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Epigenetics Update - Expansion in situ genome sequencing links nuclear abnormalities to aberrant chromatin regulation bit.ly/4jtXApb Jason D. Buenrostro (MIT/Harvard) reporting in Science #Epigenetics #Chromatin --- Gain deeper insights into gene regulation; epigenometech.com

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The #GENETICS June cover features an illustration of Starships, giant cargo-mobilising transposable elements found in fungal species of the subphylum Pezizomycotina. Starship elements are highly variable in overall length & genetic content. 1/2🧵

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Starship giant transposable elements cluster by host taxonomy using k-mer-based phylogenetics. #TransposableElements #TEs #Kmer #Phylogenetics #Genomics #Bioinformatics #G3 🧬 🖥️ academic.oup.com/g3journal/ad...

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#TEsky Factors determining chromosomal localization of transposable elements in plants doi.org/10.1111/plb....

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🔔Upcoming Wednesday, June 4th! Join us for another #FragileNucleosome series! Two amazing talks by @1995dana.bsky.social & @chrishsiung.bsky.social! If you haven’t jooned for any of 2025 talks, register here: us06web.zoom.us/webinar/regi...

submitted 7 days ago • 0 comments

New preprint from the lab led by former masters student AJ Roussel in collaboration with Alexander Suh and @fjruizruano.bsky.social. We found a ~4-fold accumulation of a Neptune #transposon in asexually reproducing "F1" fish hybrids. An unexpected and fascinating finding! #TEsky

submitted 9 days ago • 1 comment

@nadavahituv.bsky.social and colleagues use a massively parallel jumping assay to assess the ability of retrotransposons to jump and identify nucleotide changes that have the potential to reactivate them in their latest manuscript published in @natcomms.nature.com. go.nature.com/4k7pqIK

submitted 13 days ago • 0 comments

New paper "Chromatin unfolding via loops can drive clustered transposon insertion" in @biophysj.bsky.social Former postdoc Roshan Prizak & predoc Aaron Gadzekpo find that a feedback between transposon insertion and chromatin accessibility can give clustering. www.cell.com/biophysj/ful...

submitted 13 days ago • 1 comment

Modern tree-dwelling sloths are dwarf morphs of (usually) ground dwelling giant sloths 😮 reminds me the evolutionary trajectories of dinosaurs into birds. www.science.org/doi/epdf/10.... 🧪 ⚒️ #Paleobio #EvoBio #Geology

submitted 13 days ago • 0 comments

Blurring the lines between retrotransposons & viruses! sORF2 enables direct transmission of retrotransposons challenging our understanding of mobile genetic elements. #preprint @juliusbrennecke.bsky.social Lab #preLight from Ally Simpson & Alyss Humphrey! 👉 prelights.biologists.com/highlights/d...

submitted 15 days ago • 0 comments

Genome assemblies of Sargassum algae by Kim et al. suggest TE-driven genome size expansion, gene duplications, and salicylic acid responses, which could be mechanisms enabling adaptation to intertidal stress. 🔗 doi.org/10.1093/gbe/evaf084 #genome #TEsky #algae

submitted 15 days ago • 0 comments

Happy to announce that our study on the latent cis-regulatory potential of mobile DNA is officially published! TLDR: mobile DNA in bacteria (Insertion Sequences) have a proclivity for evolving new promoters. At least 25% of them probably already encode functional promoters as well.

submitted 15 days ago • 2 comments

New preprint of @trono-lab.bsky.social and my PhD work! By modulating SWI/SNF remodeling at ancient transposable elements - LINE/L2s and SINE/MIRs, a "noncanonical" KZFP called ZNF436 protects cardiomyocytes from losing their identity. 🫀heartbeat on 🔁 repeat www.biorxiv.org/content/10.1... #TEsky

submitted 17 days ago • 2 comments

Wow, what a story! And excited that it is a few loci expressing these specific SINE loci.

