Pratheek Pandesha

We’re #hiring a #postdoc @ucriverside.bsky.social 🌿
Work on cis-regulatory evolution, gene family diversification, and cell-type-specific climate responses using single-cell and comparative genomics - kenchanmanelab.com/research/

Deadline: Feb 5, 2026
Apply: aprecruit.ucr.edu/apply/JPF02058

Genome Position Does Not Impact Transgene Expression Efficiency in the Ancient Red Alga Cyanidioschyzon merolae https://www.biorxiv.org/content/10.64898/2026.01.31.703004v1

RNA decay via the nuclear exosome is essential for piwi-mediated transposon silencing https://www.biorxiv.org/content/10.64898/2025.12.16.694471v1

Intrigued by a long-standing conundrum in small RNA biology—how nuclear Argonaute proteins silence transposons when they *need* target transcription for their own recruitment—we studied the piRNA pathway.

And found a hidden RNA-decay axis from Piwi to the RNA exosome.

Excited about the future of plant epigenetics?
Join us at the Keystone Symposium Plant Epigenetics & Epigenome Engineering in Fort Collins, October 13-16, 2025! keystonesymposia-19559593.hs-sites.com/%F0%9F%8C%BF...
Registration is open!
#PlantScience #Epigenetics #KeystoneSymposia

Have you ever wondered how new DNA methylation patterns are established?

Paradigm shift ahead! We discovered a new mode of DNA methylation targeting in plants that relies on transcription factors and sequence motifs rather than chromatin modifications to regulate the methylome. rdcu.be/eQ6L5
1/8

Transcription factor-mediated recruitment of small interfering RNA production - Nature Plants Decades of research in plants has established that the protein complexes that transcribe small interfering RNAs (siRNAs) are not targeted to DNA in a sequence-specific manner. Two independent studies ...

And this great Nature Plants News & Views by Pandesha and Slotkin covering this breakthrough discovery
www.nature.com/articles/s41...
@hadse.bsky.social @KeithSlotkin @natplants.nature.com
8/8

Excited to release BoltzGen which brings SOTA folding performance to binder design! The best part of this project is collaborating with a broad network of leading wetlabs that test BoltzGen at an unprecedented scale, showing success on many novel targets and pushing the model to its limits!

50,000 years of evolutionary history of India: Impact on health and disease variation A genomic study of 2,762 individuals from India offers important insights into the genomic diversity and evolutionary history of the subcontinent and highlights the extensive genetic variation, gene f...

Our paper out today: 50,000 years of evolutionary history of India: Impact on health and disease variation: Cell www.cell.com/cell/fulltex...

It’s back! Our annual night of fun and fundraising, Party with the Plants, is September 26. 🌺 Theme is “Plants in Paradise.” 🍍 Discounted tickets on sale now: bit.ly/4kXoRSn
#STLEvents #PartyWithThePlants

Spearhead Bio, a Danforth Technology Company startup, has received a grant from NSF that will allow them to fast-track their breakthrough genome engineering technology to develop corn varieties equipped for ag’s biggest challenges. Read more: https://loom.ly/zHfitlo

T-DNAreader: fast and precise identification of T-DNA insertion sites in plant genomes using RNA sequencing data - Genome Biology Agrobacterium-mediated plant transformation, which enables the delivery of DNA using transfer DNA (T-DNA) binary vectors, is an essential technique in plant research. T-DNAs randomly integrate into th...

Very useful tool to map TDNA insertion site using RNAseq data

genomebiology.biomedcentral.com/articles/10....

Has anyone tried RUBY in a fungus?

Nice preprint! Structure of AVRcap1b from Phytophthora reveals a novel fold, and structural effector family. AVRcap1b targets the helper NLR NbNRC2. #plantimmunity

www.biorxiv.org/content/10.1...

Franklin W. Stahl, 95, Dies; Helped Create a ‘Beautiful’ DNA Experiment

As an undergraduate who loved physical chemistry and was just starting biology, I thought the Meselson-Stahl experiment was the coolest thing ever. It was so simple in its application of physical theory and experiment to prove a biological truth that it was perfect. www.nytimes.com/2025/07/07/s...

The histone acetyltransferase GCN5 regulates floral meristem activity and flower development in Arabidopsis (Amangul Hawar , Wei Chen , Tao Zhu , Xin Wang , Jiaxin Liu , Shiqi Xiong , Toshiro Ito , Dijun Chen , Bo Sun) doi.org/10.1093/plce... #PlantScience

snRNA-seq analysis of the moss Physcomitrium patens identifies a conserved cytokinin-ESR module promoting pluripotent stem cell identity Pluripotent stem cells in the apical meristem have been a key innovation that allows plants to flourish. Hata et al. identified transcriptomic characters of a pluripotent stem cell in Physcomitrium pa...

