Zeynep Baharoglu

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TF...

Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq | Nature Genetics www.nature.com/articles/s41...

Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station - Scientific Reports Scientific Reports - Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station

New species from space 🦠💫Genomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station www.nature.com/articles/s41...

A new family of ribosome hibernation factors in Archaea Ribosome hibernation preserves translation machinery during stress, yet its mechanisms in Archaea remain poorly defined. Here we identify Hib, a previously unrecognized family of archaeal hibernation ...

Ribosome hibernation in archea #microsky #ribosome 💫 www.biorxiv.org/content/10.1...

RNase Y + Y-complex initiate rRNA cleavage in B. subtilis, shrinking ribosome pools under stress while ppGpp limits synthesis. => Dual control -> better fitness. Bonus: Y-complex includes YmcA doi.org/10.1101/2025.06.27.661978

#MicroSky OLD amputates the anticodon arm of tRNAs during P2–Lambda interference #PhageSky #RNASky 🧪

"Figure 8. Proposed model"

Mycobacterial TrmI (m¹A58) is linked to aminoglycoside tolerance. Ribosomes stall in an alanine-rich region that controls whiB7, and trans-translation increases this stalling, keeping WhiB7 active and helping mycobacteria survive antibiotic stress.🦠#rnasky => preprint www.biorxiv.org/content/10.1...

tRNA-modifying enzymes in bacterial stress adaptation | Open Biology Transfer RNAs (tRNAs) and their modifications are central to bacterial translation and physiology, yet their roles in stress adaptation remain underexplored. While extensively studied in eukaryotes, a...

Happy to share our new review in Royal Society Open Biology 🎉
tRNA-modifying enzymes in bacterial stress adaptation:
How tRNA mods rewire translation under oxidative + antibiotic stress (MoTTs, moonlighting, therapy angles).
Read: doi.org/10.1098/rsob...
#RNAsky #microsky #AMR #RNAmodifications

Dual CRISPRi-seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle Dénéréaz et al. introduce dual CRISPRi-seq, a broadly applicable method to chart gene-gene interactions across whole genomes. Applying it to the pathogen Streptococcus pneumoniae, they uncovered over ...

And the crispri genetic interaction screen 👏💫🤯 #microsky from J-W Veening lab. Dual CRISPRi-seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle: Cell Systems www.cell.com/cell-systems...

📰 RNA Modifications Newsletter – October 1st, 2025 issue #4

New RNA Modifications Newsletter (October) is out! 🚀 open.substack.com/pub/rnamodif...

Check out the first preprint from our lab describing a direct molecular cross-talk between (p)ppGpp and c-di-GMP nucleotide messengers! Great work from first-author Corentin Jaboulay who was a postdoc in our lab, and great collaborations! @mmsb-lyon.bsky.social @cnrsbiologie.bsky.social

Staggering analysis here linking ciprofloxacin resistance to specific mutations in #Klebsiella.

In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below).

Loving the splitting of MIC and disk diffusion data as well.

#AMR #MicroSky #IDSky

With Chloramphenicol used here as a readout

''including ORFs within tRNA loci.'' 🤷🏻‍♀️🧐 study detects significant ORF hits at 10 distinct tRNA loci under high chloramphenicol selection 🦠

www.science.org/doi/10.1126/... 🦠 #AMR

Synthetic lethal TN-seq! #microsky 🦠

Cold shock adaptation and ribosomal RNA modifications 🦠#rnasky www.biorxiv.org/content/10.1...

Vibrio2026: The International Meeting on the Biology of Vibrios Fourwaves - Vibrio2026: The International Meeting on the Biology of Vibrios

Delighted to announce that The International Meeting on the Biology of Vibrios will be back next year!

Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists!

event.fourwaves.com/vibrio2026/p...

Expanding the genetic toolbox of the obligate predatory bacterium Bdellovibrio bacteriovorus with inducible gene expression and CRISPR interference Inducible gene expression and CRISPR interference-mediated depletion in the predatory bacterium Bdellovibrio bacteriovorus.

🚨New paper out! #MicroSky
Studying obligate predators like Bdellovibrio bacteriovorus is tricky—essential genes for predation are also essential for survival.
We expanded its genetic toolbox:
🧬promoters to fine-tune expression
🧬IPTG-inducible system
🧬CRISPRi for rapid knockdown
bit.ly/46GUn2c
1/4

Two microbiome metabolites compete for tRNA modification to impact mammalian cell proliferation and translation quality control - Nature Cell Biology Zhang, Lahry, Cipurko et al. show that the microbial metabolites queuine and preQ1 modify the same host tRNA. PreQ1-tRNA reduces cell proliferation, slows tumour growth, decreases the translation of r...

Two microbiome metabolites compete for tRNA modification to impact mammalian cell proliferation and translation quality control #rnasky www.nature.com/articles/s41...

Thanks Olivier ! Happy to read this :)

✨ RNA Modifications Newsletter – September 15, 2025 issue #3

🧬 Fresh RNA modifications newsletter out now: viral tRNA hijacking, hidden rRNA mods, dynamic Ψ, antibiotic resistance & more.

👉 open.substack.com/pub/rnamodif...

#RNAsky #Epitranscriptomics #microsky #ribosome

Ribosomal RNA tentacles are targets of free radical damage in mammalian cells during oxidative and inflammatory stress Chemical damage to ribosomal RNA (rRNA) during oxidative or inflammatory stress can impact protein synthesis. Human cells were exposed to a H2O2 titration series to induce oxidative stress or to tumor...

Ribosomal RNA tentacles are targets of free radical damage in mammalian cells during oxidative and inflammatory stress #ribosome #rnasky www.biorxiv.org/content/10.1...

Idiosyncratic evolvability among single-point ribosomal mutants towards multi-aminoglycoside resistance Author summary Identifying features that predict an organism’s ability to evolve (evolvability) is highly desirable in fundamental and applied microbial genetics. Here we show that outstanding dispari...

Idiosyncratic evolvability among single-point ribosomal mutants towards multi-aminoglycoside resistance 🦠 #ribosome dx.plos.org/10.1371/jour...

WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing Abstract. Transfer RNA (tRNA) plays an essential role in protein translation, and tRNA modifications are important to their function. Recently, nanopore di

WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing #rnasky💫👏 academic.oup.com/nar/article/...

Thank you Jonathan 🙏

Thank you David! 🙏

Thank you so much 🙏

Thank you 🙏🌸