Emiliano Sotelo

a 3d rendering of a colorful dna molecule with a black background ALT: a 3d rendering of a colorful dna molecule with a black background

Happy #RNA Day everyone!!! 🎉🎉🎉

#AUG1st #RNASky

DNA mutagenesis driven by transcription factor competition with mismatch repair Competition between transcription factors and mismatch repair machinery drives localized hypermutation at regulatory elements, with implications for cancer and genome evolution.

'Here, we show that transcription factor (TF) proteins, key players in gene regulation, can increase mutagenesis from replication errors by directly competing with the recognition of DNA mismatches by MutSα, the primary initiator of eukaryotic mismatch repair'
www.cell.com/cell/abstrac...

[1/8] *New Open-Access Long Read Resource*. We sequenced 1,019 genomes from the 1000 Genomes Project sample cohort using @nanoporetech.com long-read sequencing (LRS) to median 17x coverage. Publication at go.nature.com/4ffPb8f.

@hhu.de @crg.eu @embl.org @impvienna.bsky.social

Complex genetic variation in nearly complete human genomes - Nature Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Structural variation in 1,019 diverse humans based on long-read sequencing - Nature Intermediate-coverage long-read sequencing in 1,019 diverse humans from the 1000 Genomes Project, representing 26 populations, enables the generation of comprehensive population-scale structural varia...

Researchers have significantly expanded the catalogue of known human genetic variation. Two studies in @nature.com resequenced data from the landmark 1000 Genomes Project with long-read tech, creating what may be the most complete overview of the human genome to date. www.nature.com/articles/s41...

Over 1,000 human genomes sequenced using long-read tech—Siegfried Schloissnig, computer scientist at the IMP, shares how it happened, key findings, and what it means for the future of genomics: www.imp.ac.at/news/article...

➡️Read the paper here: www.nature.com/articles/s41...

Speaker presenting at SMBE 2025 meeting

Listening to former #RegRNALab member (now in the Moreno Lab) Jose Antonio Corona, presenting the #LatinCells project,seeking to characterise the genetic diversity of immune cells. Lots of extreme field work done for sampling indigenous populations across Latin America! 🌎

#SMBE2025

MexOMICs Maps the Genetic and Social Landscape of Disease in Mexico By focusing on twins and patients with lupus and Parkinson’s disease, a Mexican consortium is generating critical data to understand health and disease in the country.

Thanks @lecteroide.bsky.social for the opportunity to share the efforts developed in MexOmics

www.the-scientist.com/mexomics-map...

Barbara McClintock portrait

🧬🌽 Happy Transposon Day! 🌽🧬

Today we celebrate the birthday of Barbara McClintock - scientist extraordinaire and discoverer of jumping genes. Still the only woman to have an unshared Nobel Prize in the biomedical sciences #TransposonDay2025

VFB works closely with the FlyBase team and we rely on their hard work to provide many of our features. Due to the current funding situation at FlyBase (flybase.org), we encourage our users to donate and help maintain this essential resource.

Check out our new preprint!
How can we get more out of existing protein/genome language models without retraining them?

A 🧵 to walk those interested through this paper...

Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...

I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...

Participate in the Bioconductor community by sharing your work in a meeting designed to maximize interactivity and productivity at the seafront of Barcelona! 👩‍💻🏖️🧬 #EuroBiocC2025

EuroBioC2025 hex sticker design featuring the Sagrada Família in the centre, vibrant mosaic patterns inspired by Park Güell at the bottom, and other Barcelona landmarks like the crane and towers. The Bioconductor logo replaces the "i" in "BioC", and "bioconductor.org" is written across the top left. The overall shape is a yellow-bordered hexagon.

🎉 Announcing the EuroBioC2025 Sticker Winner!

🏆 Chaima Hkimi’s design features the Sagrada Família, Park Güell colours, and a nod to Bioconductor in the text. Pick up the sticker at #EuroBioC2025!

#Bioconductor #Bioinformatics #RStats #StickerContest

"We should include eugenics in our undergraduate classes, reminding students that scientists must speak out when others lie about science and use it to further their political views," says professor @peiferlabunc.bsky.social.

www.cell.com/trends/genet...

@cp-trendsgenetics.bsky.social

Newly published in Genetics:
academic.oup.com/genetics/adv...
We ask what gene flow & introgression do to gene coexpression networks. The answer is: a lot.

