Thomas Blein

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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

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.

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.

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

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

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

DR Kiran Mysore

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

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.

📜 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

In defense of funding foundational plant science

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...

Dr Marianne Kramer

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

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

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.

🧬🌱 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 🧪

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

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.

🌱🧬 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

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.

📜 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

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 ...

📜 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

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

Looking for regulatory features in your RNA? (Tool made for non-plant species)

academic.oup.com/nar/advance-...

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 👇

Root expansion microscopy: A robust method for super resolution imaging in Arabidopsis (Magali S Grison , Guillaume Maucort , Amandine Dumazel , Dorian Champelovier , Yutaro Shimizu , Yohann Boutté , Mónica Fernández-Monreal , Emmanuelle M Bayer) doi.org/10.1093/plce... #PlantScience

Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster in Solanaceae | PNAS Biosynthetic gene clusters (BGCs) are sets of often heterologous genes that are genetically and functionally linked. Among eukaryotes, BGCs are mos...

Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster in Solanaceae

From: www.pnas.org/doi/10.1073/...

#PlantScience #SecMet

Construction of multi-targeted CRISPR libraries in tomato to overcome functional redundancy at genome-scale level - Nature Communications Genetic variance is vital for breeding programs and mutant screening, yet traditional mutagenesis methods wrestle with genetic redundancy and a lack of specificity in gene targeting. Here the authors ...

📜 Construction of multi-targeted CRISPR libraries in tomato to overcome functional redundancy at genome-scale level

🧑‍🔬 Amichai Berman, Ning Su, Yuqin Zhang, @eilonshani.bsky.social, et al.

📔 @natcomms.nature.com

🔗 www.nature.com/articles/s41...

#️⃣ #PlantScience #PlantTools #Tomato #PlantCRISPR

Image generated via AI

Reflections from the “Plant Sciences in the Anthropocene” Workshop – Two Weeks of Conversations, Insight, & Impact

From the very 1st talk to the final wrap-up, the event was a deep dive into the challenges #plantscience faces in a changing world.

buff.ly/tKLsxQI w @spsplantsciences.bsky.social

#RNASky

plants.peercommunityin.org, new Peer Community In .. PLANTS !

Integrating Arabidopsis and crop species gene discovery for crop improvement Summary. Genome sequence assemblies form a durable and precise framework that supports nearly all areas of biological research, including evolutionary biol

📜 Integrating Arabidopsis and crop species gene discovery for crop improvement

🧑‍🔬 Michael W. Bevan, Klaus F. X. Mayer, et al.

📔 @theplantcell.bsky.social

🔗 academic.oup.com/plcell/advan...

#️⃣ #PlantScience #AppliedPlantScience #Crops #Agriculture #PlantBreeding #PlantGMOs #PlantGenomics

A comprehensive all-in-one CRISPR toolbox for large-scale screens in plants (Yanhao Cheng , Gen Li , Aileen Qi , Rushil Mandlik , Changtian Pan , Doris Wang , Sophia Ge , Yiping Qi) doi.org/10.1093/plce... #PlantScience

Figure 1 of the article.

New OA Letter: "Re-analysis of mobile mRNA datasets raises questions about the extent of long-distance mRNA communication" rdcu.be/ehZmi

A substantial number of transcripts, currently annotated as graft-mobile, lack statistical support from available RNA-seq data. #PlantScience

A comprehensive all-in-one CRISPR toolbox for large-scale screens in plants An all-in-one CRISPR toolbox is developed to aid guide RNA library-based loss-of-function and gain-of-function screens in plants.

📜 A comprehensive all-in-one CRISPR toolbox for large-scale screens in plants

🧑‍🔬 Yanhao Cheng, Yiping Qi, et al.

📔 @theplantcell.bsky.social

🔗 academic.oup.com/plcell/advan...

#️⃣ #PlantScience #PlantCRISPR #PlantMethods #PlantGenomics #PlantNGTs #PlantGE #PlantGenomeEditing

Dr. Pablo Manavella

Seminar by Dr. Pablo Manavella , Monday May 05, 2025 at 2:00 p.m. in the Amphitheater(teaching building): The coupling between transcription, processing, and transport during miRNA biogenesis . You are all welcome #PlantScience

An RNA condensate model for the origin of life The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA Wor…

An interesting perspective and framework: #RNA condensates-not individual RNAs-may have acted as replicative units in early life. RNAs in condensate recruit similar RNAs, then the condensate divides once it reaches a critical size.

#RNAsky