Johan Jakobsson

Anxa1+ dopamine neuron vulnerability defines prodromal Parkinson's disease bradykinesia and procedural motor learning impairment Progressive degeneration of dopamine neurons (DANs) defines Parkinson's disease (PD). However, the identity and function of the most vulnerable DAN populations in prodromal PD remain undefined. Here, ...

first thing to share here!

excited to share lab’s first study in Parkinson’s disease revealing the prodromal vulnerability and function of the dopamine neuron subtype defined by Anxa1 expression - a specialized system controlling procedural motor learning

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

MORC2 directs transcription-dependent CpG methylation of human LINE-1 transposons in early neurodevelopment Methylation of CpG dinucleotides is essential for silencing genomic repeats such as LINE-1 retrotransposons (L1s) in the germline and soma. Evolutionarily-young L1s are transcribed in human pluripoten...

Very proud of this work where we define how the MORC2 ATPase directs CpG methylation of active human L1 transposons in early development.

Thanks to co-authors, funders & wonderful environment @lundstem.bsky.social

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

Brief thread below (do people still do that?) 1/X

#TransposonDay2025 New manuscript from our center to which we contributed. Great work led by @chdouse.bsky.social ! Provides a mechanistic explanation for how L1s are silenced during early human development.

doi.org/10.1101/2025...

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

#TransposonDay2025 New manuscript from our center to which we contributed. Great work led by @chdouse.bsky.social ! Provides a mechanistic explanation for how L1s are silenced during early human development.

doi.org/10.1101/2025...

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

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

Good times in Lund 🇸🇪 with @jakobssonlab.bsky.social. Beautiful campus, great food, and awesome science! Thanks Johan!

We had a fantastic guest speaker at our lab meeting this week who talked about the beautiful life of transposons and how they contributed to the evolution of the vertebrate brain. Thanks for the visit @cedricfeschotte.bsky.social !!

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...

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

💥🥳 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

Reactivation of retrotransposable elements is associated with environmental stress and ageing Nature Reviews Genetics, Published online: 02 April 2025; doi:10.1038/s41576-025-00829-yIn this Review, Della Valle et al. discuss the role of retrotransposable elements (RTEs) in the onset and progression of ageing and ageing-related disease, including evidence that environmental stressors act through RTEs to shift the trajectory towards unhealthy ageing.

New online! Reactivation of retrotransposable elements is associated with environmental stress and ageing

The mobile genome: genetic and physiological impacts of transposable elements

Do you have transposon-related research cooking, with some cool results you are exciting to share? Start thinking about registering to #EMBOMobileGenome workshop! Nov 4-7 2025 in Heidelberg. One of the historical TE meetings, with a diverse and welcoming community. www.embl.org/about/info/c...
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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...

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...

Last week, some of us from Team Jakobsson had a great time in Arizona at the 2025 CRN Collaborative Meeting! Plenty of insightful talks and networking. Shoutout to @kirkebylab.bsky.social for a fantastic talk on PSC-based therapies and models of PD 🌟🧬🏜️ #CRNPhoenix2025 @asapresearch.bsky.social

ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers O’Neill et al. present a deep exploration of molecular subtypes in ALS postmortem tissues from the NYGC ALS Consortium. Matched bulk and single-cell profiles demonstrate that ALS subtypes are a combin...

Super happy to announce the latest work from my lab together with Hemali Phatnani @nygenome.org & NYGC ALS Consortium!

We've combined ALS patient profiling (100s!), ML classifiers and matched bulk/single-cell data to dive into ALS Molecular Subtypes

#NIHfundedResearch
www.cell.com/cell-reports...

Today… 🇸🇪

Interesting study on cell-type-specific aging using single-nuclei transcriptomics in the human neocortex. Not clear to me based on this graph that pace of aging is striking different across cell types.
doi.org/10.1101/2025...
see also
https://doi.org:10.1038/s41593-024-01742-z

Human brain cell-type-specific aging clocks based on single-nuclei transcriptomics Aging is the primary risk factor for most neurodegenerative diseases, yet the cell-type-specific progression of brain aging remains poorly understood. Here, we developed human cell-type-specific trans...

New preprint from our lab! Great collaboration with the labs of Karolina Pircs and Csaba Kerepesi from Budapest. We built molecular aging clocks for the human brain using single-nuclei RNA-seq data.

doi.org/10.1101/2025...

Human brain cell-type-specific aging clocks based on single-nuclei transcriptomics Aging is the primary risk factor for most neurodegenerative diseases, yet the cell-type-specific progression of brain aging remains poorly understood. Here, we developed human cell-type-specific trans...

New preprint from our lab! Great collaboration with the labs of Karolina Pircs and Csaba Kerepesi from Budapest. We built molecular aging clocks for the human brain using single-nuclei RNA-seq data.

doi.org/10.1101/2025...

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

CSH-Asia "The Repetitive and Mobile Genome" meeting announcement poster

Don't miss the first edition of the CSH-Asia meeting on "The Repetitive and Mobile Genome" taking place in Suzhou, China.
📅 Abstract submission deadline extended: Feb 21, 2025
👉 www.csh-asia.org?content/2544
#transposon #mobileDNA #TEsky

Randomizing the human genome by engineering recombination between repeat elements We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into re...

We're delighted to share our work on scrambling the human genome using prime editing, repetitive elements, and recombinases in @science.org , led by @jonaskoeppel.bsky.social , @f-raphael.bsky.social , with @proftomellis.bsky.social and George Church.
www.science.org/doi/10.1126/...

We had this wonderful paper for TE-JC this week. Will be very interesting (and challenging) to dissect the functional role all these elements play in early development…

www.cell.com/cell/fulltex...

Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition - Nature Genetics Simultaneous profiling of the genome, methylome, epigenome and transcriptome using single-molecule chromatin fiber sequencing and multiplexed arrays isoform sequencing identifies the genetic and molec...

Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition
www.nature.com/articles/s41...
@mrvollger.bsky.social @naturegenet.bsky.social

📣 #EMBOMobileGenome is open for registrations!

Assembling experts in genomics, epigenetics, structural biology, evolutionary biology, and developmental biology to discuss the broad impact of TEs on organismal biology. 🧬🔍

📜 Submit abstract by 29 July!
👉🏼 https://s.embl.org/mge25-01-bl

Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues - Nature Methods Spatial-Mux-seq offers a multimodal spatial platform capable of profiling multiple molecular modalities, including the transcriptome, chromatin accessibility, histone modifications and targeted protei...

Our paper presenting spatial-Mux-seq is now out 🥳 pushing the frontiers of spatial Multiomics! It has been a great pleasure to work alongside with Yanxiang. DBiT is a really flexible platform and this paper clearly demonstrates that. Congrats to all involved!
www.nature.com/articles/s41...

TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states - Nature Cancer Panzeri et al. use a Trim28+/D9 mouse model with intrinsic developmental heterogeneity to show that ‘heavy’ and ‘light’ developmental morphs exhibit different timing, type and severity of cancer, link...

Online now!

TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states

🖊️by Ilaria Panzeri & John Andrew Pospisilik and colleagues
@ilariapanzeri.bsky.social @andrewpospisilik.bsky.social

👇
www.nature.com/articles/s43...

A mechanism for maintaining and spreading H3K9me3 in heterochromatin from the Fejes Toth and Aravin labs that depends on the local H3K9me3 density: HP1 dimers recruit SetDB1 to chromatin by simultaneously binding H3K9me3 on histone H3 and auto-methylated SetDB1. www.biorxiv.org/content/10.1...