Polymorphic transposable elements contribute to variation in recombination landscapes (drosohila 🪰) www.pnas.org/doi/full/10.... #TEsky

GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller A local-haplotagging-based small and structural variant caller - yangao07/longcallD

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...

The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition DNA hypomethylation in human tumor cells results in the activation of the LINE-1-derived RNA-binding protein L1TD1 and its interactions with LINE-1 transposons.

#TEsky The domesticated transposon protein L1TD1 associates with its ancestor L1 ORF1p to promote LINE-1 retrotransposition doi.org/10.7554/eLif...

Naturally occurring variation in gene-associated transposable elements impacts gene expression and phenotypic diversity in woodland strawberry Transposable elements (TEs) constitute a major portion of plant genomes and play key roles in shaping genome architecture, regulating gene expression, and driving genome evolution. In this study, we g...

Does the smell and flavor of strawberries depend on variations in gene-associated transposons? It seems so! Check out our new preprint! www.biorxiv.org/content/10.1...

The latent cis-regulatory potential of mobile DNA Transposable elements can alter gene regulation in their host genome, either when they integrate into a genome, or when they accrue mutations after integration. However, the extent to which transposon...

Sending our manuscript back to review after getting some great constructive feedback!

Read here to see how random mutations in transposons can create new promoters. Any feedback is, of course, much appreciated.

www.biorxiv.org/content/10.1...

Drosophila follicle showing retrotransposons (pink & yellow) expressed in somatic cells infecting the oocyte

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇

What advice or resources would you give someone who is about to make their first #python package?

3D Epigenome Evolution Underlies Divergent Gene Regulatory Programs in Primate Neural Development The expansion of the neocortex is a hallmark of human evolution and is closely linked to neural stem cell biology. Yet, the epigenetic mechanisms driving divergent gene regulation during primate neuro...

🚨New preprint from @bonevlab.bsky.social 🚨: What are the key epigenetic mechanisms that drive species-specific gene regulation during primate neurogenesis - and how do they contribute to the evolution of the human neocortex?
Here’s what we discovered 👇
www.biorxiv.org/content/10.1...

Did you know that two jumping sequences (LINE-1 and Alu) make up nearly 30% of our genomes? Ever wonder how they jump into new genomic sites? We have some exciting discoveries to share new in @science.org on the structural mechanisms of LINE-1 retrotransposition (aka jumping 🧬➡️🧬) 🧪 #ScienceResearch

Figure from https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087053 showing lazy corn hanging from a basket on the left and wild-type corn growing straight on the right. Below is a gene diagram showing transposon insertions in an exon of the lazy1 gene, and some DNA sequence gibberish below.

Lazy corn is a natural mutant in the lazy1 gene (great name). My favorite of course is a transposon insertion. A CACTA transposon jumps in, inactivates the gene, plant falls down. To the extent you can actually grow corn as a hanging plant. 4/4

Science magazine front cover. Picture of a walnut in its opened shell. The text reads "All about timing. Mating type evolution in walnuts and pecans"

graphical abstract: "In Juglans (top left) and Carya, two morphs show complementary temporal separation between male and female flowering (heterodichogamy). Mating types are controlled by two nonhomologous single-locus mechanisms that arose in the common ancestor of each genus, respectively. (Bottom left) Simplified schematic of a putative functional regulatory element at the Juglans locus. (Bottom right) Strong genotypic correlations across the Carya locus indicate a lack of recombination between two colinear haplotypes with similar gene content."

Congrats to @jeffgroh.bsky.social et al on publication of "Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories"

www.science.org/doi/10.1126/...

Boundaries between TADs often extend over considerable distance. But how variable is this width of boundaries? And does it matter? Find out in our new pre-print with the group of David Holcman. www.biorxiv.org/content/10.1...

L1-ORF1p nucleoprotein can rapidly assume distinct conformations and simultaneously bind more than one nucleic acid Abstract. LINE-1 (L1) is a parasitic retrotransposable DNA element, active in primates for the last 80–120 Myr. L1 has generated nearly one-third of the hu

How does the ORF1p perform its multiple functions to facilitate LINE1 retrotransposition? And what enables its ability to also facilitate replication of other retrotransposons? Find out in our newly published paper in Nucleic Acids Research doi.org/10.1093/nar/...