ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 19/09/2026Farewell 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 · 04/09/2026pubs.acs.org/jacsat/artic...pubs.acs.orgProgrammable Recognition of Organyl 5′-Phosphates by Human Argonaute-2Abstract. 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 · 26/08/2026www.nature.com/articles/s41...nature.comDICER1-related tumour predisposition mutations increase 3p-miRNA function and HERVH activity - Nature CommunicationsDICER1 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 · 25/08/2026link.springer.com/article/10.1...link.springer.comThe clinical and molecular spectrum of AGO2-associated Lessel-Kreienkamp neurodevelopmental syndrome - Genome MedicineBackground 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.socialNobel Prize @nobelprize.org · 24/08/2026We'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 · 10/08/2026How 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 #siRNApnas.orgCentral guide–target pairing activates human Argonaute2 by uncoupling the N-PAZ and MID–PIWI lobes | PNASSmall 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 · 08/08/2026www.biorxiv.org/content/10.6...biorxiv.orgtinyRNA-seq: An optimized approach to sequencing tiny RNAs and primitive RNA genomesVery 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 · 24/07/2026We'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.comPost Doctoral ScholarScreen 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 · 24/07/2026www.science.org/doi/10.1126/...science.orgThe AGO2 adaptor LIMD1 expands the functional and evolutionary reach of microRNA targetingLIMD1 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 · 23/07/2026www.nature.com/articles/s41...nature.comLicense to slice: duplex deformation gates Argonaute catalysis - Nature Structural & Molecular BiologyHuman 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 · 06/07/2026www.biorxiv.org/content/10.6...biorxiv.orgThe structure of the apo-PIWI HSP90 complexPIWI 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 · 30/06/2026journals.plos.org/plosgenetics...journals.plos.orgArgonaute proteins orchestrate Meiotic Sex Chromosome Inactivation and timing of the spermatogenic transcriptional programAuthor 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 · 24/06/2026www.nature.com/articles/s41...nature.comCatalytic activation of human Argonaute 2 requires RNA duplex deformation - Nature Structural & Molecular BiologyHuman 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 · 19/06/2026journals.plos.org/plosbiology/...journals.plos.orgArgonaute 2 drives resistance to immune checkpoint inhibitors in immunorefractory non-small cell lung cancerImmune 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 · 19/06/2026www.nature.com/articles/s41...nature.comYolk transports miRNAs to embryos and enhances progeny stress resilience - Nature Structural & Molecular BiologyThis 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.socialJulius Brennecke @juliusbrennecke.bsky.social · 13/06/2026a small attempt to capture this enormous loss and what Greg meant and means to so many. www.cell.com/cell/fulltex...cell.comGregory 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 · 10/06/2026Narry 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.comStructural basis for RISC assembly of human Argonaute2Zhang 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 · 10/06/2026www.nature.com/articles/s41...nature.comStructural basis for chaperone-guided assembly of RNA-induced silencing complex - NatureStructures 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.socialChristine Mayr @christinemayr.bsky.social · 08/06/2026Finally 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.commRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activityHighly 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 · 07/06/2026The 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 · 26/05/2026Have 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 · 25/05/2026www.biorxiv.org/content/10.6...biorxiv.org 000
Reposted by @ktr-nakanishi.bsky.socialIgor Ulitsky @igorulitsky.bsky.social · 15/05/2026Now 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 · 08/05/2026www.nature.com/articles/s41...nature.comCLASHub is an integrated database and analytical platform for microRNA-target interactions - Nature CommunicationsMicroRNAs 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 · 30/04/2026I’m so excited to start a new R35! 000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 10/04/2026www.cruk.cam.ac.uk/news/in-memo...cruk.cam.ac.uk 012
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 31/03/2026Congratulations to Andrew Savidge on successfully defending his Ph.D. dissertation🎉 000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 30/03/2026www.biorxiv.org/content/10.6...biorxiv.org 000
Reposted by @ktr-nakanishi.bsky.socialDavid Bartel's Lab @bartellab.bsky.social · 19/03/2026Our 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/Z8TDMDtinyurl.comThe E3 ubiquitin ligase mechanism specifying targeted microRNA degradation - NatureTarget-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 · 23/02/2026www.biorxiv.org/content/10.6...biorxiv.org 000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 17/02/2026www.science.org/doi/10.1126/...science.orgAccessory microRNA byproducts expand RNA interference via microprocessor-mediated cleavage activationInsights 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 · 07/02/2026www.science.org/doi/10.1126/...science.orgExtracellular vesicles mediate stem cell signaling and systemic RNAi in planariansPlanarian extracellular vesicles carry small RNAs that mediate systemic gene silencing and coordinate regeneration. 000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 04/02/2026www.biorxiv.org/content/10.6...biorxiv.org 000
Reposted by @ktr-nakanishi.bsky.socialKatja Petzold @katjapetzold.bsky.social · 03/02/2026Interested 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 #biophysicsuu.sePostdoktortjänst inom Excellenscentrat Livets Kemiska Mekanismer vid Uppsala universitet - Uppsala universitetPostdoktortjänst inom Excellenscentrat Livets Kemiska Mekanismer vid Uppsala universitet, Institutionen för kemi - LV, Uppsala universitet 023
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 29/01/2026www.pnas.org/doi/10.1073/...pnas.orgGermline fate determination by a single ARGONAUTE protein in Ectocarpus | PNASARGONAUTE (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.socialeric lai @lucksmith.bsky.social · 23/01/2026new 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.orgSeparable 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.socialDavid Bartel's Lab @bartellab.bsky.social · 23/01/2026We’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 · 22/01/2026academic.oup.com/nar/article/...academic.oup.comValidate User 000
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 20/01/2026www.nature.com/articles/s41...nature.comBiochemical principles of miRNA targeting in flies - Nature CommunicationsMicroRNAs 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 · 18/01/2026academic.oup.com/nar/article/...academic.oup.comAn AI-guided framework reveals conserved features governing microRNA strand selectionAbstract. 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 · 15/01/2026www.cell.com/cell-reports...cell.comStructure of the MIWI endoribonuclease bound to pachytene piRNAs from mouse testesRaad 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 · 12/01/2026academic.oup.com/nar/article/...academic.oup.comPresence 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 vivoAbstract. 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 · 09/01/2026link.springer.com/article/10.1...link.springer.comClient Challenge 000
Reposted by @ktr-nakanishi.bsky.socialDavid Bartel's Lab @bartellab.bsky.social · 06/01/2026We 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.socialJakob Farnung @jakobfarnung.bsky.social · 06/01/2026When 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 · 06/01/2026www.nature.com/articles/s41...nature.comNow with oligos: antibody–oligonucleotide conjugates are the new drug modality to watch - Nature BiotechnologyDevelopers 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.socialProceedings of the National Academy of Sciences @pnas.org · 25/11/2025One 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. 0164
ktr-nakanishi.bsky.social @ktr-nakanishi.bsky.social · 14/11/2025Just 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.orgNeurodevelopmental disorder–linked Argonaute mutations permit delayed RISC formation and unusual shortening of miRNAs by 3′→5′ trimming | PNASMutations in Argonaute proteins (AGOs) cause Argonaute syndrome, a neurodevelopmental disorder (NDD), yet the underlying molecular mechanism remain... 020
Reposted by @ktr-nakanishi.bsky.socialJosh Mendell @mendell-lab.bsky.social · 10/11/2025Regulated 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.orgPlagl1 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.socialCity Therapeutics @citytx.bsky.social · 10/11/2025Excited 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