Sign in

ktr-nakanishi.bsky.social

@ktr-nakanishi.bsky.social
51 followers 54 following 48 posts

ASC Distinguished Professor / PI of the Nakanishi Lab u.osu.edu/nakanishilab/) I study tinyRNAs, cityRNAs and other small noncoding RNAs. twitter.com/ktr_nakanishi

PostsRepliesMedia
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 19/09/2026
Farewell dinner for Huaqun Zhang! 🎉 He made significant contributions to elucidating gene silencing by cityRNAs and determining the cryo-EM structures of RISC assembly and AGO2 activation. We’ll miss you, Huaqun! Wishing you all the best in your new position in China!
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 04/09/2026
pubs.acs.org/jacsat/artic...
pubs.acs.org
Programmable Recognition of Organyl 5′-Phosphates by Human Argonaute-2
Abstract. To effectuate RNA interference (RNAi), Argonaute (AGO) proteins recognize and load RNA guide strands by their requisite 5′-phosphate (5′-P). Howe
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 26/08/2026
www.nature.com/articles/s41...
nature.com
DICER1-related tumour predisposition mutations increase 3p-miRNA function and HERVH activity - Nature Communications
DICER1 is often mutated in cancer, including in DICER1-related tumour predisposition. Here, the authors show that cancer-associated DICER1 mutations shift microRNA processing and reactivate HERVH endo...
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 25/08/2026
link.springer.com/article/10.1...
link.springer.com
The clinical and molecular spectrum of AGO2-associated Lessel-Kreienkamp neurodevelopmental syndrome - Genome Medicine
Background Pathogenic variants in AGO2, encoding a central component of the RNA-induced silencing complex (RISC), cause the neurodevelopmental disorder Lessel-Kreienkamp syndrome (LESKRES). The varian...
000
Reposted by @ktr-nakanishi.bsky.social
Nobel Prize @nobelprize.org · 24/08/2026
We've arrived on Bluesky! We hope you will follow along as we share inspiring, motivational and exciting content about the achievements and individuals that have been awarded a Nobel Prize. Stay tuned.
3074244752
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 10/08/2026
How does human AGO2 distinguish cleavable from non-cleavable RNA targets? Our cryo-EM structures reveal that central guide–target pairing pries open AGO2’s central cleft, driving AGO2 into the preactive state required for target cleavage. www.pnas.org/doi/10.1073/... #RNAi #CryoEM #siRNA
pnas.org
Central guide–target pairing activates human Argonaute2 by uncoupling the N-PAZ and MID–PIWI lobes | PNAS
Small interfering RNAs (siRNAs) are widely used to repress gene expression. For human Argonaute2 (AGO2) to cleave target RNA, siRNAs must be almost...
0154
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 08/08/2026
www.biorxiv.org/content/10.6...
biorxiv.org
tinyRNA-seq: An optimized approach to sequencing tiny RNAs and primitive RNA genomes
Very short RNAs play critical roles in modern biology, and are thought to have been crucial for genome replication during the origin of life. Next-generation sequencing is an essential tool for charac...
020
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 24/07/2026
We're hiring! Join the Nakanishi Lab at The Ohio State University as a Postdoctoral Scholar. Seeking candidates with experience in protein expression/purification (baculovirus or human cells). Cryo-EM experience is a plus. Apply: osu.wd1.myworkdayjobs.com/OSUCareers/j...
osu.wd1.myworkdayjobs.com
Post Doctoral Scholar
Screen reader users may encounter difficulty with this site. For assistance with applying, please contact hr-accessibleapplication@osu.edu. If you have questions while submitting an application, pleas...
011
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 24/07/2026
www.science.org/doi/10.1126/...
science.org
The AGO2 adaptor LIMD1 expands the functional and evolutionary reach of microRNA targeting
LIMD1 helps AGO2 silence microRNA targets more effectively, revealing an additional layer of control beyond RNA sequence alone.
010
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 23/07/2026
www.nature.com/articles/s41...
nature.com
License to slice: duplex deformation gates Argonaute catalysis - Nature Structural & Molecular Biology
Human Argonaute2 (AGO2) binds siRNAs to target complementary mRNAs. Although guided–target complementary is required for slicing, there is a wide range of slicing efficacy. A study now shows the preci...
