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Thomas Blein

@bleinthomas.bsky.social
576 followers 1.7K following 9 posts

Plant molecular biologist 🥼 / @cnrs.bsky.social researcher working at @ips2parissaclay.bsky.social (Paris-Saclay university) 🇫🇷 Interested in quantitative growth control and non-coding RNAs specialy #lncRNA 🌱🧫🧬🖥️🔬 thomas.blein.me

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Reposted by Thomas Blein
Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 27/07/2026
Theses defended in late 2025 or early 2026 ips2.u-psud.fr/en/articles/... #PlantScience
Michel, Azhin and Tao
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Reposted by Thomas Blein
Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 27/07/2026
Ancient WIP transcription factors regulate auxin-dependent development in the moss Physcomitrium patens. Their conserved function reveals an ancestral genetic toolkit that has shaped land plant evolution for over 450 million years. ips2.u-psud.fr/en/articles/... #PlantScience
Overview of gametophores in the wild-type and the wip1wip2 mutant
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Reposted by Thomas Blein
Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 23/07/2026
Have a look at the new study from the F. Frugier’s SILEG & M. Benhamed’s ChromD teams published in Plant Communications, on 3D genome reorganization during symbiotic nodulation www.cell.com/plant-commun... #PlantScience
The distal enhancer region located upstream of the NODULE INCEPTION (NIN) gene becomes accessible in response to cytokinins
ATAC-Seq signals in untreated and 1h cytokinin-treated roots. The position of the Cytokinin Element (CE) chromatin loop is indicated at the top.
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Reposted by Thomas Blein
valeriegeffroy.bsky.social @valeriegeffroy.bsky.social · 23/07/2026
Have a look at our review “Bridging paradoxes in recombination at NLR cluster: A structural genomics perspective” out in Current Opinion in Plant Biology doi.org/10.1016/j.pb...
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Reposted by Thomas Blein
valeriegeffroy.bsky.social @valeriegeffroy.bsky.social · 23/07/2026
Excited to share our paper “The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean” out in @natcomms.nature.com Huge structural variation at NLR cluster and insertion of a transposable element in the I gene leading to a natural I mutant doi.org/10.1038/s414...
doi.org
The I gene defines a dynamic NLR cluster conferring broad potyvirus resistance in common bean - Nature Communications
Potyviruses seriously affect common bean production worldwide. Here, the authors combine genome assembly and characterization of loss-of-function mutants to reveal a dynamic NLR cluster conferring dur...
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Reposted by Thomas Blein
Molecular Plant & Plant Communications @mplantpcom.bsky.social · 21/12/2025
Enhancing apple disease resistance using magnetic nanoparticles carrying artificial miRNAs that suppress a tRNA-derived small RNA targeting a disease-resistant gene #research #PlantCommunications cell.com/plant-commun...
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Reposted by Thomas Blein
Molecular Plant & Plant Communications @mplantpcom.bsky.social · 25/12/2025
PlantscRNAdb 4.0: Improved marker identification and annotation under a cell type uniformity for plants #resource #MolecularPlant cell.com/molecular-pl...
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Reposted by Thomas Blein
Journal of Experimental Botany @jxbotany.bsky.social · 31/12/2025
🧬 EXPERT VIEW 🧬 In this review, Lee & Seo highlight the hierarchical organization of plant genomes, emphasizing recent advances in understanding local chromatin structures shaped by cohesins and gene borders as fundamental structural units. 🔗 doi.org/10.1093/jxb/... #PlantScience 🧪
Box 1 (shortened, full legend in paper): Key developments in elucidating hierarchical chromatin organizations in plants
Chromosome territories
Each chromosome occupies a distinct territory within the nucleus, as evidenced by strong intra-chromosomal contacts
in a Hi-C contact map.
Large A/B compartments
Each chromosome is partitioned into large A and B compartments. The heterochromatic B compartment is usually located near the nuclear membrane, whereas the euchromatic A compartment tends to be positioned toward the inner regions of the nucleus.
TAD-like domains and compartment domains
Large A and B compartments can be further partitioned into TAD-like domains and/or compartment domains.
Yin et al. (2023) demonstrated that the Arabidopsis genome is partitioned into compartments, each with different histone modifications, including H3K4me3, H3K27me1, and H3K27me3.
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Reposted by Thomas Blein
Journal of Experimental Botany @jxbotany.bsky.social · 24/12/2025
🧬 SPECIAL ISSUE REVIEW 🧬 In this review, Lee & Seo highlight the hierarchical organization of plant genomes, emphasizing recent advances in understanding local chromatin structures shaped by cohesins and gene borders as fundamental structural units. 🔗 doi.org/10.1093/jxb/... #PlantScience 🧪
Box 1 (shortened, full legend in paper): Key developments in elucidating hierarchical chromatin organizations in plants. 
Chromosome territories

