It was such a pleasure writing this with @incarnatolab.bsky.social! There has been so much exciting progress in probing the complexity of RNA folding in cells. Although we couldn't cover it all, we did our best to highlight several major emerging areas. I’m excited to see where the field goes next!

Danny IncaRNAto@incarnatolab.bsky.social · 2d ago

Thrilled to share the latest review I had the incredible pleasure to write together with @amustoe.bsky.social, out today in #COSB, about probing #RNA structural ensembles, non-equilibrium intermediates and isoforms. Check it out: www.sciencedirect.com/science/arti...

Thrilled to share the latest review I had the incredible pleasure to write together with @amustoe.bsky.social, out today in #COSB, about probing #RNA structural ensembles, non-equilibrium intermediates and isoforms. Check it out: www.sciencedirect.com/science/arti...

New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.

Excited to share the very first #preprint since I started my lab at @utrechtuniversity.bsky.social We explored the area of small molecule- #RNA interaction, and present SOLiD-MaP: a #photoproximity labeling platform for mapping small molecule binding site on RNA. www.biorxiv.org/content/10.6...

SOLiD-MaP: A Photoproximity Labeling Platform for Small Molecule Binding Site Mapping on RNA

RNA-targeting small molecules are emerging as promising therapeutic modalities, but their development requires methods that define binding sites and evaluate RNA target selectivity. Existing approache...

biorxiv.org

Today I am so incredibly excited to share with you a new tool from the lab, #RFviewJS (and its stand-alone version #RFview). Two tools I built to fill a gap that has frustrated me for years. #RNA secondary structure visualization (1/n)

#RNA Framework 2.9.7 is out! Several additions, important fixes and improvements. Please update! Check it out: github.com/dincarnato/R... & see the CHANGELOG (buff.ly/4gtJ67u) for the details!

GitHub - dincarnato/RNAFramework: RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework

github.com

To all the #RNAFramework users who updated to v2.9.6: please issue a "git pull" to ensure the latest Core::Utils module gets updated as this escaped the last commit. Apologies for the inconvenience!

#RNA Framework 2.9.6 is out! Several additions, important fixes and improvements. Please update! Check it out: buff.ly/4guLWsP & see the CHANGELOG (buff.ly/4gtJ67u) for the details!

As it's almost Christmas, here're 2 presents from the lab! 🎄 First: #RNA Framework 2.9.5 is out! Several additions, fixes and improvements. Check it out: lnkd.in/gi3QDNeq & see the CHANGELOG (shorturl.at/Lcobs) for the details! (1/n)

#RNA Framework 2.9.4 is out! Several additions, fixes, improvements. Check it out: github.com/dincarnato/R... & see the CHANGELOG (buff.ly/4gtJ67u) for the details! (1/n)

GitHub - dincarnato/RNAFramework: RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework

github.com

Please join us for our next seminar, featuring Danny IncaRNAto, PhD: “Discovery of RNA regulatory structural switches via ensemble mapping” @incarnatolab.bsky.social #rna #casprnasig #rnastructure

So excited to see this out in @natgenet.nature.com! An amazing collaboration with @gagneurlab.bsky.social, I am happy I was (a small) part of. Nucleotide dependencies can capture regulatory elements, including #RNA structures! Congrats to the whole team! Check it out: www.nature.com/articles/s41...

Nucleotide dependency analysis of genomic language models detects functional elements - Nature Genetics

Mapping pairwise nucleotide dependencies by leveraging genomic language models highlights functional genomic elements and predicts deleterious genetic variants more effectively than alignment-based conservation metrics.

nature.com

Looking forward!

Marcin Magnus@mmagnus42.bsky.social · 10mo ago

Please join us for our next seminar, featuring Danny IncaRNAto, PhD: “Discovery of RNA regulatory structural switches via ensemble mapping” @incarnatolab.bsky.social #rna #casprnasig #rnastructure

Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.