010
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 06/07/2026
www.biorxiv.org/content/10.6...
biorxiv.org
The structure of the apo-PIWI HSP90 complex
PIWI proteins are members of the Argonaute family and together with piRNAs protect metazoan germlines from transposons. PIWI proteins adopt a bi-lobed architecture with a central RNA-binding channel. ...
011
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 30/06/2026
journals.plos.org/plosgenetics...
journals.plos.org
Argonaute proteins orchestrate Meiotic Sex Chromosome Inactivation and timing of the spermatogenic transcriptional program
Author summary In order to make spermatozoa, germ cells undergo the meiotic specialized cell division, during which the sex chromosomes are temporarily shut down in a process called Meiotic Sex Chromo...
100
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 24/06/2026
www.nature.com/articles/s41...
nature.com
Catalytic activation of human Argonaute 2 requires RNA duplex deformation - Nature Structural & Molecular Biology
Human Argonaute 2 requires distortion of the paired small interfering RNA (siRNA)–target RNA duplex, not just base pairing, to cleave targets. Structures show how RNA shape and key residues enable cat...
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 19/06/2026
journals.plos.org/plosbiology/...
journals.plos.org
Argonaute 2 drives resistance to immune checkpoint inhibitors in immunorefractory non-small cell lung cancer
Immune checkpoint inhibitors are used to treat advanced non-small cell lung cancer to activate an antitumor immune response, however they fail in many patients due to resistance. This study shows that...
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 19/06/2026
www.nature.com/articles/s41...
nature.com
Yolk transports miRNAs to embryos and enhances progeny stress resilience - Nature Structural & Molecular Biology
This study shows that yolk, a conserved vehicle for nutrient provisioning to developing eggs, also transports regulatory small RNAs, such as microRNAs, from somatic tissues to the germline and embryos...
001
Reposted by @ktr-nakanishi.bsky.social
Julius Brennecke @juliusbrennecke.bsky.social · 13/06/2026
a small attempt to capture this enormous loss and what Greg meant and means to so many. www.cell.com/cell/fulltex...
cell.com
Gregory J. Hannon (1964–2026)
Gregory J. Hannon passed away in April 2026 at the age of 61. A towering figure in modern molecular biology, Greg influenced remarkably diverse areas of science. His work reshaped our understanding of...
17132
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 10/06/2026
Narry Kim & Soung-Hun Roh's paper and our recent paper nicely complement each other. Their study reveals an early chaperone-assisted step in AGO2 loading. Our work captures the subsequent assembly intermediates and uncovers target-assisted passenger ejection (TAPE). www.cell.com/molecular-ce...
cell.com
Structural basis for RISC assembly of human Argonaute2
Zhang et al. report cryo-EM structures of AGO2-siRNA complexes capturing RISC assembly intermediates. They reveal MID-PIWI-mediated duplex loading, α14-guided end sensing, and stepwise passenger peeli...
173
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 10/06/2026
www.nature.com/articles/s41...
nature.com
Structural basis for chaperone-guided assembly of RNA-induced silencing complex - Nature
Structures of the AGO maturation complex reveal how chaperones and an RNA duplex drive assembly of the RNA-induced silencing complex.
0124
Reposted by @ktr-nakanishi.bsky.social
Christine Mayr @christinemayr.bsky.social · 08/06/2026
Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...
cell.com
mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity
Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.
522597
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 07/06/2026
The supplementary videos (S1–S7) in our Molecular Cell paper were inadvertently reordered during production. Here is the correct sequence of the seven videos until the journal updates the webpage.
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 26/05/2026
Have you ever used siRNAs? We reveal the structural basis of human AGO2 RISC assembly by cryo-EM. Surprisingly, target-assisted passenger ejection (TAPE) promotes RISC maturation, suggesting that mRNAs actively contribute to RNA silencing. www.cell.com/molecular-ce...
030
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 25/05/2026
www.biorxiv.org/content/10.6...
biorxiv.org
000
Reposted by @ktr-nakanishi.bsky.social
Igor Ulitsky @igorulitsky.bsky.social · 15/05/2026
Now out @natbiotech.nature.com ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones.
27725
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 08/05/2026
www.nature.com/articles/s41...
nature.com
CLASHub is an integrated database and analytical platform for microRNA-target interactions - Nature Communications
MicroRNAs control gene expression, but their direct RNA targets and turnover mechanisms remain difficult to study. Here, the authors present CLASHub, an integrated database and analysis platform that ...
