Rebecca Berrens
@rberrens.bsky.social
📤 2193
📥 1233
📝 51
Group leader of transposon group in Oxford at IDRM.
#new_pi
https://sites.google.com/view/berrenslab
reposted by
Rebecca Berrens
Surfin' NuRD
10 days ago
OK Kids, our ERK story is finally heading out into the world. After 9 years of having funding, losing funding, losing staff, getting funding, gaining staff...it's ready! We discovered a novel stage of what is an otherwise extensively studied process: how cells respond to extracellular signals. 1/n
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https://www.biorxiv.org/content/10.64898/2026.03.27.714694v1
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Rebecca Berrens
Mafalda Almeida 🇵🇹 🇪🇺
13 days ago
Do you want to move to Oxford and join our lab? There is a computational biologist position open atm to develop and implement tools to analyse TE expression in single cell long read data and more. Apply!
#TEsky
#UniversityofOxford
#postdoc
add a skeleton here at some point
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reposted by
Rebecca Berrens
Josh Dubnau
about 1 year ago
Fun primer with @ForeverYHChang highlighting a lovely Travis Thomson lab paper! Did animals co-opt viral gag for intercellular (trans synaptic) communication? Or did viruses co-opt retrotransposon gags that animals had previously co-opted for intercellular use?
add a skeleton here at some point
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Rebecca Berrens
Navin B. Ramakrishna
23 days ago
Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis
www.nature.com/articles/s41...
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Integrated small and long RNA sequencing reveals piRNA mediated transposon repression during human oogenesis - Nature Communications
The roles of the piRNA pathway in human oocytes are poorly understood. Here, the authors profile small and long RNAs in single oocytes and show that short piRNAs broadly repress transposable elements,...
https://www.nature.com/articles/s41467-026-70296-4#author-information
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Rebecca Berrens
Toby Baril
23 days ago
🎉🧬 Multiple genomes/pangenome? Time for a parTEA! 🧬 ☕️ Tired of annotating TEs one genome at a time? Same. So we organised a parTEA! Introducing EarlGrey ParTEA v0.1.3 — consistent TE annotation across all your genomes, in parallel, with one command:
github.com/TobyBaril/Ea...
#TEworldwide
#TEsky
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Rebecca Berrens
Dr. Tyler A. Elliott
23 days ago
#TEsky
TEffectBayes: a nextflow pipeline for exploring the potential effect of transposable elements in gene regulatory network with multi-omic Bayesian network model
doi.org/10.1007/s004...
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TEffectBayes: a nextflow pipeline for exploring the potential effect of transposable elements in gene regulatory network with multi-omic Bayesian network model - Molecular Genetics and Genomics
Molecular Genetics and Genomics - Transposable elements (TEs) are critical contributors to gene regulatory networks, yet their repetitive and abundant nature complicates efforts to elucidate their...
https://doi.org/10.1007/s00438-026-02365-8
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reposted by
Rebecca Berrens
Evolution Soup
29 days ago
This fish has cloned itself for 100,000 years. Scientists just figured out how.
#evolutionsoup
#evolution
#gynogenesis
#science
#fossils
#cloning
👇🏿👇🏽
is.gd/PUwN0s
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Rebecca Berrens
Molecular Biology and Evolution
28 days ago
Potapenko et al. studied two species of barley, finding that TE silencing is central to genome size regulation, with selection maintaining smaller genomes among individuals with higher fitness in favorable habitats. 🔗
doi.org/10.1093/molbev/msag051
#evobio
#molbio
#TEsky
#PlantSky
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Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species
Abstract. A substantial variation in genome size has been observed among individuals of the same species. Theory predicts that increased genome size may co
https://doi.org/10.1093/molbev/msag051
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We are looking for a Postdoc to join our lab at
@oxfordbiochemistry.bsky.social
. This is a dry-lab focused post on the computational analysis of long read single-cell sequencing data to understand the role of transposable elements (TEs) in early development.
my.corehr.com/pls/uoxrecru...
#TEsky
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LinkedIn
This link will take you to a page that’s not on LinkedIn
https://lnkd.in/eUQbpPHk
28 days ago
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Rebecca Berrens
Amelia Cervera 🍉
about 1 month ago
#TEsky
add a skeleton here at some point
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Rebecca Berrens
Dr. Tyler A. Elliott
about 1 month ago
#TEsky
A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions
pubmed.ncbi.nlm.nih.gov/41797537/
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A retroelement-derived mammalian ARC protein exhibits selective RNA recognition and nucleic acid chaperone functions - PubMed
Activity-regulated cytoskeleton-associated protein (ARC) is an RNA-binding protein that also serves as a central hub for neuronal protein-protein interactions. It is essential for intercellular signaling and contributes to synaptic plasticity. ARC includes Gag-like sequences of Ty3/Gypsy retrotransp …
https://pubmed.ncbi.nlm.nih.gov/41797537/
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Rebecca Berrens
Ana Gázquez-Gutiérrez
about 1 month ago
I'm so happy to share our latest paper! Now out in
@narjournal.bsky.social
🥳 Did you know that transposable elements embedded in mRNAs can form dsRNA and activate innate immunity? 🧬🦠 Have a look!
academic.oup.com/nar/article/...