Cytokinin-ESR module promoting pluripotent stem cell identity in moss.

From: www.cell.com/developmenta...

🧪🧵 Check out this preprint dealing with one of my favorite gene families:
✨✨the Reproductive Meristem (REM) transcription factor family!✨✨
REMs are B3 TFs just like ARFs or RAVs but they are much less studied than their other B3 “cousins”. 1/4

Amazing. First cell cycle, then DNA methylation (paper/preprints posted somewhat recently), now sex determination. A class of TF that definitely needs more love.

a maize shoot apical meristem labeled with a plasma membrane marker fused to cyan fluorescent protein

maize shoot apical meristems are the cutest! 😍
plasma membrane labeled with PIP2A-CFP

Fig. 1. (short legend see paper for full description): Null met1-1 mutants cannot be produced by crossing TILLING lines with disruptions in the three MET1-1 homoeologues. (A) Evolutionary relationships between MET1 homologues in Arabidopsis (AtMET1), rice (OsMET1a and OsMET1b), and wheat (homoeologue groups TaMET1-1, TaMET1-2, and TaMET1-3). (B) Crossing schematic showing the generation of the hexaploid MET1-1 populations: the C0465×C0884 population (top) and the C0451×C2028×C1292 population (bottom). (C) Structure of the three MET1-1 homoeologues. Filled rectangles represent exons, open rectangles represent untranslated regions, and lines represent introns. Triangles indicate the positions of the premature termination codon mutations in the TILLING lines used to produce the two hexaploid F2 populations (C0465×C0884, orange; C0451×C2028×C1292, purple). The green box signifies the Bromo adjacent homology domain (BAH) and the blue box signifies the C-5 cytosine methyltransferase domain.

🌾🧬 SPECIAL ISSUE RESEARCH 🌾🧬

📝 Varying gene dosage through mutating DNA methyltransferase 1-1 (MET1-1 ) in polyploid wheat generates quantitative changes to CG methylation without the lethal consequences observed in other crops - Burrows et al.

🔗 doi.org/10.1093/jxb/...
#PlantScience 🧪

Transcription factors instruct DNA methylation patterns in plant reproductive tissues DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail ...

Here it is!

www.biorxiv.org/content/10.1...

REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes - Nature Cell Biology Wu et al. demonstrate that REM transcription factors and GDE1 guide RNA polymerase IV to specific genomic loci, establishing a DNA sequence-dependent mechanism for siRNA biogenesis and DNA methylation...

Transcription factors targeting RNA-directed DNA methylation machinery in Arabidopsis reproductive tissues.

From: www.nature.com/articles/s41...

I think I saw another preprint on this by another lab too.

Joanna Friesner- NAASC- honored for her support of the Arabidopsis community #ICAR2025

Assistant Professor - Genetics, Genomics, Evolution and Development - Department of Molecular and Ce... University of California, Berkeley is hiring. Apply now!

Our department mcb.berkeley.edu is soliciting applications for an Assistant Professor position studying fundamental aspects of genetics, genomics, evolution, and/or developmental biology. Bring it on! aprecruit.berkeley.edu/JPF04110

I've 4 invite codes and would love to recruit some #plantscience folks. Pass it on!

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler https://www.biorxiv.org/content/10.1101/2023.08.31.555833v1 Genomic imprinting is observed in endosperm, a placenta-like seed tissue, where transposable element

Upstream regulator of genomic imprinting in rice endosperm is a small RNA-associated chromatin remodeler https://www.biorxiv.org/content/10.1101/2023.08.31.555833v1

I'm writing up the @root-shoot.bsky.social Inclusive Conferences Working Group efforts to date & next steps.
Q for #PlantScience community.
What in your opinion / experiences are biggest barriers to inclusion + belonging at meetings, & how to remedy?
We've got funds to put towards this objective!

In addition to the updated manuscript, we have expanded our online browser to enable the viewing of all transcripts detected in each of our single-nucleus RNA-seq datasets!

arabidopsisdevatlas.salk.edu

BlueSky for Scientists BlueSky for Scientists Authors: Steve Haroz and Mark RubinURL: http://blueskyscience.steveharoz.com Features you may miss from Twitter or Mastodon As BlueSky is in beta, some features are not impleme...

Scientist?

New to BlueSky?

Trying to figure out what the hell a "feed" is and why hashtags aren't working the same as on Twitter?

Check out this quick start guide by @steveharoz.com and me 👇