Suja Jagannathan

Thank you! That's the hope :)

That's an interesting thought. We were thinking that termination may be highly efficient at start-proximal PTCs to reduce the risk of ribosome collisions... But the exact distance is puzzling for sure.

That would be very cool to look at, @timtriche.bsky.social! I suppose it would depend on how translation is impacted as well. 🤔

Genomic stop codon scanning reveals quantitative principles of nonsense-mediated mRNA decay Nonsense-mediated mRNA decay (NMD) degrades transcripts containing premature termination codons (PTCs), critically shaping the disease outcomes of protein-truncating variants. While existing NMD rules...

www.biorxiv.org/content/10.6...

Thanks also to our collaborator,
@zcoban.bsky.social for providing ASE data that helped us expand the scope of our findings!

Excited for this work by Michael Cortazar, an @JagannathanLab Postdoc, to be out as a preprint.

So much hard work went into it, but it was well worth it 🤓

Known for decades: DNA sequence drives nucleosome "rotational positioning" (which face of DNA contacts histones)

But: How does this persist when remodelers & transcription constantly mobilize nucleosomes? Our new preprint 1/ :

www.biorxiv.org/content/10.6...

Hello Fly Folks. quick note FlyBase is under duress due to termination NIH$ to Harvard and intl collabs. The hardworking folks @flybase.bsky.social are doing their darndest to ensure access to current data. For US, there will soon be a new site to donate. Please spread the word, ideas and support 🪰💪

I will unfortunately miss the meeting this year. 😞 So much FOMO! Have fun on my behalf!

This preprint is now out after peer review! Check it out: www.cell.com/cell-genomic.... Huge congrats (and thanks!) to the whole team that contributed!

Absolutely!

Excited to have this out as a preprint!

It was a pleasure to work with @calhoujd.bsky.social and all the coauthors brought together by @varianteffect.bsky.social.

Evidence Aggregator: AI reasoning applied to rare disease diagnostics Retrieving, reviewing, and synthesizing technical information can be time-consuming and challenging, particularly when requiring specialized expertise, as is the case of variant assessment for rare di...

New preprint! We worked with @msftresearch.bsky.social and @broadinstitute.org to see whether large language models (LLMs) can be useful to variant scientists in deciding whether genetic variants seen in a patient are responsible for their disease. tl;dr yes they can: www.biorxiv.org/content/10.1...

Wish i could claim credit! 😂

Antisense oligonucleotide-mediated TRA2β poison exon inclusion induces the expression of a lncRNA with anti-tumor effects Nature Communications - The oncogenic splicing factor TRA2β is reported to be upregulated in human cancers partly by increased TRA2β poison exon (PE) skipping. Here the authors show that...

Our latest work on targeting the poison exon in #RNA #splicing factor TRA2B in #cancer reveals a role for this non coding transcript and opportunities for targeting splicing factor levels across multiple tumor types
rdcu.be/d90Ra
#RNAsky @jacksonlab.bsky.social

If you have been affected by the fires in LA, or are concerned about your ability to keep precious Drosophila strains going during the latest funding crisis, we will host your strains as a backup. Please email me.

Please amplify. If you are also able to host fly strains, add your name as well.

GGNBP2 regulates MDA5 sensing triggered by self double-stranded RNA following loss of ADAR1 editing GGNBP2, CNOT10, and CNOT11 are required for innate immune response after the loss of ADAR1-mediated editing of self dsRNA.

Time for a 🧵 on our new paper from the Walkley lab in @scienceimmuno.bsky.social.

If you're into RNA editing by ADARs, double-stranded RNA (dsRNA) sensing, post-transcriptional gene regulation and CRISPR screening, then read on! 1/X

www.science.org/doi/10.1126/...

#RNASky #ImmunoSky

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...

Question for FULL Professors:

I'm preparing myself to go up for Full soon, and I'm just curious to hear from additional voices: What changed for you as Full? Did it open up any additional opportunities? What new/different expectations came with it?

#AcademicSky #CommSky

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...

I'm excited to share the preprint for the first chunk of my PhD work! We combined DMS structure probing with nascent RNA enrichment to report high-resolution, dynamic structures of transcripts just after synthesis - inside cells. @karlaneugebauer.bsky.social
www.biorxiv.org/content/10.1...

I know many of you have been awaiting us launching transcript expression data in gnomAD. We were waiting for the GTEx v10 release which is now out so we are finally able to launch this. Enjoy!!

m6A sites in the coding region trigger translation-dependent mRNA decay Zhou et al. discovered a specific role of adenosine modifications in the coding region of mRNAs. These chemical alterations slow down the movement of the ribosome during translation and trigger degrad...

Interesting role of m6A in the coding sequence of RNA

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

Thanks for the shoutout, Megan!

Excited to share the latest work from the lab, led by Divya Kolakada, the first PhD from our group 🎓🤓🎉

Peptidyl-tRNA hydrolysis rate influences the efficiency of nonsense-mediated mRNA decay www.biorxiv.org/content/10.1...

Created an #RNAbiology feed to talk RNA science! Let's use it.

@onamy.bsky.social @mgblango.bsky.social @graveley.bsky.social @nickingolia.bsky.social @hogglab.bsky.social @quaidmorris.bsky.social @snf.bsky.social @lucksmith.bsky.social