Each chromosome occupies a distinct territory within the nucleus, as evidenced by strong intra-chromosomal contacts in a Hi-C contact map.

Large A/B compartments

Each chromosome is partitioned into large A and B compartments. The heterochromatic B compartment is usually located near the nuclear membrane, whereas the euchromatic A compartment tends to be positioned toward the inner regions of the nucleus.

TAD-like domains and compartment domains

Large A and B compartments can be further partitioned into TAD-like domains and/or compartment domains.
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Reposted by Thomas Blein
The Arabidopsis Information Resource (TAIR) @tairnews.bsky.social · 22/12/2025
Meet the volunteer researchers behind #TAIR12... beginning with Emmanuel Boutet of the Swiss Institute of Bioinformatics. Please join us in expressing gratitude to everyone who contributed to this new annotation. #plantbiology #plantscience #TAIR #Arabidopsis bit.ly/4p6FagQ
phoenixbioinfo.org
Meet the volunteer researchers behind TAIR12: Emmanuel Boutet, Swiss Institute of Bioinformatics - Phoenix Bioinformatics
Over the past two years TAIR has led a community effort to reannotate the Arabidopsis thaliana genome with support from scientists like Emmanuel Boutet, a plant biocurator for the Swiss Institute of B...
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Reposted by Thomas Blein
Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 21/12/2025
AI based framework for RNA modif detection using nanopore #RNAbiology
biorxiv.org
SWARM: A Single-Molecule Workflow for High-Precision Profiling of RNA Modifications
Nanopore direct RNA sequencing promises to decode the epitranscriptome by detecting multiple modifications on individual RNA molecules, but its potential for biological discovery is hampered by high f...
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Reposted by Thomas Blein
Plantae.org @plantaeofficial.bsky.social · 18/12/2025
📅New #PlantSciEvents Event Added: SPS Summer School 2026 - "Plant single cell RNAseq workshop: From current technologies to data analyses" 👉 buff.ly/cCZZ5kq #PlantScience
buff.ly
SPS Summer School 2026 - "Plant single cell RNAseq workshop: From current technologies to data analyses"
(2026) Sun 28 Jun, 2:00 PM - Fri 3 Jul, 6:00 PM [CEST]: This Summer school is organized by the Saclay Plant Sciences (SPS) network, one of the largest European plant sciences communities. scRNAseq…
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Reposted by Thomas Blein
Blanca Jazmin Reyes-Hernandez @bjazminrh.bsky.social · 18/12/2025
📢 Online event: International Society of Root Research - Mini Symposium — Wed 28 Jan 2026, 10:00–17:00 UK (12:00–18:30 UTC). Talks + discussion for anyone into root research & related topics. @rootscientists.bsky.social @rootarchitecture.bsky.social #roots #RootResearch #PlantScience #Rhizosphere
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The Arabidopsis Information Resource (TAIR) @tairnews.bsky.social · 18/12/2025
It's our birthday! Twenty-five years ago, in December 2000, the Arabidopsis thaliana genome was published and #TAIR was born. Now, we're preparing for the release of #TAIR12 early in the new year. What a long way we've come! bit.ly/3KDJciT #plantbiology #plantscience #genomics #Arabidopsis
bit.ly
Get ready: TAIR12 is coming - Phoenix Bioinformatics
More than two years ago, TAIR took the lead in a volunteer-driven project to reannotate the Arabidopsis thaliana genome
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Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 12/12/2025
🎉 Congratulations to Leandro Quadrana (@leandroquadrana), @CNRS researcher at @IPS2ParisSaclay, for obtaining the prestigious #ERCCoG HosTEome! #ERC #Genomics #Research #AIinBiology #CNRS #UniversitéParisSaclay #PlantScience ips2.u-psud.fr/en/articles/...
Leandro Quadrana
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Molecular Plant & Plant Communications @mplantpcom.bsky.social · 28/10/2025
In vivo RNA structure influences the translation and stability of plant long noncoding RNAs #research #PlantCommunications cell.com/plant-commun...
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Reposted by Thomas Blein
Molecular Plant & Plant Communications @mplantpcom.bsky.social · 20/11/2025
