Patricia Gerdes

New preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.

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

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...

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system Transposable elements (TEs) make up about half of the human and mouse genomes and play important regulatory roles in immune responses. However, the cis -regulatory contribution of TEs to immune cell d...

New Year, New Paper!🎊

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system
www.biorxiv.org/content/10.6...

Centerpiece of Jason Chobirko's PhD, talented PhD student co-mentored by Andrew Grimson & me. Really excited about it!🧵

Postdocs at Center for Gene Expression in Department of Cellular and Molecular Medicine - Copenhagen, Hovedstaden (DK) job with University of Copenhagen | 12849488 We are looking for 2 or more highly motivated postdocs interested in ribosome biology, 3D chromatin organisation, or regulation of protein turnove...

We are looking for a Postdoc at the Center for Gene Expression in Copenhagen. Deadline for applications is the 11th of January. If you are interested in 3D chromatin, SMC complexes, and super-resolution microscopy, join us. www.nature.com/naturecareer...

Very happy that this part of my postdoc work is now out as a preprint!! Our findings reveal a new mechanism by which retroviral pandemics may have shaped primate brain evolution 🧬🐒🧠 This was a true team effort! w/ @ofeliakarlsson.bsky.social @raquelgarza.bsky.social @jakobssonlab.bsky.social #TEsky

Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells. The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, ...

How do pluripotent stem cells resist harmful interferon responses to safeguard development? Through total epigenetic lockdown of ligands, sensors and effectors of IFN-I. In our preprint, James Holt shares his PhD discoveries on the ground state of immune evasion 😊: www.biorxiv.org/cgi/content/...

Wonderful highlight of our work! 🧬

LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early brain development Adami et al. demonstrate that evolutionarily young L1s are expressed in human pluripotent stem cells and are dynamically regulated throughout neural differentiation. The study examines the role of L1s...

New paper from our lab! We found that LINE-1 transposons contribute to early human brain development.

Funded by @asapresearch.parkinsonsroadmap.org

www.cell.com/cell-genomic...

Long-read RNA sequencing of transposable elements from single cells using CELLO-seq - Nature Protocols Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors fro...

Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...

A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage A phylogenetic approach reveals cryptic LTR subfamilies and functional insights at nucleotide resolution in primates.

Is the annotation of viruses in the human genome accurate? We think not. Take a look at our new paper and let us know if you agree! www.science.org/doi/10.1126/...

Come to Lund! We are looking for a postdoc to join the team. #transposons #epigenetics

Join our team as a postdoc and explore the exciting world of transposable elements and developmental biology with us! @imbavienna.bsky.social @vbcscitraining.bsky.social

Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons Heterochromatin is characterised by an inaccessibility to the transcriptional machinery and associated with the histone mark H3K9me3. Heterochromatin erosion is a hallmark of human ageing and H3K9me3 ...

New preprint from our lab! Why is not everyone working on Transposons?

Loss of H3K9me3 maintenance in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons

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

Another successful year with our workshop at #UniStemDay2025. We explained to high school students how we study human brain evolution using human and monkey brain organoids and looking at gene expression 🧠🐒🔬🧬 w/ @vivienhorvath.bsky.social @ofeliakarlsson.bsky.social @lundstem.bsky.social

I am thrilled to share our story online at @cellpress.bsky.social . Big thanks to all authors: Zhiping, Bill, @lubanlab.bsky.social, Keith & bluesky-less!

authors.elsevier.com/c/1kjdaL7PXu...

How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA

More below 👇

LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human development...

Read this preprint today from @jakobssonlab.bsky.social lab that profiles and CRISPRi perturbs L1 transcription in hiPSCs and cerebral organoids. It is extremely well done. The L1 CRISPRi phenotype in the organoids is subtle and variable but interesting. 1/n

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

#TEsky

We are hiring! 3-year BBSRC-funded postdoc position available. TEs, epigenetics, pregnancy: if you love one or more of these keywords, apply through the link below.
Please spread the word.

We profiled the effects of our CRISPRi system targeting young L1 elements in human pluripotency & brain development. These elements deeply impact our transcriptome, but also have very distinct effects on their nearby genome. Check it out!! 🧬👾

#TEsky #CRISPR #L1 #development #epigenetics

Profiling and targeting young L1s is no easy matter 🧐 check out our new preprint to see how we delve into transcriptional and epigenomic profiling of L1s, and investigate their involvement in pluripotency and early brain development 🧠

LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human development...

🚨 New pre-print from Team Jakobsson! LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development.

This work was led by @anitaada.bsky.social, @raquelgarza.bsky.social and @jakobssonlab.bsky.social from the Jakobsson Lab.

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

LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human development...

New preprint from our lab. Led by the outstanding @anitaada.bsky.social and @raquelgarza.bsky.social. Funded by @asapresearch.bsky.social and @vetenskapsradet.bsky.social.

LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development

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

Don't miss the first CSH Asia meeting on transposons in April in Suzhou, China. Truly fantastic line-up! Abstract deadline at the end of the month... (why is not everyone working on transposons?).

We're thrilled to announce that our project has been funded by @asapresearch.bsky.social in partnership with the Michael J. Fox Foundation! 🚀 Excited to continue exploring the role of transposable elements in Parkinson’s disease. Learn more here:
www.lunduniversity.lu.se/article/52-m...

Fantastic line up of speakers at the 7th Max Planck Freiburg Epigenetics Meeting! Looking forward to hear about all the interesting science done in the epigenetics field!! 🧬🤓 @mpi-ie.bsky.social

YY1 is a transcriptional activator of the mouse LINE-1 Tf subfamily Abstract. Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element in human and mouse genomes. L1 transcription is contro

Well done paper from Wenfeng An's lab showing Yy1 activates L1 TF monomers but surprisingly not GF monomers. More monomers = stronger Yy1 activation

academic.oup.com/nar/advance-...

The HuSH complex silences retrotransposable elements. We identify HuSH2, centered on TASOR2, targeting KRAB-ZNFs and interferon genes, balancing retrotransposon silencing and immune regulation. www.nature.com/articles/s41...

🧬 🧠 Excited to see it printed! We bring key insights on the epigenetic regulation of SVAs, including SVA-XDP: a polymorphic SVA driving a rare neurodegenerative disorder

@jakobssonlab.bsky.social @vivienhorvath.bsky.social
#TEworldwide #Transposons #XDP #NSMB
+ the volume has the cutest cover 🦔

If you like #Transposons 👾 check out this feed and tag your posts with #TEsky! Thanks @tobybarilbio.bsky.social 🤗 bsky.app/profile/did:...

The mobile genome: genetic and physiological impacts of transposable elements

Thrilled to announce that the EMBO workshop «Mobile Genome» will be back in Heidelberg, Nov 4-7th 2025 @EMBLEvents @EMBO. Registration open soon but you can already register interest. Organized with fantastic colleagues @juliusbrennecke @GonzalezLab_BCN @JoePetersLab

www.embl.org/about/info/c...