Yanjie Chao
@yjchao.bsky.social
Bacterial RNA Biologist, Group Leader and Professor at Chinese Academy of Sciences, Shanghai Institute of Materia Medica (Formerly Institut Pasteur of Shanghai). Homepage: https://yanjiechao.wordpress.com
Major Chinese funder to stop paying fees for 30 pricey open-access journals | Science | AAAS www.science.org/content/arti...
Major Chinese funder to stop paying fees for 30 pricey open-access journals
Move comes amid effort to grow the country’s own journals
science.org
🚨 Group Leader Opportunity Alert! 🚀 Apply by February 15 and join us in Würzburg. ⬇️
Jens Hör@jenshoer.bsky.social · 6mo agoWe are looking for a junior group leader in RNA biology to join us in Würzburg at the @helmholtz-hiri.bsky.social ! A generous funding package, a great collaborative environment, and a beautiful city are all included :) Deadline for application is Feb 15; more information below 👇
I’m thrilled to share our work on phage triggers of the bacterial immune system in its final form @natmicrobiol.nature.com www.nature.com/articles/s41...
A phage protein screen identifies triggers of the bacterial innate immune system - Nature Microbiology
A library of 400 phage protein-coding genes is used to find a trove of antiphage systems, revealing systems that target tail fibre and major capsid proteins.
nature.com
NLR-like immunity in bacteria A new study from the Alex Gao lab. The scope of this work is incredible!!! www.biorxiv.org/content/10.6...
Diverse bacterial pattern recognition receptors sense the conserved phage proteome
Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...
biorxiv.org
Nature Microbiology turns 10! 🎂 As a special treat, we take you back to the editorial team that started it all and then fast forward to take a peek into the future of microbiology through some brilliant microbiologists. #MicroSky 🦠 www.nature.com/nmicrobiol/v...
Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
biorxiv.org
How does a bacterial small RNA evolve new functions? Our new study reveals the stepwise evolutionary journey of UhpU, a 3′UTR-derived sRNA in E. coli and relatives. It evolved from a metabolically-focused regulator to one with expanded targets and biogenesis manner. www.pnas.org/doi/10.1073/...
Check this out for the 2026 SISB (phage defense) meeting in NYC. Mark your calendar! (and note the Zoom option, if needed) sisb2026.rockefeller.edu
SISB2026
sisb2026.rockefeller.edu
Sharing the link to our updated Vibrio preprint, where we compare and contrast Ecospecies with other genetic structures, and using the opportunity to fix typos and update some bluesky handles! with @danielfalush.bsky.social @whqqq.bsky.social @yjchao.bsky.social @chaooo.bsky.social
Evolution of hunt, kill, devour in a Vibrio ecospecies
Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Coadaptation within the “Molassodon” ecospecies of Vibrio parahaemo...
biorxiv.org
Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides tinyurl.com/ch3damp We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity Revealed by the amazing Ilya Osterman. See his thread below👇
Osterman Ilya@ostermanilya.bsky.social · 9mo agoBacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...
I'm happy to co-organize the 2nd Microbial RNA Symposium in Shanghai! Looking forward to these inspiring talks this weekend! @rnasociety.bsky.social @natmicrobiol.nature.com @cellpress.bsky.social
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
biorxiv.org
🚨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
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.
academic.oup.com
Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide www.nature.com/articles/s41...
Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution
A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...
nature.com
tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa 🦠👏High-throughput tRNA epitranscriptome profiling using mass spec on P. aeruginosa transposon insertion library and links with metabolic networks #microsky #rnasky doi.org/10.1093/nar/...
tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa
Abstract. Transfer RNA (tRNA) modifications have emerged as critical post-transcriptional regulators of gene expression affecting diverse biological and di
doi.org
New preprint! We characterise the small, regulatory RNA Arp which controls DNA uptake and twitching motilty in A. baumannii. Led by our Dr Fergal Hamrock @hamrockfergal.bsky.social and in collaboration with @westermannlab.bsky.social and Mike Gebhardt's lab!
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last yr.DNA uptake and twitching motility are controlled by the small RNA Arp through repression of pilin translation in Acinetobacter baumannii https://www.biorxiv.org/content/10.1101/2025.07.19.665661v1
Evolution of hunt, kill, devour in a Vibrio ecospecies Great paper 'Molassodon' - genetically distinct ecospecies from typical V. parahaemolyticus, it has evolved a predatory strategy that devour other bacteria in viscous environments @campy-bara.bsky.social www.biorxiv.org/content/10.1...
Evolution of hunt, kill, devour in a Vibrio ecospecies
Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Using coadaptation analysis as a foundation for laboratory experime...
biorxiv.org
#NatMicroPicks Vibrio in competition! 🦠💉 An orphan T6SS effector in non-toxigenic Vibrio cholerae targets susceptible strains by disrupting ion balance, shaping Vibrio population dynamics and offering a model for precision antimicrobials. #MicroSky www.cell.com/cell-host-mi...
