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@jameswalker303.bsky.social

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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

I'm thrilled to share that our study is now published in Cell:
Extensive N4 cytosine methylation is essential for Marchantia sperm function.
www.cell.com/cell/fulltex...
This paper confirms our 4mC discovery in Marchantia sperm and takes it much further.
A thread: 0/13

Extensive N4 cytosine methylation is essential for Marchantia sperm function

Global N4 cytosine methylation in Marchantia polymorpha sperm regulates gene expression and promotes sperm fertility.

www.cell.com

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Dr Radu Zabet @raduzabet.bsky.social · 18d

Excited to see our story on epigenetic mediated aclimation of plants to fluctuating light patterns out today in doi.org/10.1111/nph..... This work started 6 years ago co-supervised with the amazing @proftlawson.bsky.social and led by the brilliant @robynemm.bsky.social. 1/2

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Pierre Baduel @pierrebaduel.bsky.social · 20d

Happy to share the results of a long-haul post-doc project, now online @science.org, aiming at understanding the rules of transgeneration epigenetic inheritance over TEs in plants and its extent and impact in nature. More below!
doi.org/10.1126/scie...

Transposable elements are vectors of recurrent transgenerational epigenetic inheritance

DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...

doi.org

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Reposted

Oxford Biology @biology.ox.ac.uk · Sep 4

@tinaschreier.bsky.social has been awarded an @erc.europa.eu Starting Grant for research into the cell biology of C4 photosynthesis 🌱

Tina’s project will explore the cell biology that leads to the formation of specialised bundle sheath cells in C4 plants 👇
bit.ly/4mWFGhh

Dr Tina Schreier awarded ERC Starting Grant

bit.ly

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ARC Centre of Excellence in Plants for Space @plants4space.bsky.social · Jul 29

We are pleased to share that P4S Research Fellow @jamespblloyd.bsky.social from the University of Western Australia was recently awarded a Grains Research and Development Corporation Mid-Career Research Fellowship 🌟

Read more 👉 www.linkedin.com/feed/update/...

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Tatsuya Nobori @tatsuyanobori.bsky.social · Jul 26

#PlantBio2025
I’ll be speaking in the final plenary—sharing the story behind this paper and some new, unpublished work from my lab at TSL. Hope people stick around till the end (though a few already warned me they’re leaving early 😅)!

Tatsuya Nobori @tatsuyanobori.bsky.social · Jan 8

New year, new paper! Now published in @nature.com. We identified and characterised diverse immune cell states in plants under pathogen attack. My postdoc work in the Ecker lab at @salkinstitute.bsky.social. A thread (0/n)
#PlantScience
www.nature.com/articles/s41...

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Facundo Romani @fromani.bsky.social · Jul 21

New Pre-print! A long-standing question for transcription factor biology is how their chromatin context dependency works in plants. In this collaboration with Fred Berger lab, we present some new ideas not only in Arabidopsis but also in Marchantia. www.biorxiv.org/content/10.1...

Conservation of chromatin states and their association with transcription factors in land plants

The complexity of varied modifications of chromatin composition is integrated in archetypal combinations called chromatin states that predict the local potential for transcription. The degree of conse...

www.biorxiv.org

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Rebecca Berrens @rberrens.bsky.social · Jul 16

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...

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...

doi.org

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Andy Plackett @seedrevolutionlab.bsky.social · Jul 10

I have a Postdoctoral Research Fellow position starting in January to study the evolution of seed gene networks using the fern Ceratopteris! Interested? More info here:
www.jobs.ac.uk/job/DNU179/r...

Closing date 31st July. 🙂
#PlantScience
#PlantSciencejobs

Research Fellow (Postdoctoral) at University of Birmingham

An opportunity for an academic position as a Research Fellow (Postdoctoral) is available, as advertised on jobs.ac.uk. Apply now and explore other academic job openings.

www.jobs.ac.uk

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Reposted

Mary Williams @PlantTeaching @plantteaching.bsky.social · Jun 7

I’m sharing my very personal story to encourage everyone to participate in and celebrate Pride month. All our voices are needed to protect diversity and support the queer community. #PRIDEmonth 🌈.
rootandshoot.org/forever-prid...

Inclusive pride flag, showing the rainbow flag with the trans flag and brown and black stripes to represent racial diversity.

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Alexandre Marand @marand-lab.bsky.social · Apr 17

Grateful to share that our study on "The genetic architecture of cell type–specific cis regulation in maize" is now published in @science.org! Huge thank you to all co-authors and the 4 tough, but fair, reviewers who all helped to improve the study 🌽🧬 www.science.org/doi/10.1126/...

The genetic architecture of cell type–specific cis regulation in maize

Gene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, ...

www.science.org

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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 12

Thanks Max!! 😁😁

jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 10

A putative 4mC methyltransferase is found in rotifers (N4CMT) that's also thought to have arisen through horizontal gene transfer from bacteria which we talk about briefly in the paper. Wouldn't be surprised if there are others examples out there to be found!

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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 10

Thanks Jake!! 😄

jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 10

Thanks Sean!! 😁😁😁

jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 10

Thanks Li! 😎

jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 10

Thanks Tatsuya!! :)

jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

#DNA #methylation #4mC #epigenetics #germline #Marchantia #sperm #fertility #chromatin #reproduction #plantbiology #evolution

jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

This work completes a story that started with strange bisulfite-seq anomalies during my PhD and ends with the discovery of a new epigenetic layer in eukaryotic reproduction.
Huge thanks to all co-authors, collaborators, and especially Xiaoqi Feng for guidance throughout.
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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

In summary, our study establishes:
4mC is a functional DNA modification in eukaryotes
MpDN4MT1a is a eukaryotic 4mC writer
5mC and 4mC mark distinct chromatin domains in sperm
4mC coordinates transcriptional shutdown, chromatin compaction, sperm motility, and fertility
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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

We also propose that 4mC could act as a paternal imprint—for example, guiding PRC2 targeting after fertilization. This may explain why loss of paternal 4mC reduces embryo viability and disrupts development.
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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

Why deposit 4mC in Marchantia sperm?
We see no evidence of dual-modified 4,5mC, suggesting that 5mC blocks 4mC. This creates a clear division: 4mC marks genes, 5mC marks repeats.
This allows global methylation for compaction while preserving the TE-specific 5mC signature.
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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

The motility defect is rescued by reintroducing wild-type MpDN4MT1a.
By contrast, sperm from global 5mC mutants show none of these distinctive phenotypes.
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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

We now know that 4mC is essential for multiple aspects of sperm function.
Sperm lacking 4mC are motility-defective, outcompeted by wild-type sperm, and produce developmentally compromised embryos.
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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

By contrast, transcripts for key sperm function genes—like CENTRIN1 and DYNEIN LIGHT CHAIN 7—are reduced, likely due to a dilution effect, helping explain the sperm motility defect in 4mC mutants.

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jameswalker303.bsky.social @jameswalker303.bsky.social · Apr 9

ATAC-seq shows widespread open chromatin in mutants—especially where 5mC is absent at transcription start sites.
Careful RNA-seq analysis uncovered globally elevated expression. As a result, the mutant transcriptome resembles wild-type spermatids before 4mC is established!
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