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 30/04/2026
I’m so excited to start a new R35!
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 10/04/2026
www.cruk.cam.ac.uk/news/in-memo...
cruk.cam.ac.uk
012
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 31/03/2026
Congratulations to Andrew Savidge on successfully defending his Ph.D. dissertation🎉
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 30/03/2026
www.biorxiv.org/content/10.6...
biorxiv.org
000
Reposted by @ktr-nakanishi.bsky.social
David Bartel's Lab @bartellab.bsky.social · 19/03/2026
Our work on the E3 ligase mechanism of target-directed microRNA degradation is now published! Amazing collaboration with Brenda Schulman’s lab led by @jakobfarnung.bsky.social and @elenaslo.bsky.social, with special thanks to @wyppeter.bsky.social, Lianne Blodgett, and Daniel Lin! tinyurl.com/Z8TDMD
tinyurl.com
The E3 ubiquitin ligase mechanism specifying targeted microRNA degradation - Nature
Target-directed microRNA degradation is driven by the atypical ZSWIM8–CUL3 E3 ubiquitin ligase that uses a two-RNA-factor authentication mechanism to specifically recognize AGO–miRNA–trigger...
06120
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 23/02/2026
www.biorxiv.org/content/10.6...
biorxiv.org
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 17/02/2026
www.science.org/doi/10.1126/...
science.org
Accessory microRNA byproducts expand RNA interference via microprocessor-mediated cleavage activation
Insights into microRNA processing guide the design of an RNA medicine strategy that enables precise multitargeting against cancer.
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 07/02/2026
www.science.org/doi/10.1126/...
science.org
Extracellular vesicles mediate stem cell signaling and systemic RNAi in planarians
Planarian extracellular vesicles carry small RNAs that mediate systemic gene silencing and coordinate regeneration.
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 04/02/2026
www.biorxiv.org/content/10.6...
biorxiv.org
000
Reposted by @ktr-nakanishi.bsky.social
Katja Petzold @katjapetzold.bsky.social · 03/02/2026
Interested in RNA structural biology/dynamics/biophysics and how they explain RNA regulation? Want to push further and this this in cells? Join our lab: 1 PhD and 1 Postdoc position (apply via links) www.uu.se/om-uu/jobba-... www.uu.se/om-uu/jobba-... #NMR #RNA #biophysics
uu.se
Postdoktortjänst inom Excellenscentrat Livets Kemiska Mekanismer vid Uppsala universitet - Uppsala universitet
Postdoktortjänst inom Excellenscentrat Livets Kemiska Mekanismer vid Uppsala universitet, Institutionen för kemi - LV, Uppsala universitet
023
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 29/01/2026
www.pnas.org/doi/10.1073/...
pnas.org
Germline fate determination by a single ARGONAUTE protein in Ectocarpus | PNAS
ARGONAUTE (AGO) proteins are a highly conserved family of RNA-binding proteins that play central roles in gene regulation and developmental process...
000
Reposted by @ktr-nakanishi.bsky.social
eric lai @lucksmith.bsky.social · 23/01/2026
new paper from the Lai lab! Renfu Shang performs careful mechanistic dissection of miRNA cluster assistance and reveals many insights and surprises to this enigmatic regulatory strategy that gives suboptimal miRNAs a boost. if you love Northerns, you'll ♥️ this! 🧬 genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
Separable roles for Microprocessor and its cofactors, ERH and SAFB1/2, during microRNA cluster assistance
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
12611
Reposted by @ktr-nakanishi.bsky.social
David Bartel's Lab @bartellab.bsky.social · 23/01/2026
We’re excited to share our latest preprint on the mechanism of excised linear intron stabilization in yeast! This work was led by PhD student @glennli.bsky.social and was a wonderful collaboration with @maxewilkinson.bsky.social. Link: www.biorxiv.org/content/10.6... (1/4)
15925
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 22/01/2026
academic.oup.com/nar/article/...
academic.oup.com
Validate User
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 20/01/2026
www.nature.com/articles/s41...
nature.com
Biochemical principles of miRNA targeting in flies - Nature Communications
MicroRNAs guide Argonaute proteins to repress gene expression. Here, the authors define the binding rules for five Drosophila miRNAs, showing a narrow preference for canonical seed sites and identifyi...
