Johan Jakobsson
@jakobssonlab.bsky.social
📤 574
📥 1109
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Transposons and heterochromatin
reposted by
Johan Jakobsson
Raquel Garza
8 days ago
Always a joy to join
#EMBOMobileGenome
-A week full of cool nature’s quirks and science along the friendliest crowd 🧬 Happy to have shared our work on ERVs in human brain evolution (talk by
@jakobssonlab.bsky.social
) and Parkinson’s disease (poster by yours truly) 🧠
#ASAP
@jakobssonasap.bsky.social
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reposted by
Johan Jakobsson
Updated version of our preprint on how SETDB1-mediated H3K9me3 controls the expression of L1 elements in human neural progenitor cells. The new analysis in this revised version supports a role for active DNA demethylation of L1s in the absence of H3K9me3.
www.biorxiv.org/content/10.1...
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Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
Heterochromatin is characterised by an inaccessibility to the transcriptional machinery and is associated with the histone mark H3K9me3. However, studying the functional consequences of heterochromati...
https://www.biorxiv.org/content/10.1101/2025.03.28.645885v2
10 days ago
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Updated version of our preprint on how SETDB1-mediated H3K9me3 controls the expression of L1 elements in human neural progenitor cells. The new analysis in this revised version supports a role for active DNA demethylation of L1s in the absence of H3K9me3.
www.biorxiv.org/content/10.1...
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Loss of SETDB1-mediated H3K9me3 in human neural progenitor cells leads to transcriptional activation of L1 retrotransposons
Heterochromatin is characterised by an inaccessibility to the transcriptional machinery and is associated with the histone mark H3K9me3. However, studying the functional consequences of heterochromati...
https://www.biorxiv.org/content/10.1101/2025.03.28.645885v2
10 days ago
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Wonderful highlight of our work! 🧬
add a skeleton here at some point
about 1 month ago
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reposted by
Johan Jakobsson
Gael Cristofari
about 1 month ago
It was fun to write this preview with Larisa Okorokova. Congrats to
@jakobssonlab.bsky.social
and all coauthors for this nice piece of work !
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🇸🇪
about 1 month ago
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reposted by
Johan Jakobsson
PLOS Biology
about 1 month ago
Join
@embl.org
for this conference exploring genetic and physiological impacts of transposable elements. Virtual registration is open until October 28. Learn more at
plos.io/4nuqeZA
.
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Todays labmeeting became a tribute to Jane Goodall. Such an outstanding role model. 🙊
about 1 month ago
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reposted by
Johan Jakobsson
New preprint from my lab! We describe how transposable elements are activated in Parkinson’s disease, which is linked to an interferon response. We believe this study significantly advances our understanding of transposons and their role in human brains.
www.biorxiv.org/content/10.1...
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Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson's disease
Parkinson's disease (PD) is a common age-related neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TE) have been linked to i...
https://www.biorxiv.org/content/10.1101/2025.09.03.673956v1
2 months ago
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reposted by
Johan Jakobsson
bioRxiv Neuroscience
2 months ago
Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson's disease
https://www.biorxiv.org/content/10.1101/2025.09.03.673956v1
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New preprint from my lab! We describe how transposable elements are activated in Parkinson’s disease, which is linked to an interferon response. We believe this study significantly advances our understanding of transposons and their role in human brains.
www.biorxiv.org/content/10.1...
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Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson's disease
Parkinson's disease (PD) is a common age-related neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TE) have been linked to i...
https://www.biorxiv.org/content/10.1101/2025.09.03.673956v1
2 months ago
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New collaborative paper from our lab! We developed cell-type specific transcriptional ageing clocks using snRNA-seq data from human brain.
doi.org/10.1002/advs...
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Human Brain Cell‐Type‐Specific Aging Clocks Based on Single‐Nuclei Transcriptomics
Muralidharan and colleagues develop cell-type-specific transcriptomic aging clocks using single-nucleus RNA sequencing of human post mortem prefrontal cortex samples. These clocks accurately predict ....
https://doi.org/10.1002/advs.202506109
3 months ago
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Johan Jakobsson
ASAP Team Jakobsson
3 months ago
Team Jakobsson gathered in southern Sweden for a few inspiring days discussing PD, transposable elements and future plans. We even squeezed in a hike and enjoyed some beautiful views ☀️🌊
@jakobssonlab.bsky.social
@kirkebylab.bsky.social
@mollygale.bsky.social
@asapresearch.parkinsonsroadmap.org
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www.stemcellcenter.lu.se/article/why-...
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Why repetitive DNA matters for human brain evolution and disease
Lund University. DNA carries the complete set of instructions an organism needs to develop and survive, but only about 1.5% of it consists of protein-coding genes that determine traits such as eye col...
https://www.stemcellcenter.lu.se/article/why-repetitive-dna-matters-human-brain-evolution-and-disease
3 months ago
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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...
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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...
https://www.cell.com/cell-genomics/fulltext/S2666-979X(25)00235-6
3 months ago
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reposted by
Johan Jakobsson
Dinos Meletis
11 months ago
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...
