to many fields, and triple drug therapies for CF represent an amazing story in chemical biology and protein folding and I often teach this to undergrads.
Bede Portz@ysptsps.bsky.social · last yr.Major Medical Prizes Given to Cell Biology and Cystic Fibrosis Pioneers www.nytimes.com/2025/09/11/h...