#TEsky
#RNAsky
#RNAbiology
#immunity
#NAR
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Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8
Abstract. The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prev
https://academic.oup.com/nar/article/54/5/gkag190/8506905?searchresult=1
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reposted by
Rebecca Berrens
Astrid Haase
about 1 month ago
Join us at the EMBO Workshop “RNA-guided genome protection” 🇨🇭 June 16–20. Transposon silencing • stem cell biology • RNA-guided immunity. Keynotes: Déborah Bourc’his + Ian MacRae. Register now + submit your abstract!
meetings.embo.org/event/26-gen...
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RNA-guided genome protection
The genome carries information across generations, ensuring species survival. To preserve faithful transmission of genetic information, RNA-directed mechanisms safeguard the genome integrity in diver…
https://meetings.embo.org/event/26-genome-protection
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reposted by
Rebecca Berrens
Antonio Scialdone
about 1 month ago
Transposable elements are increasingly studied in single-cell data, but how reliable are current locus-level quantification methods in short-read scRNA-seq data? If you work with single-cell RNA-seq or TEs, we hope this is a useful resource — feedback very welcome!
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Rebecca Berrens
Veronica Finazzi
about 1 month ago
Happy to share our new preprint! 📊 We benchmarked methods for locus-level transposable element quantification in short-read scRNA-seq, using both real datasets and simulations with read-level ground truth. Huge thanks to
@catavallejos.bsky.social
and
@antonio-scialdone.bsky.social
!
#TEsky
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reposted by
Rebecca Berrens
🧬Jacob L Steenwyk
about 1 month ago
How does the piRNA system first recognize a new transposon or virus as foreign?
https://www.biorxiv.org/content/10.1101/2024.01.24.577019
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Rebecca Berrens
Johann Confais
about 2 months ago
🚨📢📄 Article in press in Genome Biology
doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics
#TEsky
🧵👇
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A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology
Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variabil...
https://doi.org/10.1186/s13059-026-03984-5
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reposted by
Rebecca Berrens
Dominik Handler
about 2 months ago
How does the piRNA pathway solve the self vs. non-self problem? 🧬 Since piRNAs come from single-stranded RNA, how does the cell choose the right ones? For years, "piRNA clusters" were seen as THE privileged source. But are they really special and earmarked for biogenesis? (1/19)
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reposted by
Rebecca Berrens
Bardin Lab
about 2 months ago
Very last chance to join us (Deadline tomorrow Feb 10!) at this Developmental Biology meeting! Have a nice story? Come and discuss it with editors from
@embojournal.org
@plosbiology.org
and
@dev-journal.bsky.social
! A one hour info session from
@erc.europa.eu
will also be presented!
add a skeleton here at some point
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reposted by
Rebecca Berrens
Naomi Moris
2 months ago
We're recruiting a
#devbio
Postdoctoral Fellow to explore the hTLS system! If you know any fab PhD students finishing, or candidates wanting to get their hands on
#SCBEM
embryo models, do get them to apply! 🌟https://www.crick.ac.uk/careers-study/vacancies/2026-02-03-postdoctoral-fellow-moris-lab
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reposted by
Rebecca Berrens
FragileNucleosome
2 months ago
We've got two exciting chromatin talks coming up on Wednesday next week:
@epijenatics.bsky.social
from
@jbuenrostro.bsky.social
's lab and
@ambystoma22.bsky.social
! register and join us:
us06web.zoom.us/webinar/regi...
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reposted by
Rebecca Berrens
Alex Crits-Christoph
3 months ago
Sad to hear that Oxford Nanopore wants to discontinue the P2Solo later this year in favor of the P2i (the very pricey P2Solo that comes with a GPU to do the basecalling in it) It feels like such a big step in the wrong direction. They are a great sequencing company, not a great GPU upseller...
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nanoporetech-customers - Sign In
https://community.nanoporetech.com/posts/product-update-p2
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reposted by
Rebecca Berrens
Etienne Bucher 🌾🧬🇪🇺
3 months ago
The speed at which Oxford Nanopore is cancelling support for their devices is just mind boggling 😳 P2 solo will be decommissioned soon!!! This is not sustainable!
@nanoporetech.com
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Rebecca Berrens
Toby Baril
3 months ago
🍄Transposon traffic in the mycocosmos🍄 Fascinating work reveals extensive horizontal TE transfer across fungi (
@jromeijn.bsky.social
, Iñigo Bañales &
@mfseidl.bsky.social
;
doi.org/10.1016/j.cu...