A telomere-to-telomere reference genome assembly of tomato cultivar Heinz 1706 #correspondence #PlantCommunications cell.com/plant-commun...
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Reposted by Thomas Blein
Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 27/11/2025
Registrations are open for the Summer School "Saclay Plant Science" (SPS) 2026 on Plant Single Cell at Versailles ! ips2.u-psud.fr/en/articles/... #PlantScience
Summer School 2026
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Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 27/11/2025
A review from F. Frugier' team aiming at identifying the common molecular mechanisms associated to the different beneficial plant-microbe symbiotic and endophytic interactions ips2.u-psud.fr/en/articles/... #PlantScience
Plants establish beneficial interactions with both fungi and bacterial microbes that they attract from the soil rhizosphere by producing signalling molecules under conditions of nutritional deficiency. 
(A) arbuscular mycorrhizal (AM) symbiosis, (B) nitrogen-fixing rhizobial nodulation symbiosis, (C) other beneficial plant-fungi interactions, such as the ectomycorrhizal symbiosis (ECM) and the association with Trichoderma or Mucoromycotina ‘fine root endophytes’ (MFRE), (D) interactions with Plant Growth-Promoting Rhizobacteria (PGPR) Figure generated using BioRender (https://biorender.com/).
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Reposted by Thomas Blein
Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 03/11/2025
Welcome and congratulations to Bruno Guillotin on joining IPS2 as a permanent researcher! May the spirit of science always be with you and inspire your future discoveries. #PlantScience ips2.u-psud.fr/en/articles/...
Dr. Bruno Guillotin
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Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 14/11/2025
9 international PhD students, 17 partners, 1 goal: coordinated by Université Paris-Saclay, the HeatDDR Doctoral Network is training the next generation of plant scientists to boost crop resilience to heat and climate change 🌱🔥 ips2.u-psud.fr/en/articles/... #PlantScience
HeatDDR is funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them
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Reposted by Thomas Blein
bioRxivpreprint @biorxivpreprint.bsky.social · 29/10/2025
plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters www.biorxiv.org/content/10.1101/202…
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Reposted by Thomas Blein
Molecular Plant & Plant Communications @mplantpcom.bsky.social · 25/06/2025
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 · 11/09/2025
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 · 22/10/2025
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 · 18/10/2025
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.org
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...
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Reposted by Thomas Blein
Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 22/08/2025
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 · 20/08/2025
Check out the open access paper here: www.nature.com/articles/s41...
nature.com
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.
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 20/08/2025
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.eurosky.social · 20/08/2025
The histone variant H3.14 is an early player in the abiotic stress response of Arabidopsis. #PlantScience 🌾🧪 www.sciencedirect.com/science/arti...
sciencedirect.com
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…
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Nature Reviews Molecular Cell Biology @natrevmcb.nature.com · 09/08/2025
ICYMI: New Online! A histone variant that manages abiotic stress in plants
bit.ly
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.
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Amelia Cervera 🍉 @ameliacervera.eurosky.social · 09/08/2025
#RNAsky #RNAbiology #PlantScience 🌾🧪
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in silico Plants @insilicoplants.bsky.social · 06/08/2025
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
Please DM me for full text
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Memorial Sloan Kettering Cancer Center @mskcancercenter.bsky.social · 28/07/2025
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.
