Author | Lightnews

Reposted by Thomas Blein

bioRxivpreprint @biorxivpreprint.bsky.social · 4d

plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters https://www.biorxiv.org/content/10.1101/2025.10.28.683968v1

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Reposted by Thomas Blein

Molecular Plant & Plant Communications @mplantpcom.bsky.social · Jun 25

From non-coding to chromatin regulators: VIVIpary and the rise of lncRNAs in plant biology #spotlight #MolecularPlant cell.com/molecular-pl...

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Reposted by Thomas Blein

Molecular Plant & Plant Communications @mplantpcom.bsky.social · Sep 11

Long noncoding RNAs as molecular architects: Shaping plant functions and physiological plasticity #review #MolecularPlant cell.com/molecular-pl...

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Thomas Blein @bleinthomas.bsky.social · 11d

Interested in #lncRNA and #ArtificiaIntelligence?
In the frame of our recently founded French-Korean bilateral project DHARP, we are recruiting a post-doc in bioinformatics and artificial intelligence in our team at
@ips2parissaclay.bsky.social
Application limit: 01/12/2025

PostDoc position in bioinformatics and artificial intelligence. PDF available upon request.

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Thomas Blein @bleinthomas.bsky.social · 15d

New academic year and we are lucky to host two new PhD students in our group at @ips2parissaclay.bsky.social. Welcome Laura and Valentin!

funrna.org/post/2025-10...

FunRNA Team Welcomes two new PhD students this Fall: Laura Chabes Pereira and Valentin Bourdin | FunRNA team

The FunRNA team is growing! We are excited to welcome Laura Chabes Pereira and Valentin Bourdin, two talented new PhD students whose research will expand our exploration into the world of long non-cod...

funrna.org

Thomas Blein @bleinthomas.bsky.social · 15d

We were very happy about your stay and the nice exchanges. Next time in Chile!

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Reposted by Thomas Blein

Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · Aug 22

Have a look to the new study from the Frugier team at IPS2, about the sTDIF signaling peptide that modulates the root stele diameter and primary metabolism to accommodate symbiotic nodulation. ips2.u-psud.fr/en/articles/... #PlantScience

Model describing the promoting effect on symbiotic nodulation of TDIF signaling peptides through increasing the root stele diameter and adapting the primary metabolism

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Reposted by Thomas Blein

Millennium Science @mscience.bsky.social · Aug 20

Check out the open access paper here: www.nature.com/articles/s41...

A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle - Nature Plants

This study presents an extensive single-nucleus and spatial transcriptomic atlas of the Arabidopsis life cycle that represents ten distinct developmental time points inclusive of six diverse organs.

www.nature.com

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Reposted by Thomas Blein

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Aug 20

Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...

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Amelia Cervera 🍉 @ameliacervera.bsky.social · Aug 20

The histone variant H3.14 is an early player in the abiotic stress response of Arabidopsis.

#PlantScience 🌾🧪

www.sciencedirect.com/science/arti...

The histone variant H3.14 is an early player in the abiotic stress response of Arabidopsis

The combinatorial changes in DNA methylation, post-translational histone modifications, and histone variants underlie the complexity of chromatin stru…

www.sciencedirect.com

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Reposted by Thomas Blein

Nature Reviews Molecular Cell Biology @natrevmcb.nature.com · Aug 9

ICYMI: New Online! A histone variant that manages abiotic stress in plants

A histone variant that manages abiotic stress in plants

Nature Reviews Molecular Cell Biology, Published online: 06 August 2025; doi:10.1038/s41580-025-00884-7H3.14, a histone variant of unknown role, has a dual transcriptional function in the abiotic stress response in plants: activation of stress response genes and inhibition of growth genes.

bit.ly

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Reposted by Thomas Blein

Amelia Cervera 🍉 @ameliacervera.bsky.social · Aug 9

#RNAsky #RNAbiology #PlantScience 🌾🧪

Amelia Cervera 🍉 @ameliacervera.bsky.social · Aug 8

RNA elements and their biotechnological applications in plants.

nph.onlinelibrary.wiley.com/doi/full/10....

RNA elements and their biotechnological applications in plants

Engineering of plants for improved traits and efficient heterologous protein production can be achieved by modifying or introducing cis- or trans-acting RNA elements. The function of these elements d...

nph.onlinelibrary.wiley.com

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Reposted by Thomas Blein

in silico Plants @insilicoplants.bsky.social · Aug 6

PhD Position: Root System Architecture and Plant Adaptation to Climate Change at the Institute of Plant Sciences of Montpellier (IPSiM) and the PhenoMEn team at the Amélioration Génétique et Adaptations des Plantes méditerranéennes et tropicales (AGAP)
#PlantSciJobs

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Reposted by Thomas Blein

Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · Jul 28

New in @natbiotech.nature.com: a team led by scientists at MSK and ‪University of Toronto have developed a new platform to facilitate the study of RNA-biding proteins (RBPs) across hundreds of species of plants, insects, and animals.