). I wrote a Dispatch to prime non-specialists,check it out here:
doi.org/10.1016/j.cu...
.
#TEworldwide
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Rebecca Berrens
Teif lab
3 months ago
Schaepe et al, 2026. Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells
www.cell.com/cell/fulltex...
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Rebecca Berrens
Molly Gale (Gale-Hammell Lab)
3 months ago
📣Excited to announce a new pre-print from the lab 📣 Led by my student
@storiesofisobel.bsky.social
in collab with Hemali Phatnani
@nygenome.org
We discovered a novel class of TDP-43 dependent cryptic gene-TE spliced transcripts: crypTEs
#TEsky
#RNAsky
#ALS
doi.org/10.64898/2026.01.09.698641
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TDP-43 dysfunction leads to the accumulation of cryptic transposable element-derived exons, crypTEs, in iPSC derived neurons and ALS/FTD patient tissues
TDP-43 is an RNA and DNA binding protein that plays major roles in regulating RNA processing. In particular, TDP-43 dysfunction leads to the accumulation of cryptic splice isoforms that result from im...
https://doi.org/10.64898/2026.01.09.698641
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Really excited to share our recent work here today and connect all of you :)
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3 months ago
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What a cool story. Particularly like the fact of expansion and different TF bdg sites! Really speaks for each locus being differential key regulated.
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3 months ago
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Rebecca Berrens
Toby Baril
3 months ago
☕Earl Grey v7.0.0 brewed fresh☕ Nested TEs finally get the treatment they deserve: iterative detection of deep nesting, cleaner GFF annotations, and coverage stats that don’t double-count genomic space + a RepeatCraft edge-case fix. Happy new year to the TE folks! 🧬
github.com/TobyBaril/Ea...
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GitHub - TobyBaril/EarlGrey: Earl Grey: A fully automated TE curation and annotation pipeline
Earl Grey: A fully automated TE curation and annotation pipeline - TobyBaril/EarlGrey
https://github.com/TobyBaril/EarlGrey/
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#TEsky
still have to read the paper but sounds very interesting.
add a skeleton here at some point
3 months ago
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reposted by
Rebecca Berrens
Dr. Tyler A. Elliott
3 months ago
#TEsky
Heterogeneous Lineages of DNA Transposons Encode a TET/JBP Dioxygenase in Fungi
doi.org/10.3390/biol...
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https://doi.org/10.3390/biology14121741
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Rebecca Berrens
Alejandro Burga
5 months ago
🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.
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Rebecca Berrens
Waggoner Lab
3 months ago
@biorxivpreprint.bsky.social
Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells
www.biorxiv.org/content/10.6...
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Rebecca Berrens
Lars Velten
4 months ago
ISCO (Innovations in Single-Cell OMICS) will be back in beautiful Barcelona! 🗓️ 28th/29th of May 2026 📍Barcelona Biomedical Research Park
@prbb.org
(beachfront!) Keynotes:
@bartdeplancke.bsky.social
and
@bocklab.bsky.social
Submit your abstract and present your research!
www.isco-conference.eu
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Rebecca Berrens
Hiten Madhani
3 months ago
Nice paper from
@robertife.bsky.social
on how metabolism-induced H4K16 acylations correlate with (and may cause) chromatin opening through disruption of tail-acidic patch internucleosomal interactions.
www.cell.com/molecular-ce...
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H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations
Nitsch et al. show that short-chain acylations of histone H4K16, acetylation (C2), propionylation (C3), and butyrylation (C4) modulate chromatin structure in vitro. These effects can translate in vivo...
https://www.cell.com/molecular-cell/fulltext/S1097-2765(25)00971-2
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Rebecca Berrens
RB Kollannur
4 months ago
More than one-third of polar bear genome is made up of transposable elements. By contrast, transposons make up about 45% of the human genome Polar bears in southern Greenland are 'using jumping genes to rapidly rewrite their own DNA' to survive melting sea ice
www.livescience.com/animals/pola...
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Polar bears in southern Greenland are 'using jumping genes to rapidly rewrite their own DNA' to survive melting sea ice
Warming temperatures appear to be driving genetic mutations in some polar bears to help them survive the shifting climatic conditions.
https://www.livescience.com/animals/polar-bears/polar-bears-in-southern-greenland-are-using-jumping-genes-to-rapidly-rewrite-their-own-dna-to-survive-melting-sea-ice
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Rebecca Berrens
Michelle Percharde
4 months ago
🚨Our story is published! Same bones but + dissection of MERVL’s role integrating signals from
#ZGA
factors, & + about pathological DUX4 activation of NOXA
#TEsky
. Thanks to all revs for their helpful comments improving the ms. Even
#rev3
- until they ghosted us 😜
www.science.org/doi/epdf/10....
