Fernando Rabanal

New paper in @PNASNews : “Standing genetic variation fuels rapid evolution of herbicide resistance in #blackgrass” Led by @Kersten_Sonja at @plantevolution lab, in collaboration with @christiandhuber @kjschmid @YvesVandePeer & colleagues from @BASF pnas.org/doi/10.1073/pn…

Modifying meiotic recombination by targeting chromatin regulators to crossover hotspots in Arabidopsis science.org/doi/10.1126/sc… excellent new work from Ziolkowski group @Piotraz1 @SzymanskaLejman

Visualizing pairwise genome comparisons? No need to run BLAST separately anymore! 🧬 ​#gbdraw has implemented #LOSAT, a WASM-powered Rust reimplementation of BLASTN/TBLASTX. ​✅ No local installation ✅ No data transfer (Serverless) ​Try it here: gbdraw.app

📢 New paper from our lab! Ribo-BiFC enables direct visualisation of assembled 80S ribosomes in vivo in plants 🌱 — allowing observation of active translation across tissues. 🔗 link.springer.com/article/10.118… 👏 Big congratulations to the whole team! 1/2

The (Yoav) Voichek lab has opened its gates at the Weizmann Institute, and is actively recruiting students and researchers at all levels - come explore gene regulation and computational genomics in a fun, friendly sprouting lab 🤗🥼⚗️🧪 weizmann.ac.il/plants/voichek/

Finally out! We introduce NoLMseq, a #nucleolus laser microdissection method to capture single-cell genome-nucleolus interactions in normal and stressed nucleoli, revealing novel insights into genome organization & function. nature.com/articles/s4146…

Many people think of the genome as a string of "letters." The human genome, say, has 3.2 billion base pairs of DNA organized across 23 pairs of chromosomes. But the genome is a 3D object. Genes located on entirely different chromosomes might be clustered together. Mutations in these "distant" genes can lead to disease in surprising ways. For a new paper in @Nature, researchers released several "maps" of human genomes from two types of cells: embryonic stem cells and fibroblasts. They compared methods to see which ones are least biased, and found many long-range interactions between genes. The article does a good job explaining how “the genome is organized at different scales”: > On a single chromosome, histones control which parts of the DNA sequence are accessible and expressed. > At the scale of hundreds of thousands of bases, “chromatin loops in a dynamic manner,” the authors write, bringing distant genes closer together. > Across chromosomes, sequences "cluster together in space to form subnuclear compartments." Examples abound. Enhancers, for example, are short DNA sequences that regulate the expression of far away genes. They do this by *physically* touching the genes they control; a protein called cohesin grabs the DNA and tugs it into big loops. Even promoters, which are thought of as being associated with one gene or operon, can cluster together across many genes! A protein, Ronin, grabs promoters and pulls them together. This is apparently done mostly for genes that tend to be "on," as it helps enzymes find genes faster/not have to diffuse far away to find targets. (This also happens with genes that tend to be "off;" so-called polycomb proteins grab onto promoters, cluster them up, and silence all of them at once. It's a way for the cell to conserve energy.) One consequence of this spooky "action-at-a-distance" is that diseases might arise from mutations in unexpected locations. Editing these regulatory sequences, in other words, might in turn affect a gene located on an entirely different chromosome that *is* associated with that disease. Genetic mutations linked to autism, for example, are known to disrupt the 3D organization of the genome. A single deletion at a gene, TAL1, also affects its ability to form long-range chromatin interactions with other genes, leading to leukemia. There are probably many other, as-yet-undiscovered, instances of this.

Excited to share our @NaturePlants News & Views article highlighting how two independent studies uncover transcription factor mediated recruitment of the key siRNA-producing protein, RNA polymerase IV to specific DNA sequences in plants. Full article: doi.org/10.1038/s41477… 1/3

Our paper is out in @Nature! Oncogenes are often copy-number amplified on extrachromosomal DNA (ecDNA) in cancer, but how is ecDNA inherited by dividing cells? Here we identified elements within ecDNA that promote its retention in dividing cells. 1/11 nature.com/articles/s4158…

At last! This long-awaited effort fills a critical gap in plant science that has remained elusive for so long. Huge congratulations to this team for creatively uncovering CNSs across so many complex plant genomes.

Functional diversity of Arabidopsis late embryogenesis abundant proteins in response to changes in the physicochemical environment biorxiv.org/content/10.110… #biorxiv_biophys

We are thrilled to have our spatial single-cell atlas of the Arabidopsis lifecycle in @NaturePlants. It turns out that it is easy to generate aesthetic images when the spatial expression of 1,000 genes is available! 1/n @NatanellaE @nobolly @JoeEcker nature.com/articles/s4147…

Finally published~! science.org/doi/10.1126/sc… 1. Strong evidence of adzuki domestication in Japan 2. The Jomons are not merely hunter-gatherers 3. Tracing evolutionary changes in domestication traits difficult to observe from archaeological evidence

📢 Excited to share our work out now in @Nature! 📢 We present the phased pan-genome of the European tetraploid potato, based on 10 historical cultivars representing 85% of European potato diversity. Learn more below! 🔗 nature.com/articles/s4158… 1/7

Abundant clock proteins point to missing molecular regulation in the plant circadian clock | Molecular Systems Biology embopress.org/doi/full/10.10… We predicted and measured the abundance of clock proteins in Arabidopsis thaliana.

Beautiful collaboration led by Tetsuji Kakutani and Sayuri Tsukahara on unravelling the fine changes that can make a centrophobic TE become centrophilic and vice versa! The devil is in the details for these TEs. nature.com/articles/s4158…

Natural variation modifies centromere proximal meiotic crossover frequency and segregation distortion in Arabidopsis thaliana biorxiv.org/content/10.110… new work from us on centromere inheritance and organisation @njgorringe @MpNaish @malacopa_genome

This work follows a 15K young allotetraploid Arabidopsis suecica through its origin and evolution along a polyploid cycle♻️. Robin Rurns,@Gauri1488, @liverworks, @Uliana_Kolesni, @FilipKolar7, @alisondawnscott biorxiv.org/content/10.110…

Does the aggregation of complex multicellularity follow a universal developmental pattern across the eukaryotic tree of life? Thrilled to announce that we found a convergently evolved transcriptomic hourglass pattern in brown algal development. @Nature 👉nature.com/articles/s4158…

Excited to share our team's discovery on tissue-like multicellularity in archaea under mechanical compression! Led by @theopi, Olivia Leland & @Archaeon_Alex, it rethinks the evolution of multicellularity beyond eukaryotes. @HFSP @MPI_Bio biorxiv.org/cgi/content/sh…

Preprint alert 🚨 As we gear up to share out exploits in red algae, we took a detour down the green lineage to piece together the evolutionary dyanmics of epigenetic gene silencing in plants 🌱🤓 biorxiv.org/content/10.110…