nature.com
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.
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RNA Society Journal @rnajournal.bsky.social · 29/07/2025
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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The Plant Cell @theplantcell.bsky.social · 28/07/2025
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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Vandepoele lab @vandepoelelab.bsky.social · 16/07/2025
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
vandepoelelab.be
Jobs | Vandepoele Lab
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Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 11/07/2025
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
DR Kiran Mysore
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Marc Somssich @somssich.bsky.social · 07/07/2025
📜 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
nature.com
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.
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North American Arabidopsis Steering Committee @naascarabidopsis.bsky.social · 15/05/2025
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...
academic.oup.com
In defense of funding foundational plant science
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Institute of Plant Sciences - Paris-Saclay (IPS2) @ips2parissaclay.bsky.social · 03/07/2025
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
Dr Marianne Kramer
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Reposted by Thomas Blein
The Plant Cell @theplantcell.bsky.social · 01/07/2025
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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Journal of Experimental Botany @jxbotany.bsky.social · 02/07/2025
🧬🌱 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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Dave Shechner @shechnerlab.bsky.social · 30/06/2025
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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Journal of Experimental Botany @jxbotany.bsky.social · 01/07/2025
🌱🧬 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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Marc Somssich @somssich.bsky.social · 18/06/2025
📜 Small DNA elements can act as both insulators and silencers in plants 🧑‍🔬 @tobiasjores.bsky.social, Christine Queitsch, et al. 📔 @theplantcell.bsky.social 🔗 academic.oup.com/plcell/advan... #️⃣ #PlantScience #PlantGenetics #PlantGenomics #PlantSynBio #PlantPromoters
academic.oup.com
Small DNA elements can act as both insulators and silencers in plants
Small DNA elements can insulate or repress transcription in Nicotiana benthamiana, Arabidopsis thaliana, maize, and rice in a context-dependent manner.
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Marc Somssich @somssich.bsky.social · 28/05/2025
📜 Hormonal regulation of primary root development 🧑‍🔬 Michela De Nittis, Mirko De Vivo, @raffolab.bsky.social, Sabrina Sabatini 📔 @cp-cellreports.bsky.social 🔗 www.cell.com/cell-reports... #️⃣ #PlantScience #RootBiology #PlantRoots #Phytohormones #Auxin #Cytokinin #PlantDevelopment
cell.com
Hormonal regulation of primary root development
Dynamic hormone networks orchestrate Arabidopsis root meristem growth. In this review, Nittis et al. highlight recent advances in how these regulatory systems shape root development and discuss their ...
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Rodrigo Reis @rodrigoreislab.com · 26/05/2025
Looking for regulatory features in your RNA? (Tool made for non-plant species) academic.oup.com/nar/advance-...
academic.oup.com
RegRNA 3.0: expanding regulatory RNA analysis with new features for motif, interaction, and annotation
Abstract. Functional RNA molecules are crucial for biological processes from gene regulation to protein synthesis, and analyzing functional motifs and elem
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Marc Somssich @somssich.bsky.social · 25/05/2025
I have created some #PlantScience resources here on Bluesky, including 𝐂𝐨𝐧𝐭𝐞𝐧𝐭 𝐅𝐞𝐞𝐝𝐬 & 𝐒𝐭𝐚𝐫𝐭𝐞𝐫 𝐏𝐚𝐜𝐤𝐬. The Feeds deliver plant science content with relevant hashtags to your timeline. The Starter Packs help you connect to other plant scientists. See this thread 🧵 for all feeds and starter packs 👇
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