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Rebecca Berrens
Julius Brennecke
4 months ago
Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway. And found a hidden RNA-decay axis from Piwi to the RNA exosome.
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Very excited to share our work on locus level transposable elements in development with the
@fnucleosome.bsky.social
community!
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4 months ago
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Very excited to take part in ISCO in Barcelona next year. Looking forward to great discussions and new ideas!
add a skeleton here at some point
4 months ago
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Rebecca Berrens
Miguel Branco
4 months ago
Despite having been scooped big time by this paper from William Pastor's lab, really quite enjoyed reading it. Congrats to the authors.
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Divergent roles of DNA methylation, TRIM28, and p53 surveillance in human embryonic and trophoblast stem cells
Transcriptional regulation of transposons and genes by TRIM28 and 5mC is critical for proper mammalian embryonic development, but the specific roles for these mediators in human embryonic and placenta...
https://www.biorxiv.org/content/10.1101/2025.10.19.683051v2
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Rebecca Berrens
Toby Baril
5 months ago
TEs aren’t just genomic parasites, they’re also engines of genomic novelty. Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion. With
@danielcroll.bsky.social
&
@guidopuccetti.bsky.social
🧬
www.nature.com/articles/s41...
#TEworldwide
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Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications
In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...
https://www.nature.com/articles/s41467-025-64944-4
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Rebecca Berrens
5 months ago
www.nature.com/articles/s41...
Human inflammatory responses have been linked to adaptive genetic changes during human evolution. It is proposed that primate-specific transposons facilitated the evolution of inflammatory responses in great apes, w/Alus shaping adaptive potential in modern humans.
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Transposon invasion of primate genomes shaped human inflammatory enhancers and susceptibility to inflammatory diseases - Nature Communications
Here, the authors propose that primate-specific transposons facilitated the evolution of inflammatory responses in great apes, with Alus shaping adaptive potential in modern humans.
https://www.nature.com/articles/s41467-025-64690-7
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Rebecca Berrens
Dr. Tyler A. Elliott
5 months ago
#TEsky
A comparative analysis of transposable element diversity and evolution across 75 bee genomes
doi.org/10.1186/s128...
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A comparative analysis of transposable element diversity and evolution across 75 bee genomes - BMC Genomics
Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...
https://doi.org/10.1186/s12864-025-12190-9
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Rebecca Berrens
Karim-Jean Armache
5 months ago
@ckadoch.bsky.social
and I are excited to welcome you to Geneva for the 2026 Keystone Symposium on Epigenetics and Gene Regulation in Health and Disease — short talk and poster slots are still open. Don’t miss the deadlines. Video:
youtu.be/sLfyuQuH8F0
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KSQA: Dr Karim-Jean Armache / Dr. Cigall Kadoch (Epigenetics and Gene Regulation)
YouTube video by KeystoneSymposia
https://youtu.be/sLfyuQuH8F0
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reposted by
Rebecca Berrens
Toby Baril
5 months ago
1/ Ever needed to annotate TEs in a fungal genome, but didn't know where to start? We have released
#MycoMobilome
, a community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom, constructed from >4,000 fungal genomes!
www.biorxiv.org/content/10.1...
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Rebecca Berrens
Svetlana Dodonova
5 months ago
Lab’s first paper is out!! We show the first structures of
#Asgard
#chromatin
by
#cryo-EM
🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across
#Archaea
, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here:
www.cell.com/molecular-ce...
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Rebecca Berrens
Olivier Borkowski
6 months ago
Emergence of population-level feedback control by transposon-plasmid coevolution
doi.org/10.1101/2025...
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reposted by
Rebecca Berrens
Molecular Biology and Evolution
6 months ago
Guo et al. generated haplotype-resolved genome assemblies of black carp, identifying dmrt1 as the sex-determining locus, with a 13.4 kb insertion containing TEs functioning as cis-regulatory modules that mediate Y-specific activation. 🔗
doi.org/10.1093/molbev/msaf239
#evobio
#molbio
#TEsky
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Transposable Element-Mediated Cis-Regulation Drives the Evolution of dmrt1 as a Candidate Master Sex-Determining Gene in Black Carp
Abstract. Sex determination in vertebrates exhibits remarkable evolutionary plasticity, with diverse mechanisms and master sex-determining (MSD) genes aris
https://doi.org/10.1093/molbev/msaf239
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reposted by
Rebecca Berrens
Mandy Jeske
6 months ago
Excited to share our new
@narjournal.bsky.social
paper! Using ReLo and AlphaFold, we described a network of interactions between Drosophila piRNA pathway factors suggesting new links how they coordinate to ensure transposon silencing and genome integrity.
academic.oup.com/nar/article/...
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