010
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 18/01/2026
academic.oup.com/nar/article/...
academic.oup.com
An AI-guided framework reveals conserved features governing microRNA strand selection
Abstract. MicroRNAs (miRNAs) are central regulators of gene expression, yet how cells choose between the two strands (5p or 3p) of a miRNA duplex during bi
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 15/01/2026
www.cell.com/cell-reports...
cell.com
Structure of the MIWI endoribonuclease bound to pachytene piRNAs from mouse testes
Raad et al. describe the cryo-EM structure of mouse MIWI in complex with pachytene piRNAs to reveal a larger RNA-binding channel. They also identify a putative tryptophan-binding pocket on the PIWI do...
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 12/01/2026
academic.oup.com/nar/article/...
academic.oup.com
Presence of phosphodiester backbone, but not nucleobases, in the guide’s 3′ terminal region is necessary for RISC loading and target cleavage in vitro and in vivo
Abstract. Short interfering RNAs (siRNAs) represent a novel class of therapeutic modalities, where, in the context of complex chemical modification pattern
000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 09/01/2026
link.springer.com/article/10.1...
link.springer.com
Client Challenge
000
Reposted by @ktr-nakanishi.bsky.social
David Bartel's Lab @bartellab.bsky.social · 06/01/2026
We are thrilled to share our latest work uncovering the mechanistic basis of target-directed microRNA degradation (TDMD). This work was driven by @jakobfarnung.bsky.social and @elenaslo.bsky.social in a fantastic collaboration with Brenda Schulman's lab. tinyurl.com/E3TDMD (1/5)
29630
Reposted by @ktr-nakanishi.bsky.social
Jakob Farnung @jakobfarnung.bsky.social · 06/01/2026
When RNA Degradation 🤝 meets 🤝 Protein Degradation! tinyurl.com/E3TDMD In a collaboration of @bartellab.bsky.social and Schulman lab, we show that, in target-directed microRNA degradation (TDMD), 2-RNA-factors recruit an E3 ligase and induce the degradation of not only a protein but also RNA (1/5).
111850
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 06/01/2026
www.nature.com/articles/s41...
nature.com
Now with oligos: antibody–oligonucleotide conjugates are the new drug modality to watch - Nature Biotechnology
Developers have married gene-modulating oligonucleotides with the targeted precision of antibodies, and the first filings using such conjugates in Duchenne muscular dystrophy are imminent.
000
Reposted by @ktr-nakanishi.bsky.social
Proceedings of the National Academy of Sciences @pnas.org · 25/11/2025
One of the most-viewed PNAS articles in the last week is “Neurodevelopmental disorder–linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3′→5′ trimming.” Explore now: ow.ly/hwP450XxHM6 For more trending articles, visit ow.ly/q6Cl50XxHGN.
AGO1(ΔF180) retains the ability to form functionally mature RISCs.
0164
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 14/11/2025
Just published! AGO syndrome mutants slow passenger ejection, leaving the guide’s 3′ end exposed to 3′→5′ exonucleases that generate tyRNAs. This atypical trimming may occur during periods of stress or viral infection, potentially leading to neurodevelopmental disorders. www.pnas.org/doi/10.1073/...
pnas.org
Neurodevelopmental disorder–linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3′→5′ trimming | PNAS
Mutations in Argonaute proteins (AGOs) cause Argonaute syndrome, a neurodevelopmental disorder (NDD), yet the underlying molecular mechanism remain...
020
Reposted by @ktr-nakanishi.bsky.social
Josh Mendell @mendell-lab.bsky.social · 10/11/2025
Regulated decay of microRNAs plays a critical role in controlling body size in mammals! Check out our new paper in @genesdev.bsky.social and see thread previously posted with our pre-print 👇 for more info. Congrats to Collette LaVigne, Jaeil Han, and all authors! genesdev.cshlp.org/cgi/content/...
genesdev.cshlp.org
Plagl1 and Lrrc58 control mammalian body size by triggering target-directed microRNA degradation of miR-322 and miR-503
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
1218
Reposted by @ktr-nakanishi.bsky.social
City Therapeutics @citytx.bsky.social · 10/11/2025
Excited to announce the submission of our CTA to the @mhragovuk.bsky.social to initiate a Phase 1 study of CITY-FXI, an investigational RNAi therapeutic targeting Factor XI w/ the potential to safely & effectively prevent blood clots without increasing bleeding risk. www.citytx.com/news/city-th...
012