Guillaume Hummel 🌱 🇪🇺 🇫🇷 🥨 🇮🇹
@guillaumehummel
RNA biologist and physiologist studying how plants regulate the expression of invasive and foreign DNA elements, and how this regulation shapes tissue identity IBMP-CNRS, University of Strasbourg
Yes, Marchantia polymorpha is included in the dataset. We cannot identify obvious gap-inference for this species as you can see below (distinct centromere type?). As said, it works well for angiosperms for instance.
This works particularly well in angiosperms, where tRNA gene dispersal is highly ordered. It could help compare centromere organization across species and explore how different centromere configurations evolved in plant genomes.
🔎 Want to explore how #tRNA genes are organized across 🌱 plant genomes yourself? We built ShinytRNA: a new @ibmp-cnrs.bsky.social interactive web app that standardizes the metrics used in this study 🛠️💻 📊 Try it here now: nebula.ibmp.unistra.fr/shinytRNA/
16) This brings us to the last Figure 5, and to what I see as one of the little gems of this manuscript. If clusters locally disrupt the otherwise ordered dispersion of tRNA genes, the next question is: what are these clusters made of?
12) Figure 4 shows that tRNA genes follow a surprisingly ordered chromosomal organization. In land plants, distances between neighboring tRNA genes are relatively homogeneous, suggesting evolutionary constraints on their dispersion.
7) Figure 3 moves from copy number to regulation. We asked whether tRNA genes carry conserved regulatory signals around the precursor tRNA sequence, especially motifs linked to RNA polymerase III transcription.
5) Figure 2 shows one of the most striking results: total tRNA gene number varies enormously across species. But the relative abundance of tRNA families remains surprisingly conserved!
4) The study spans algae, bryophytes, lycophytes, gymnosperms, angiosperms, and non-plant eukaryotes. A broad evolutionary view to ask: what is conserved, and what is lineage-specific?
The first experiment that led me to propose this idea was a comparative incubation of in vitro-transcribed tRNAs and endogenous total tRNAs with enzymatic extracts prepared from siliques, an organ in which RNases T2 accumulate prominently during senescence.
Figs and berries in season, butterfly in motion — the trésors du jardin never disappoint! #GardenVibes #Alsace 🥨
I am honoured to share that my postdoctoral work is now out in The Plant Cell @theplantcell.bsky.social ! doi.org/10.1093/plce...
A garden in full swing! Everything’s alive and buzzing. Loving this joyful abundance in every corner 🌱 #Alsace 🇫🇷🥨 #GardenVibes #SpringBurst #NatureLovers #BackyardBuddies
A piece of home in Alsace. Where my passion for plants took root — and still grows.
Spring is blooming on the Strasbourg campus! 🌸✨ @unistra.fr
Celebrating family today! 🎉 My grandfather Robert was honored by the town of Thann for 37 years of commitment to Alsatian beekeeping and biodiversity. So proud of him! 🐝🌿 #Inspiration
21) Finally, bringing the dual reporter system in syy-1 background by crossing led to the abortion of EXT19-GFP-NLS accumulation in RCC and LRC tissues, while it had no effects on the accumulation of the mCherry-NLS control 🧵
20) Results showed that RCC and LRC tissues, where the SYY cluster is reactivated, are the only tissues capable of continuously accumulating the Ser, Tyr, and Pro-rich EXT19-GFP-NLS during development 🧵
18) Therefore, we looked for proteins rich in these amino acids in the A. thaliana nuclear genome. We identified a family of cell wall and secreted components named hydroxyproline-rich glycoproteins (HRGPs) 🧵
16) Surprisingly, the two approaches revealed that the reactivation of the SYY cluster in wild-type roots occurs despite elevated CG DNA methylation levels. A gain of CHH methylation is observed in the columella and indicates a relaxed chromatin environment and RdDM activation 🧵
15) We sought to decipher how the reactivation of the SYY cluster in roots correlates with DNA methylation levels. Chop-PCR assays were designed to sensitize mC variations together with bisulfite-seq data reanalysis. The experimental design was validated using the ddm1 mutant 🧵
12) By stably agro-transforming in the syy-1 background either a SYY repeat (1xSYY) or a tyrosine tDNA engineered for high and constitutive expression as a control, we were able to demonstrate that SYY cluster tDNAs are functional loci 🧵
11) Then, using whole-mount in situ hybridizations, we precised that the root cap columella (RCC) and lateral root cap (LRC), two protective tissues of the meristem, are the main expression sites of the SYY cluster 🧵
10) We confirmed that the SYY cluster is indeed the genomic region responsible for this developmental expression pattern via its deletion with the CRISPR/Cas9 technology. We obtained two alleles named syy-1 and syy-2 🧵