submitted 20 days ago • 0 comments

Combining pangenomics and population genetics finds chromosomal re-arrangements, accessory-like chromosome segments, copy number variations and transposon polymorphisms in wheat and rye powdery mildew https://www.biorxiv.org/content/10.1101/2025.05.08.652814v1

submitted 23 days ago • 0 comments

The regulatory potential of transposable elements in maize ->Nature | More info from EcoSearch

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From the archives: Transposable elements shape the evolution of mammalian development go.nature.com/4mfy7lI #Review by Anna D. Senft & Todd S. Macfarlan

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We dive into the dynamics of #starships 🚀 in a fungal pathogen to ask: how might these giant #transposons impact human health? We find they drive genome-wide variation, encode clinically-relevant traits and even transpose within the same strain! 🍄🧪 out today in mBio #goteam doi.org/10.1128/mbio...

submitted 24 days ago • 0 comments

I am thrilled to share our preprint where we take advantage of the unique opportunities offered by human blastoids to uncover a human-specific mechanism potentially playing a role in preimplantation 🧵. www.biorxiv.org/content/10.1...

submitted 24 days ago • 2 comments

Almeida et al. show how F-box genes in C. elegans and zebrafish have fused with transposon-derived domains, contributing to functional and regulatory novelty for thermotolerance and fertility. 🔗 doi.org/10.1093/molbev/msaf097 #evolbio #TEsky @miskalab.bsky.social

submitted 24 days ago • 0 comments

Delighted to see our work now published in @currentbiology.bsky.social. A great place for Bostrychia to stake its claim as an emerging red algal model system. Check it out here: www.cell.com/current-biol...

submitted 27 days ago • 4 comments

Mind-blowing work on salamander genomes 🧬🦎🧪 In giant genomes, transposable element (TE) suppression breaks the rules: no link to deletion, expression, or host defense. Just noise, chaos, and stochastic TE bloat! Genome size ≠ genome control. nature.com/articles/s42003-025-08127-3

submitted 25 days ago • 0 comments

Lineage-Specific Evolution, Structural Diversity, and Activity of R2 Retrotransposons in Animals https://www.biorxiv.org/content/10.1101/2025.05.05.652312v1

submitted 27 days ago • 0 comments

Check out our review article on the structural and functional studies of retrotransposon proteins by @akankshathawani.bsky.social together with Kathy Collins' lab. www.sciencedirect.com/science/arti...

submitted 28 days ago • 0 comments

Kawamura Lab @ Saitama Uni 🇯🇵 “investigated widefins medaka, a spontaneous mutant displaying phenotypic variation in the number of dorsal and anal fin rays. [WGS] revealed that an extremely large transposon, Teratorn, containing a herpesvirus genome, was inserted into the 3’ UTR of the hoxc12a gene.”

submitted 28 days ago • 1 comment

Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others. www.nature.com/articles/s41...

submitted 28 days ago • 1 comment

New research by scientists of DZNE's population-based "Rhineland Study" indicate that retrotransposable elements and their repressors are markers of aging and that their dysregulation is linked to inflammation, especially in men. 👉 onlinelibrary.wiley.com/doi/10.1111/...

submitted 30 days ago • 1 comment

A megatransposon drives the adaptation of Thermoanaerobacter kivui to carbon monoxide | Nature Communications https://www.nature.com/articles/s41467-025-59103-8

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Comparative analysis of transposable element activity and host silencing pathways across gigantic genomes of different sizes reveals that gigabases of DNA can be gained and lost without clear, predictive differences in TE-host interaction dynamics. www.nature.com/articles/s42...

submitted 29 days ago • 0 comments

@fxquah.bsky.social 's paper is finally out @genomeresearch.bsky.social and we made the cover!! This was only possible due to the brilliant illustration by @sonhita.bsky.social Paper here: genome.cshlp.org/content/35/5... See below for more details 🧵

submitted 30 days ago • 1 comment

New preprint from my group! Here we studied the contribution of a subset of human- and hominoid-specific transposons (SVA, LTR5HS) to the evolution of human craniofacial development. We specifically focussed on cranial neural crest (CNCC) formation and migration 1/n www.biorxiv.org/content/10.1...

