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fabiogomezcano.bsky.social @fabiogomezcano.bsky.social · 20/09/2026

🚨How many reads in a single-cell barcode come from that cell? 🚨 We loaded maize and Arabidopsis nuclei into separate wells of the same scifi-ATAC plate. Arabidopsis barcode averaged 73% maize reads, yet standard QC looked normal! New preprint 🧵 biorxiv.org/content/10.6... 1/10

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Alexandre Marand @marand-lab.bsky.social · 17/09/2026

🚨New preprint🚨 from super postdoc, @fabiogomezcano.bsky.social, on modeling and removing ambient contamination (i.e. nuclei-free chromatin 🧬) in single-cell scifi-ATAC-seq experiments using his new tool, AmbientMapper. Feedback is welcome! www.biorxiv.org/content/10.6...

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Alexandre Marand @marand-lab.bsky.social · 26/08/2026

Congratulations to the team @fabiogomezcano.bsky.social, Andrew Luo, and Mark Minow for their enormous effort. We appreciate any feedback or insights the community is willing to offer. 10/10

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Joe Gage @joegage10.bsky.social · 27/08/2026

New preprint 1 of 3! GxE is everywhere, but what causes it at the molecular level? @skdeb.bsky.social led this project using allele-specific expression in a B73xMo17 hybrid to test whether sequence variation changes TF binding & drives cis-reg GxE in gene expression. www.biorxiv.org/content/10.6...

biorxiv.org

Cis-regulatory variation and transcription factor binding contribute to allelic genotype-by-environment interactions for gene expression in maize

Genotype-by-environment interactions (GxE), or differences in how genotypes perform across varying environments, are a pervasive source of phenotypic variation and underlie differences in local adapta...

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bioRxivpreprint @biorxivpreprint.bsky.social · 21/08/2026

Cell-type-specific regulatory variation shapes maize heterosis www.biorxiv.org/content/10.64898/20…

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Plant Cell Atlas @plantcellatlas.bsky.social · 21/05/2026

The Application deadline for the SynBio Hackathon has been EXTENDED until June 8, 2026! Apply Now Here: www.plantcellatlas.org/2026-synbio-... *Participants will be reimbursed up to $800 for travel and lodging costs.

Poster for "The Plant Cell Atlas 2026 Synthetic Biology Hackathon" at MIT, July 12-13, 2026. Green leafy background, application deadline June 8, 2026.

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Plant Science Spotlight @plant-sci.bsky.social · 22/05/2026

🌾✂️Testing >30,000 promoter mutations in sorghum. A ~500 bp core region is key.Some edits boosted protein >30fold. Precise, nontransgenic crop improvement through cis‑regulatory editing @savagecatsonly.bsky.social @evangroover.bsky.social @ucberkeleyofficial.bsky.social www.nature.com/articles/s41...

nature.com

Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression - Nature Biotechnology

Variant mapping of sorghum promoters identifies CRISPR-accessible mutations that upregulate gene expression.

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Alexandre Marand @marand-lab.bsky.social · 23/05/2026

Plants are unique in that single somatic cells have the remarkable potential to dedifferentiate and regenerate entirely new plants. However, the cell types and regulatory dynamics enabling dedifferentiation competence have not been fully explored... until now ⬇️ (1/12)

Scientific figures illustrating protoplast molecular and cellular phenotypes

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Joram Dongus @drdongus.bsky.social · 14/04/2026

New bioRxiv preprint!🌱 We found the SAUERKRAUT transposon to regulate the floral transition in a salt-dependent manner!🧂 A step toward salt-tolerant crops in a changing climate!🌞🥬 🔗 doi.org/10.64898/202... #PlantScience #SaltStress #ClimateChange @pph-wur.bsky.social @christatesterink.bsky.social

Salt stress alters plant development, including the floral transition, but regulation of timing of flowering by salt is poorly understood at the molecular level. To identify genetic loci regulating the floral transition under high soil salinity, we performed a genome-wide association study (GWAS) in Arabidopsis thaliana and identified natural variation at the UGT74E1-UGT74E2-BT3 (UUB) locus that correlates with bolting time specifically in response to salt stress. Genetic analysis revealed BT3 as a novel repressor of the floral transition in control conditions. Similarly, the putative IBA glycosylases UGT74E1 & UGT74E2 delay the floral transition in control conditions. Furthermore, we identified that IBA homeostasis regulators TOB1 and ECH2/IBR10 play a key role in the floral transition, and that ECH2/IBR10 are required for the early flowering phenotype of the ugt74e1/ugt74e2 double mutant, indicating that UGT74E1 & UGT74E2 delay flowering by altering IBA homeostasis. A pangenome analysis of the UUB locus revealed variation in the occurrence of the DNA transposon SAUERKRAUT (SKRT). CRISPR-mediated SKRT deletion in Col-0 affected gene expression both within and outside the UUB locus and caused a salt-dependent delayed floral transition. The delayed bolting phenotype of the skrt-2 mutant also depends on ECH2/IBR10 function, indicating that SKRT accelerates the floral transition by altering IBA homeostasis. Finally, targeted demethylation of SKRT resulted in delayed floral transition under salt stress. Taken together, our data show a role for SKRT and its DNA methylation levels in the salt-dependent bolting time response in Arabidopsis, revealing a novel molecular mechanism to control flowering in adverse conditions.

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