A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function - Nature Biotechnology

RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

www.nature.com

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Reposted by Thomas Blein

RNA Society Journal @rnajournal.bsky.social · Jul 29

Only 3 out of 9 tools for detecting protein-coding sequences beat a naive baseline — popular methods often fail on real data. #genomics #bioinformatics #lncRNA bit.ly/3GgrDD2

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Reposted by Thomas Blein

The Plant Cell @theplantcell.bsky.social · Jul 28

Best practices in plant fluorescence imaging and reporting: A primer (Kirk J Czymmek , Yoselin Benitez-Alfonso , Tessa Burch-Smith , et al) doi.org/10.1093/plce... #PlantScience

doi.org

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Reposted by Thomas Blein

Vandepoele lab @vandepoelelab.bsky.social · Jul 16

We are hiring! If you have experience in plant genomics + AI, or promoter engineering + synthetic biology, check out our two open postdoc positions (computational + wetlab): www.vandepoelelab.be/Jobs please re-share RT #ERC

Jobs | Vandepoele Lab

www.vandepoelelab.be

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Reposted by Thomas Blein

Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · Jul 11

Seminar by DR Kiran Mysore , Tuesday July 22, 2025 at 11:00 a.m . in the Red Room of the teaching building : " An update on Medicago Tnt1 resources and Engineering Agrobacterium to improve plant transformation and regeneration." You are all welcome #PlantScience

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Reposted by Thomas Blein

Marc Somssich @somssich.bsky.social · Jul 7

📜 Unlocking gene regulatory networks for crop resilience and sustainable agriculture

🧑‍🔬 Richalynn Leong, Xin He, Bob Sebastiaan Beijen, @dinglab.bsky.social, et al.

📔 @natbiotech.nature.com

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantImmunity #Agronomy #PlantStress #PlantGenomics

Unlocking gene regulatory networks for crop resilience and sustainable agriculture - Nature Biotechnology

Gene regulatory networks are crucial for understanding complex gene regulation in plants and could advance crop improvement for more sustainable and climate-resilient agricultural practices.

www.nature.com

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Reposted by Thomas Blein

North American Arabidopsis Steering Committee @naascarabidopsis.bsky.social · May 15

I’m happy that our commentary is out! (It would be wonderful if this made a difference!)
In defense of funding foundational plant science academic.oup.com/plcell/artic...

In defense of funding foundational plant science

academic.oup.com

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Reposted by Thomas Blein

Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · Jul 3

Seminar by Dr Marianne Kramer , Thursday July 10, 2025 at 11:00 a.m . in the Red Room of the teaching building : " Identification of a cleaved aberrant RNA associated with the initiation of transgene silencing." You are all welcome #PlantScience

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Reposted by Thomas Blein

The Plant Cell @theplantcell.bsky.social · Jul 1

Small DNA elements can act as both insulators and silencers in plants (Tobias Jores , Nicholas A Mueth , Jackson Tonnies , Si Nian Char , et al) doi.org/10.1093/plce... #PlantScience

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Reposted by Thomas Blein

Journal of Experimental Botany @jxbotany.bsky.social · Jul 2

🧬🌱 SPECIAL ISSUE EXPERT VIEW 🧬🌱

📖 Edera & Quadrana review how the interplay between histone variants and DNA methylation is essential for cellular function in Arabidopsis thaliana, with chromatin remodeling serving as a coordinating factor.

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪

Box 1 (shortened- see paper for full legend): The schematic figure illustrates recent findings on the intimate interplay between histone variants and DNA methylation in Arabidopsis thaliana.
(A) Choi et al. (2021) and Harris et al. (2024) showed that the absence of linker histone H1 leads to a redistribution of Pol IV and Pol V from euchromatin to heterochromatin, enabling RdDM to act on the body of long heterochromatic TEs.
(B) Choi et al. (2021) offered evidence that, in the absence of H1, Pol IV is still recruited to heterochromatin even when H3K9me2 is severely reduced (h1cmt2cmt3), supporting a model where RdDM functions in a feedback loop with its own targets.
(C) Bourguet et al. (2021) described that the absence of H2A.W leads to the accumulation of H1 in heterochromatin, which reduces RdDM- and CMT2-dependent DNA methylation. This indicates that H2A.W regulates H1 accumulation in heterochromatin.

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Reposted by Thomas Blein

Dave Shechner @shechnerlab.bsky.social · Jun 30

Hello! Ever wonder what's "talking to" your favorite transcript, but were too scared to ask? In our review in @cp-cellreports.bsky.social, @mardakheh.bsky.social and I highlight new RNA-focused tools for discovering RNA interactions across organizational scales. Checkit!

tinyurl.com/ydn6e3ac

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Reposted by Thomas Blein

Journal of Experimental Botany @jxbotany.bsky.social · Jul 1

🌱🧬 SPECIAL ISSUE REVIEW 🌱🧬

Tremblay & Qüesta discuss how examining the seed-to-seedling transition can reveal how non-coding RNAs and epigenetic changes regulate transcription during developmental transitions.

🔗 doi.org/10.1093/jxb/...

#PlantScience 🧪 @jiquesta.bsky.social‬

Figure 2 (shortened, see paper for full legend): Long non-coding RNAs participate in both activation and repression of genes preventing germination. (A) Under red and far-red light conditions, phytochrome B (phyB) promotes accumulation of the HIDDEN TREASURE 1 (HID1) lncRNA in the radicle of germinating seeds to repress transcription of genes which slow germination. For the repressor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3), HID1 RNA directly interacts with the chromatin in its promoter region, repressing transcription. For other genes such as the ABA biosynthesis gene 9-CIS-EPOXYCAROTENOID DIOXYGENASE (NCED9), HID1 not only interacts with the chromatin in its promoter region, but also with the histone methylase ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7) to suppress its ability to deposit the activating gene body mark H3K4me3, thus reducing transcription of NCED9. (B) Transcription of the dormancy-promoting gene DELAY OF GERMINATION1 (DOG1) is induced and repressed by different lncRNAs.

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