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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, ...
https://www.biorxiv.org/content/10.1101/2024.12.22.629963v1
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reposted by
Johan Jakobsson
Christopher Douse
5 months ago
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
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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...
https://www.biorxiv.org/content/10.1101/2025.06.11.658943v2
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reposted by
Johan Jakobsson
#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...
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https://doi.org/10.1101/2025.06.11.658943
5 months ago
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reposted by
Johan Jakobsson
Molly Gale (Gale-Hammell Lab)
5 months ago
🧬🌽 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
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#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...
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https://doi.org/10.1101/2025.06.11.658943
5 months ago
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reposted by
Johan Jakobsson
Mike Fainzilber
6 months ago
A 🧵 to walk those interested through this paper...
add a skeleton here at some point
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reposted by
Johan Jakobsson
Danica Milovanović
6 months ago
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
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reposted by
Johan Jakobsson
Cedric Feschotte
6 months ago
Good times in Lund 🇸🇪 with
@jakobssonlab.bsky.social
. Beautiful campus, great food, and awesome science! Thanks Johan!
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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
!!
6 months ago
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reposted by
Johan Jakobsson
Raquel Fueyo
6 months ago
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...
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reposted by
Johan Jakobsson
Cedric Feschotte
7 months ago
💥🥳 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
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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. ...
https://www.pnas.org/doi/10.1073/pnas.2411446122
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reposted by
Johan Jakobsson
Nature Reviews Genetics
8 months ago
New online! Reactivation of retrotransposable elements is associated with environmental stress and ageing
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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.
https://www.nature.com/articles/s41576-025-00829-y?utm_source=dlvr.it&utm_medium=bluesky
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reposted by
Johan Jakobsson
Deborah Bourc’his
8 months ago
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...
1/3
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The mobile genome: genetic and physiological impacts of transposable elements
https://www.embl.org/about/info/course-and-conference-office/events/mge25-01/
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reposted by
Johan Jakobsson
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...
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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 ...
https://www.biorxiv.org/content/10.1101/2025.03.28.645885v1
8 months ago
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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...
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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 ...
https://www.biorxiv.org/content/10.1101/2025.03.28.645885v1
8 months ago
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reposted by
Johan Jakobsson
ASAP Team Jakobsson
8 months ago
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
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reposted by
Johan Jakobsson
Molly Gale (Gale-Hammell Lab)
8 months ago
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...
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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...
https://www.cell.com/cell-reports/fulltext/S2211-1247(25)00173-1
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Today… 🇸🇪
9 months ago
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reposted by
Johan Jakobsson
Denis Jabaudon
9 months ago
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
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reposted by
Johan Jakobsson
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...
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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...
https://doi.org/10.1101/2025.02.28.640749
9 months ago
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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...
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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...
https://doi.org/10.1101/2025.02.28.640749
9 months ago
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reposted by
Johan Jakobsson
Geoff Faulkner
9 months ago
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
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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...
https://www.biorxiv.org/content/10.1101/2025.01.17.633315v1.abstract
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reposted by
Johan Jakobsson
Gael Cristofari
9 months ago
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
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reposted by
Johan Jakobsson
Leopold Parts
10 months ago
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/...
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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...
https://www.science.org/doi/10.1126/science.ado3979
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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...
10 months ago
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reposted by
Johan Jakobsson
Waggoner Lab
10 months ago
Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition
www.nature.com/articles/s41...
@mrvollger.bsky.social
@naturegenet.bsky.social
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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...
https://www.nature.com/articles/s41588-024-02067-0
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Johan Jakobsson
EMBL Events
10 months ago
📣 #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
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reposted by
Johan Jakobsson
Marek Bartosovic
10 months ago
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...
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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...
https://www.nature.com/articles/s41592-024-02576-0
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Johan Jakobsson
Nature Cancer
10 months ago
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...
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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...
https://www.nature.com/articles/s43018-024-00900-3?utm_source=bluesky&utm_medium=social&utm_campaign=natcancer
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reposted by
Johan Jakobsson
Karsten Rippe
10 months ago
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...
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reposted by
Johan Jakobsson
ASAP Team Jakobsson
10 months ago
🧠🔬 Great meeting last Friday in Copenhagen between the Kirkeby and Jakobsson labs — exciting experiments coming up to investigate transposons in PD in vitro models!
@asapresearch.bsky.social
@kirkebylab.bsky.social
@jakobssonlab.bsky.social
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reposted by
Johan Jakobsson
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.01.17.633315v1
10 months ago
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reposted by
Johan Jakobsson
Oded Rechavi
10 months ago
If there's something we don't understand I assume transposons are responsible unless proven otherwise
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reposted by
Johan Jakobsson
Anita Adami
10 months ago
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 🧠
add a skeleton here at some point
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reposted by
Johan Jakobsson
Raquel Garza
10 months ago
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
add a skeleton here at some point
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