A Vibrio-specific T6SS effector reshapes microbial competition by disrupting Vibrio bioenergetics
Liu et al. report that a Vibrio-specific T6SS effector, TseVs, selectively disrupts Vibrio bioenergetics while sparing non-target microbes via an immunity-independent mechanism. This work reveals how ...
cell.com
Happy to share the preprint from here in Shanghai, together with @danielfalush.bsky.social, as well as with team Zhizhou Jia, Huqi Wen, and Zhe Xie! www.biorxiv.org/content/10.1...
Evolution of hunt, kill, devour in a Vibrio ecospecies
Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Using coadaptation analysis as a foundation for laboratory experime...
biorxiv.org
3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages https://www.biorxiv.org/content/10.1101/2025.06.06.658255v1
Quality over quantity: Small RNA pauses translation elongation to lift protein activity: Molecular Cell www.cell.com/molecular-ce...
Quality over quantity: Small RNA pauses translation elongation to lift protein activity
Small noncoding RNAs typically regulate the translation initiation of target mRNAs and thereby protein production. In this issue of Molecular Cell, Thongdee et al. discovered a novel regulatory mechan...
cell.com
Quality over quantity: Small RNA pauses translation elongation to lift protein activity
Quality over quantity: Small RNA pauses translation elongation to lift protein activity
Small noncoding RNAs typically regulate the translation initiation of target mRNAs and thereby protein production. In this issue of Molecular Cell, Thongdee et al. discovered a novel regulatory mechanism where a bacterial small RNA modulates translation elongation and co-translational folding to alter protein activity without affecting protein abundance.
dlvr.it
I'm happy to share the first publication from my lab @hoerlab.bsky.social, now out in @narjournal.bsky.social! I take a look at the biology of RNA phages, focusing on how meta-omics methods are discovering new RNA phage families and bacterial defense strategies. #PhageSky doi.org/10.1093/nar/...
Advancing RNA phage biology through meta-omics
Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i
doi.org
Grant opportunity! 200K USD for 3 years from CAS-ANSO program. Apply by May 20th. Details in here: www.anso.org.cn/programmes/S...
Where science meets culture 🔬🎭 At the Vogel Foundation Dr Eckernkamp’s 25th anniversary gala at the Mainfranken Theater, #HIRI director Jörg Vogel emphasized the vital role of culture for cutting-edge research. Congrats & thank you for supporting our science! ➡️ www.helmholtz-hiri.de/en/newsroom/...
📅🖍️ Mark your calendars: The #HIRI & the Shanghai #RNA Club will host @rnasociety.bsky.social’s next RNA Collaborative Seminar on March 12. HIRI group leader @jenshoer.bsky.social will discuss “Insights into the role of RNA in bacterial immunity and phage replication.” us02web.zoom.us/webinar/regi...
Welcome! You are invited to join a webinar: RNA Collaborative - Helmholtz Institute for RNA-based Infection Research (HIRI) & Shanghai RNA Club. After registering, you will receive a confirmation emai...
Featuring: “Insights into the role of RNA in bacterial immunity and phage replication” Jens Hör, PhD Group Leader, Helmholtz Institute for RNA based Infection Research, Junior Professor, University...
us02web.zoom.us
It is finally out! Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)! Check it out @naturemicrobiol.bsky.social www.nature.com/articles/s41...
CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d - Nature Microbiology
Leveraging RNA-targeting dCas13d enables selective interference with phage protein translation and facilitates measurement of phage gene fitness at a transcriptome-wide scale.
nature.com
🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈 “Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo
Highly multiplexed spatial transcriptomics in bacteria
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...
science.org
My collaborators in Shanghai discovered that Within-host evolution of a transcriptional regulator contributes to the establishment of chronic Pseudomonas aeruginosa infection: Cell Reports www.cell.com/cell-reports...
Within-host evolution of a transcriptional regulator contributes to the establishment of chronic Pseudomonas aeruginosa infection
Zhou et al. identify a 9-bp deletion in a putative transcriptional regulator in P. aeruginosa. This mutation is highly associated with chronic P. aeruginosa infection and leads to pyruvate accumulatio...
cell.com
Bacterial small RNA promotes gut colonization | EurekAlert! www.eurekalert.org/news-release...
Bacterial small RNA promotes gut colonization by regulating sialic acid metabolism
Dr. CHAO Yanjie at the Shanghai Institute of Immunity and Infection of the Chinese Academy of Sciences and Dr. WANG Chuan from Fudan University revealed how a bacterial pathogen coordinates N-acetylne...
eurekalert.org