Carlos Alfonso

Regulatory paradigm of Dscam1 stochastic alternative splicing through conserved long-range RNA structures Abstract. Pancrustacean Dscam1 genes encode 2 000–120 000 distinct isoforms via mutually exclusive splicing; however, the underlying regulatory mechanisms

academic.oup.com/nar/article/...

Check this

Spligation enables programmable chimeric RNA generation in living cells
doi.org/10.64898/202...

Out now! In collaboration with Leifu Chang, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems!

Links to the published articles:
tinyurl.com/55kpavet
tinyurl.com/sk6djwx3

Previous thread for the preprint:
bsky.app/profile/did:...

Exapted CRISPR–Cas12f homologues drive RNA-guided transcription - Nature Specialized σ factors interact with nuclease-dead, CRISPR–Cas12f proteins to form potent, RNA-guided gene activation systems that function independently of fixed promoter motifs.

Just amazing what evolution can come up with. Naturally occurring nuclease deficient Cas12 family members use gRNAs to bind DNA and recruit sigmaE family members that drive txn initiation proximally. 2 papers! 1- describes 2- structure!
www.nature.com/articles/s41... www.nature.com/articles/s41...

Our most recent work on the “function and evolution” of #nuclear-speckles is now online at Cell @cp-cell.bsky.social
doi.org/10.1016/j.ce...
Read the thread👇 for the highlights of our findings.

I’m thrilled to share that my PhD work has been just published in Cell. After a long and bumpy ride, we uncovered the core function of nuclear speckles -splicing of GC-levelled exons- and traced the evolution of this gene architecture and condensates themselves to amniotes.

Age-related chromatin remodeling includes shared and specific signatures across cell types, sex, and organs
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
@science.org @junyuecao.bsky.social @rockefeller.edu

Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs Nature Structural & Molecular Biology - METALoci, a new three-dimensional genome computational tool, reveals a major rewiring of regulatory interactions during sex determination. By combining...

🤩💪 Out now! 3D regulatory hubs in sex determination

With @mamartirenom.bsky.social & Capel labs, led by @imotagom.bsky.social & @jrotwitguez.bsky.social

1️⃣ METALoci – explore #3DGenome 🧬
2️⃣ Non-coding region controlling Fgf9 🧩
3️⃣ Meis genes = new key players 🌟

👉 rdcu.be/e5sm2

1/n Bluetorial 👇

Single-cell and isoform-specific translational profiling of the mouse brain - Nature Post-transcriptional regulation of mRNA translation was explored using Ribo-STAMP and single-cell RNA sequencing to reveal cell-type-specific and isoform-specific translation patterns across hipp...

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

A pictographic model of chromatin folding in the nucleus. DNA wrapped around nucleosomes aggregates into nanoscale domains, whilst newly nucleosome depleted DNA that forms after acute degradation of FACT projects from these domains and engages in long-range interactions that can span TAD boundaries

New preprint from @anadopico.bsky.social (who I have had the great pleasure of supervising with Tom Milne) and our fantastic collaborators in the @davieslab.bsky.social

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

#genomics #GeneRegulation #chromatin

Very cool! rRNA Expansion Segments are so interesting! All eukaryotic ribosomes contain them, but what they are doing is still not entirely clear. It looks like they could have multiple roles.

Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR - Nature Biotechnology Trimodal single-cell analysis reveals gene-regulatory architecture in complex tissues.

Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR - @yaruidiao.bsky.social @dukehealth.bsky.social go.nature.com/4rZqimf

The 3 hardest things to learn as a scientist:
1. Trust the data.. especially when it’s not what you expected,
2. Trust the data.. allowing it to change your direction,
3. Trust the data.. but not too much: test with new data at every turn.

One of my favorite transposon facts. Think LTR retrotransposons are a homogeneous group? The two main kinds -- Ty1 and Ty3 -- are as evolutionary diverged as GIANT SQUID and PINE TREES.

Very cool work. I will have to integrate this into general nucleotide trends.

De novo design of GPCR exoframe modulators - Nature De novo designed proteins that target the transmembrane domain of G-protein-coupled receptors, created using iterative structural predictions, are able to act as agonist-positive, negative or biased a...

