Danny IncaRNAto

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)

Subjecting bacteria to cold shock causes an increase in the number of regions populating 2+ alternative conformations. By combining these results with covariation analysis we identified a number of novel RNA cold thermometers, such as the 5′ UTR of lpxP. (3/n)

By performing ensemble deconvolution analysis of the E. coli transcriptome, we identified a large number of regions populating 2+ alternative conformations, characterized by features such as high G+C content, low Shannon entropy, high structuredness and conservation, etc. (2/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.

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)

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!

The 1212 nt fission-yeast S. pombe telomerase RNA (TER1) secondary structure, determined by phylogenetics and bioinformatics

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.

That looks like Mol*: molstar.org

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...

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...

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

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

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

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.

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