Danny IncaRNAto

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!

Beyond significant speed-ups, this version features a complete rewrite of the rf-correlate module for calculating pairwise correlations between samples. The new version has no sample number limit, and it generates clustered correlation heatmaps.

#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!

Second: DRACO v1.3 is out! Greatly improved algorithm for increased sensitivity and accuracy in the reconstruction of #RNA conformation reactivity profiles. The biggest improvement: replicate support (for more information, check the documentation: shorturl.at/zY3nu). Check it out: lnkd.in/gBhpnisG

The biggest improvement is the introduction of paired-end support in rf-count (for more information, check the documentation: shorturl.at/LZcou). (2/n)

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)

Until a fix will be released, we advice users to install ViennaRNA v2.7.0 in a separate folder and to provide the path to RNAplot v2.7.0 via the -vrp parameter of rf-fold. (4/n)

!!! Important note: A bug was introduced in ViennaRNA v2.7.0, which breaks the pseudoknot detection functionality of rf-fold. However, RNAplot v2.7.0 is required to take advantage of the new secondary structure plotting functionality. (3/n)

Highlights: new normalization method in rf-norm (Mitchell method, pubmed.ncbi.nlm.nih.gov/37334863/), statistics plots in rf-count & rf-count-genome, and secondary structure plots in rf-fold (powered by ViennaRNA v2.7.0) (2/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

#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)

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

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.

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...

Looking forward!

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

Happy #RNA day to all my fellow RNA lovers!

Thanks Lars! It definitely was :-)

Thanks Dirk-Jan!

Thanks Rita!

Thanks Fede!

Thanks Sebastian!

Thanks Ivano!

And a huge thanks to @erc.europa.eu for funding that made all of this possible! (11/n)

Shoutout to rockstar Ivana Borovská, who led this incredible work, and to our collaborators, particularly @mtwolfinger.bsky.social and Wim Velema! (10/n)

While our study still presents many limitations, we sincerely hope this will represent a stepping stone in better understanding and characterizing the structural dynamics of cellular RNAs, and their roles in regulating gene expression. (9/n)

papers/Borovska et al., 2025 at main · dincarnato/papers Data & pipelines associated with papers from the lab - dincarnato/papers

Furthermore, we introduced the DeConStruct framework (github.com/dincarnato/p...), to aid the discovery and prioritization of conserved regulatory RNA structural switches discovered via ensemble deconvolution analysis of chemical probing data. (8/n)

For example, the 5′-UTR of the CKS2 RNA populates two conformations, one promoting increased translation of a uORF, and one reducing translation of the main ORF. (7/n)

Thanks to this method, we observed that regions of human 5′-UTRs populating 2+ alternative conformations, tend to be enriched for upstream start codons (NTG), suggesting that the switch between these conformations might regulate translation of uORFs vs. main ORF. (6/n)

Next, we sought to explore the transcriptome of human cells. Due to the extreme sequencing depth required for ensemble deconvolution analyses, we developed 5′UTR-MaP, which enables the transcriptome-scale interrogation of 5′-UTRs (and, in general, of 5′-terminal regions). (5/n)

Interestingly, the well characterized cspA thermometer already populates both ON and OFF conformations at 37°C, and completely shifts to the ON conformation at 10°C, explaining why cspA is among the top-expressed proteins in the E. coli proteome. (4/n)