De novo designed GPCR exoframe modulators restore the activity of various dopamine receptor loss of function mutants #NBThighlight www.nature.com/articles/s41...

Axolotls wow scientists by regenerating this complex organ Axolotls can completely rebuild their thymus, a key immune organ

Axolotls can completely rebuild their thymus, a key immune organ

A single-cell time-series atlas of endothelial cell embryonic development The STED-EC atlas enables inter-organ and multi-time-point comparisons of gene expression in endothelial cells, revealing substantial transcriptomic variations across endothelial cells from different embryonic organs and facilitating investigation of previously unknown molecular mechanisms that govern organ-specific vascular development.

Now online! A single-cell time-series atlas of endothelial cell embryonic development

Global mapping of circRNA-target RNA interactions reveal P-body-mediated translational repression Li et al. introduce circTargetMap, a computational framework for transcriptome-wide mapping of circRNA-target RNA interactions using RIC-seq data. They show that circRNAs such as CDR1as repress mRNA translation by base-pairing-mediated sequestration into P-bodies, independent of miRNAs, revealing a general mode of circRNA-mediated translational regulation with disease relevance.

Online Now: Global mapping of circRNA-target RNA interactions reveal P-body-mediated translational repression Online now:

Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation - Nature Genetics Acute depletion of NIPBL reveals a class of chromatin loops that are independent of NIPBL for their maintenance but not their establishment and that NIPBL is necessary for the expression of lineage-de...

Very excited to share my postdoc research in the @jesserdixon.bsky.social lab at @salkinstitute.bsky.social, out online at @natgenet.nature.com today! www.nature.com/articles/s41... We investigated the function of the cohesin accessory protein NIPBL, making two particularly interesting findings:

Wow, big time preprint drop from @jacobsenucla.bsky.social lab! One of the holy grails of DNA methylation research. Also, the 2-figure paper reminds me of the classic Science Brevia from Simon Chan and Steve showing RNA-directed DNA methylation drives de novo DNAme www.biorxiv.org/content/10.6...

This remarkable set of genetic screens done both in the Nüsslein-Volhard & Driever & Fishman labs in Tübingen & Boston revolutionized our understanding of vertebrate development. This remembrance is worth a read-it was a long road, right up to the end 🧪 1/2
journals.biologists.com/dev/article/...

The replicase???

These hungry immune cells tidy sleeping flies’ brains Hear the biggest stories from the world of science | 11 February 2026

Latest from the Nature Podcast 🔊 These hungry immune cells tidy sleeping flies' brains

go.nature.com/45W6VCk

New OA Resource: "Motif-based substrate mapping of the receptor-like cytoplasmic kinase BIK1 reveals novel components and regulatory nodes of plant immunity" rdcu.be/e29Ro

...define and use the phosphorylation motif of BIK1 to find novel substrate candidates.

🧪✨ Introducing BenchAid🧪! Our new molecular biology AI agent is live at benchaid.farnunglab.com. Over the last months, we built BenchAid🧪 to streamline many of our bench workflows to help move our lab faster. Try it out!

Stretch-induced endogenous electric fields drive directed collective cell migration in vivo - Nature Materials Electric fields guide collective cell migration in developing embryos of Xenopus laevis via a voltage-sensitive phosphatase.

REPOSTING this here just to officially leave "the other place"

Our work on the role of endogenous electric fields in guiding collective cell migration during #morphogenesis is out @naturematerials.bsky.social
nature.com/articles/s41...

Interested in antisense oligonucleotides?
Check our story about downstream-of-gene ASOs (DG-ASOs)!
Together with the Roche Innovation Center we
identified transcription termination windows of protein-coding genes as ASO target regions.

link to BioRxiv:
www.biorxiv.org/content/10.6...

Interesting work suggesting the need for different mechanisms on the establishment of patterning www.biorxiv.org/content/10.1... that echo some ‘old’ ideas along similar lines and also involving #Wnt
www.sciencedirect.com/science/arti...
www.nature.com/articles/nrg...

I am excited to share a new review @cp-molcell.bsky.social written in collaboration with @tanjamittag.bsky.social , Mikayla Eppert, and Ambuja Navalkar where we review the current evidence for and against the role of density transitions in regulating transcription www.cell.com/molecular-ce...