submitted 59 days ago • 2 comments

💥🥳 At long last, our latest paper is out! Gag proteins of endogenous retroviruses are required for zebrafish development www.pnas.org/doi/10.1073/... Led heroically by Sylvia Chang & @jonowells.bsky.social A study which has changed the way I think of #transposons! No less! 🧵 1/n

submitted 37 days ago • 14 comments

Environmentally induced variation in sperm sRNAs is linked to gene expression and transposable elements in zebrafish offspring www.nature.com/articles/s41...

submitted 42 days ago • 0 comments

In science you can always look again, deeper, and at bits missed out earlier — this time with that classic, Gregor Mendel’s peas, 159 years after Mendel published his work.

submitted 41 days ago • 1 comment

Long-read DNA and RNA sequencing reveal an intronic retrotransposon insertion in TCOF1 causing Treacher Collins syndrome https://www.medrxiv.org/content/10.1101/2025.04.24.25326319v1

submitted 40 days ago • 0 comments

#TEsky Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector doi.org/10.1038/s415...

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#TEsky The demographic history of populations and genomic imprinting have shaped the transposon patterns in Arabidopsis lyrata doi.org/10.1093/molb...

submitted 40 days ago • 1 comment

The rest of Mendel's alleles characterized! So, out of 7 traits, 3 caused by TE insertions!!! (though apparently there are two different green alleles, one cause by a TE insertion, but another a promoter deletion allele) www.nature.com/articles/s41...

submitted 41 days ago • 1 comment

It’s out! The evolutionary origins of yeast point centromeres uncovered! “Ancient co-option of LTR retrotransposons as yeast centromeres” www.biorxiv.org/content/10.1...

submitted 41 days ago • 1 comment

This is a very cool article. They did T2T (high depth, low error) sequencing on genomes from FOUR generations of a family. 🧵 "Human de novo mutation rates from a four-generation pedigree reference" www.nature.com/articles/s41...

submitted 43 days ago • 1 comment

Interested in the analysis on Transposable elements? 🧬 Have a look at our course with @valentinapeona.bsky.social & @ritarebollo.bsky.social We'll cover everything from TE biology to de novo library construction, quantification, & transcriptomic analysis. www.physalia-courses.org/courses-work...

submitted 44 days ago • 0 comments

💬 “Our findings show how k-mer-based analysis can refine how #Starships can be studied, and home in on the rare events where these complex #transposons seem to jump across large evolutionary distances. buff.ly/TsiReRA 🖥️ 🧬

submitted 46 days ago • 0 comments

#TEsky Impact of a horizontally transferred Helitron family on genome evolution in Xenopus laevis doi.org/10.1186/s131...

submitted 45 days ago • 0 comments

In this study, Hermant et al. describe the evolution of the retrotransposon MERVL and its cis-regulatory transcription factor binding motifs, highlighting the phyloregulatory adaptation at play during early embryogenesis. Learn more here: ➡️ tinyurl.com/gd352270

submitted 44 days ago • 0 comments

Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain [new] Aged mouse brain: Cell-specific TE demethylation & TAD remodeling found, mostly in non-neuronal cells.

submitted 45 days ago • 0 comments

Ancona et al. investigated transposable elements in the Apennine Yellow-Bellied Toad: TEs are more active in male gonads, while TE-silencing pathways increase in ovaries. These findings challenge a simple "genomic arms race" model of host-TE evolution. 🔗 doi.org/10.1093/gbe/... #evobio #genomics

submitted 45 days ago • 0 comments

#mDNASRC is back and stronger than ever after 30 years! Discover how transposable elements shape our genomes and impact health, featuring keynote speaker @bengrbm.bsky.social, and more! Save your space: buff.ly/QiSc4E6

submitted 52 days ago • 0 comments

#TEsky FHY3/FAR1 transposable elements generate adaptive genetic variation in the Bassia scoparia genome doi.org/10.1002/ps.8...

submitted 52 days ago • 0 comments