Check out this new fantastic method from @rivaselenarivas.bsky.social to predict #RNA structure + 3D motifs and pseudoknots guided by covariation

Elena Rivas@rivaselenarivas.bsky.social · 10mo ago

Integrated prediction of RNA secondary structure jointly with 3D motifs and pseudoknots guided by evolutionary information. @aakaran31.bsky.social and @rivaselenarivas.bsky.social link.springer.com/article/10.1...

Happy #RNA day to all my fellow RNA lovers!

I am so incredibly excited to share our latest work, on the exploration of #RNA secondary structure ensembles and discovery of RNA regulatory structural switches in bacteria and human cells, just out in @natbiotech.nature.com: nature.com/articles/s41.... A short tread! (1/n)

Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis - Nature Biotechnology

Transcriptome-scale maps of RNA secondary structure ensembles in living cells detect candidate RNA structural switches.

nature.com

The IncaRNAto lab is seeking a motivated #PhD candidate, interested in studying #RNA structural ensemble dynamics in living cells. Here's the link to the vacancy: www.rug.nl/about-ug/wor.... Please share!

#RNA Framework 2.9.3 is out! Lots of improvements! Check it out: github.com/dincarnato/R... & see the CHANGELOG (raw.githubusercontent.com/dincarnato/R...) for the details!

In a preprint published today, we are excited to report the secondary structure of the 1212 nt fission-yeast S. pombe telomerase RNA, TER1, and its roles in the physicofunctional organization of this massive, flexible enzymatic RNP complex. www.biorxiv.org/content/10.1...

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Two 2-year postdoc positions available at @unigroningen.bsky.social with @incarnatolab.bsky.social Apply here: rug.nl/about-ug/wor... Info on the group: incarnatolab.com

#RNA rules

We present Rfam-based RNA structural alignments and other structure-based inputs for RNA 3D structure prediction by deep learning. www.biorxiv.org/content/10.1...

Inaugural post "All-at-one RNA folding with 3D motif prediction framed by evolutionary information" www.biorxiv.org/content/10.1... Introducing CaCoFold-R3D by @aakaran31.bsky.social and myself @rivaselenarivas.bsky.social

All-at-once RNA folding with 3D motif prediction framed by evolutionary information

Structural RNAs exhibit a vast array of recurrent short 3D elements involving non-Watson-Crick interactions that help arrange canonical double helices into tertiary structures. We present CaCoFold-R3D...

biorxiv.org

#RNA Framework 2.9.2 is out! Several fixes and improvements, particularly for mutlithreading. Check it out: buff.ly/4guLWsP & see the CHANGELOG (buff.ly/4gtJ67u) for the details!

GitHub - dincarnato/RNAFramework: RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis

RNA structure probing and post-transcriptional modifications mapping high-throughput data analysis - dincarnato/RNAFramework

buff.ly

Amazing new paper from @rivaselenarivas.bsky.social keeps improving #RNA covariation analysis, by adding RNA 3D motif prediction from alignment in R-scape!

Elena Rivas@rivaselenarivas.bsky.social · 2y ago

Inaugural post "All-at-one RNA folding with 3D motif prediction framed by evolutionary information" www.biorxiv.org/content/10.1... Introducing CaCoFold-R3D by @aakaran31.bsky.social and myself @rivaselenarivas.bsky.social

The full #RNA conformational landscape of RNase P in solution: www.nature.com/articles/s41...

The conformational space of RNase P RNA in solution - Nature

Using a deep neural network and statistical analyses of atomic force microscopy images of individual RNA molecules enables the mapping of RNA conformational space in solution.

nature.com

Hello Bluesky 🤠 Our very first post is about our recent paper in Nucleic Acids Research: so-called PUN motifs are repetitive elements enabling proteins to catalyze #RNA folding and RNA-dependent #condensate formation ( #LLPS). 15% of human proteins contain 3 or more PUN motifs. See bit.ly/4fZ3f54.