Manikandan

Structural basis of 5′ splice site recognition by the minor spliceosome Zhao et al. present two cryo-EM structures of apo and substrate-bound U11 snRNP complexes, elucidating their architecture and the mechanism of the U12-type 5′ splice site recognition. The unique struc...

www.cell.com/molecular-ce...

This shows the C. difficile ModT locus, the genes regulated by ModT, and the conserved tertiary structures of ModT RNAs from 5 bacterial species.

Bacterial ncRNAs influence various cellular functions & often have complex 3ry structures. ModT is a conserved #ncRNA found in 2,500 bacterial spp, shown here to regulate growth transition & sporulation in #Cdifficile via changes in c-di-GMP @helmholtz-hiri.bsky.social #PLOSBiology plos.io/4iIpgYm

Super cool #RNA stuff!

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...

Model depicting the early steps during production of a membrane protein

Huping Wang and Manu Hegde, in @cellbiol-mrclmb.bsky.social have found a factor that accelerates protein deliveries to the endoplasmic reticulum

Click here to read more about it: www2.mrc-lmb.cam.ac.uk/discovery-of...

#LMBResearch

First paper of our lab today @natureportfolio.bsky.social by Nussi!

We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping!

@embl.org #RNAbiology #RNASky

t.co/a24Xxcxdo0

Portrait picture of Romain Linares, with computers in the background.

Meet Romain Linares, cryo-electron microscopy (cryo-EM) expert at EMBL Grenoble.

In this interview, he talks about his role in managing the cryo-EM platform to explore molecules at the atomic level and his passion for stargazing.

🧪 🧬🧶 #MolBiol
www.embl.org/news/people-...

EMBL Group Leader @olivierduss.bsky.social and his research team discovered how two molecular machines in bacteria work together and watched their interactions as a real-time movie.

Discover how they put snapshots in motion 👉 www.embl.org/news/science...

#MolBiol 🧪 @natureportfolio.bsky.social

Congratulations, Olivier Duss, Simone Köhler, and Eva Kowalinski! 👏

The three EMBL Group Leaders have received ERC Consolidator Grants #ERCCoG for their innovative research projects aimed at understanding fundamental cellular mechanisms.

#MolBiol 🧪👇
Read more here: www.embl.org/news/awards-...

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...

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...

Very cool work on single mRNA visualisation inside cells!

‘Dark proteome’ survey reveals thousands of new human genes Database confirms that overlooked segments of the genome code for a multitude of tiny proteins

‘Dark proteome’ survey reveals thousands of new human genes | Science www.science.org/content/arti...

Stereochemistry in the disorder–order continuum of protein interactions - Nature Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.

We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???

www.nature.com/articles/s41...

The PNUTS phosphatase complex controls transcription pause release Kelley et al. discover that the PNUTS phosphatase complex plays an essential role in gene transcription by controlling RNA polymerase II pause release. PNUTS achieves this through its TND, which recog...

Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with @edimitrova.bsky.social and the rest of the @robklose.bsky.social lab www.cell.com/molecular-ce... A short thread: (1/8)

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...

The ribotoxic stress response drives acute inflammation, cell death, and epidermal thickening in UV-irradiated skin in vivo Solar UVB light causes damage to the outermost layer of skin. This insult induces rapid local responses, such as dermal inflammation, keratinocyte cel…

sunburn is from ribosomes stalled by UV damage to RNA? super cool www.sciencedirect.com/science/arti...

Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis An RNA′s catalytic, regulatory, or coding potential depends on RNA structure formation. Because base pairing occurs during transcription, early structural states can govern RNA processing events and d...

Super method linking GROseq/DMSMaPseq shedding light on co-transcriptional #RNA folding. Really enjoyed seeing this presented recently. #RNAStructure www.biorxiv.org/content/10.1...

‘Dark proteome’ survey reveals thousands of new human genes Database confirms that overlooked segments of the genome code for a multitude of tiny proteins

Do you want to go further with your proteomics? Looking for something new in cancer?

Check out microproteins!

Thanks to @science.org for featuring this work, in collaboration with @sebastiaanvheesch.bsky.social, #HUPO, @gencodegenes.bsky.social

www.science.org/content/arti...

🔎 microprotein
🧬 💻

Hi, could you please add me? Thanks :)

The ribosome comes to life The ribosome is an ancient molecular machine that coverts the genetic information carried by mRNA into protein, a crucial step in linking genotype to phenotype. This review discusses landmark advances...

www.cell.com/cell/fulltex...

Graphical abstract of the paper.

How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...

Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing ... RNA begins to fold as the nascent transcript emerges from a transcribing RNA polymerase. Here, the authors develop a concise method for mapping RNA folding pathways that couples in vitro transcription...

The final version of our article describing a modernized procedure for cotranscriptional RNA structure probing is online! www.nature.com/articles/s41...

RNA-mediated double-strand break repair by end-joining mechanisms - Nature Communications Double-strand breaks (DSBs) in DNA are challenging to repair. Here, the authors show that transcript RNAs impact the DSB repair outcomes in human and yeast cells by promoting NHEJ or MMEJ in a sequenc...

RNA-mediated DNA damage repair:
www.nature.com/articles/s41...
#RNAbiology
#RNAsky

Accurate RNA 3D structure prediction using a language model-based deep learning approach - Nature Methods RhoFold+ is an end-to-end language model-based deep learning method to predict RNA three-dimensional structures of single-chain RNAs from sequences.

A language model-based deep learning approach for #RNA 3D structure prediction www.nature.com/articles/s41...

First attempt in a (loosely defined) Single-Molecule Biophysics starter pack. Please share and (self-) nominate. go.bsky.app/CteFZM5

First snow at @embl.org❄️

Hi, Could you please add me! Thanks :)

Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting | Molecular Systems Biology imageimageTranscriptome-wide measurement of subcellular mRNA dynamics in mouse ES cells reveals that nuclear retention is the rate-limiting step in the life-cycle of most mRNAs and provides a resource for understanding spatiotemporal gene ...

Our fantastic collaboration with the lab of Nils Blüthgen @molsysbio.bsky.social has been published:
www.embopress.org/doi/full/10....

#RNASky #RNAbiology @mdc-berlin.bsky.social

Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation....

Last #RNAbiology work for the day. This one by the Mendell lab: www.science.org/doi/10.1126/...