High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2

Becker, Winston R., Ober-Reynolds, Benjamin, Jouravleva, Karina, Jolly, Samson M., Zamore, Phillip D., Greenleaf, William J.·2019·Molecular Cell
DOI 10.1016/j.molcel.2019.06.012

Cited by (163)

Items 101–163 of 163

  1. Near Sequence Homology Does Not Guarantee siRNA Cross-Species Efficacy
    Iris Valeria Rivera Flores, Kathryn R. Monopoli, Samuel Jackson, Dimas Echeverria, Daniel O’Reilly, Robert H. Brown, Anastasia Khvorova · 2024 · Nucleic Acid Therapeutics
  2. Systematic Evaluation of Position-Specific Tolerability of Seven Backbone and Ribose Modifications in Fully Chemically Stabilized siRNAs
    Daniel O’Reilly, Raymond Furgal, Vignesh Narayan Hariharan, Clemens Lochmann, David Cooper, Dimas Echeverria, Anastasia Khvorova · 2025 · Nucleic Acid Therapeutics
  3. Transcriptome-Wide Analysis of microRNA–mRNA Correlations in Tissue Identifies microRNA Targeting Determinants
    Juan Manuel Trinidad-Barnech, Rafael Sebastián Fort, Guillermo Trinidad Barnech, Beatríz Garat, Marı́a Ana Duhagon · 2023 · Non-Coding RNA
  4. Engineering supramolecular dynamics of self-assembly and turnover of oncogenic microRNAs to drive their synergistic destruction in tumor models
    Daria Chiglintseva, David J. Clarke, Сенькова Александра Васильевна, Thomas Heyman, Svetlana K. Miroshnichenko, Fangzhou Shan, Valentin V. Vlassov, Зенкова Марина Аркадьевна, Olga Patutina, Elena V. Bichenkova · 2024 · Biomaterials
  5. Opening new frontiers with catalytic nucleic acids in miRNA inhibition
    Olga Patutina, Svetlana K. Miroshnichenko, Daria Chiglintseva, Зенкова Марина Аркадьевна · 2025 · Frontiers in Pharmacology
  6. mir-21 is associated with inactive low molecular weight Argonaute complexes in thyroid cancer cell lines
    Bonita H. Powell, Andrey A. Turchinovich, Yongchun Wang, Zhaohao Liao, Mohammad Aasif Dar, Gaspare La Rocca, George K. E. Umanah, Martha A. Zeiger, Christopher B. Umbricht, Kenneth Whitaker Witwer · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  7. The conserved zinc-finger protein GTSF1 helps PIWI proteins achieve their full catalytic potential
    Amena Arif, Shannon Bailey, Natsuko Izumi, Todd A. Anzelon, Deniz Mahmut Özata, Cecilia Andersson, Ildar V. Gainetdinov, Ian J. MacRae, Yukihide Tomari, Phillip D. Zamore · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  8. Relaxed targeting rules allow PIWI-clade Argonaute proteins to silence ever-mutating transposons
    Ildar V. Gainetdinov, Katharine R. Cecchini, Joel Vega‐Badillo, Ayca Bagci, Cansu Colpan, Amena Arif, Pei‐Hsuan Wu, Phillip D. Zamore · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  9. MicroRNAs' Significance in Retinoblastoma Diagnosis and Treatment: The Little Heroes
    Maryam Zamani Sani, Mohammad Mirzaei, Ali Mota, Jamal Mohammadian, Elmira Aboutalebi Vand Beilankouhi, Mohammad Rahmati‐Yamchi · 2025 · Biochemical Genetics
  10. PAIRNet: Predicting PIWI cleavage specificity via position-aware RNA interaction modeling
    Lin Zeng, Zhenzhen Li, Enzhi Shen, Shikui Tu, Lei Xu · 2026 · PLoS Computational Biology
  11. Toward learning the rules that predict siRNA efficacy
    Xavier Bofill‐De Ros · 2023 · Molecular Therapy — Nucleic Acids
  12. Circ_0026579 knockdown ameliorates lipopolysaccharide‐induced human lung fibroblast cell injury by regulating CXCR1 via miR‐370‐3p
    Yuanhong Zhuang, Yuyun Yang, Lihong Peng · 2023 · Clinical and Experimental Pharmacology and Physiology
  13. Expression, not sequence, distinguishes miR-238 from its miR-239ab sister miRNAs in promoting longevity in Caenorhabditis elegans
    Laura B. Chipman, San Luc, Ian A. Nicastro, Jesse J. Hulahan, Delaney C. Dann, Devavrat M. Bodas, Amy E. Pasquinelli · 2023 · PLoS Genetics
  14. Biochemistry-informed design selects potent siRNAs against SARS-CoV-2
    Élisabeth Houbron, Sophie Mockly, Sophia Rafasse, Nathalie Gros, Delphine M. Muriaux, Hervé Seitz · 2023 · RNA Biology
  15. Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage
    Emily K. Matozel, Nathaniel Dale, Allen C. Price · 2020 · Journal of Visualized Experiments
  16. Dynamics of RNA–protein interactions studied in living cells
    Olivia S. Rissland · 2021 · Nature
  17. Big Insights into Small RNAs
    Olivia S. Rissland · 2020 · Biochemistry
  18. Noncanonical targeting contributes significantly to miRNA-mediated regulation
    Jennifer Y. Tan, Baroj Abdulkarim, Ana Claudia Marques · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  19. Decoding RNA–protein interactions using high-throughput methods
    Marianne Régis, Paola Pulcina, Dmitry A. Kretov · 2026 · RNA Biology
  20. Specificity of DNA targeting by RNA-guided pAgo nucleases
    Lidiya Lisitskaya, А. А. Кузнецова, Ivan Petushkov, Maya K. Alieva, Yuliya S Zaitseva, Anna Olina, Ekaterina Kropocheva, M. S. Lavrova, Anton A. Musabirov, Nikita A. Kuznetsov et al. · 2026 · Nucleic Acids Research
  21. Distribution of divalent small interfering RNA into neurons of sensory ganglia produces selective, durable knockdown of Nav1.7 and strong analgesia
    Corrie L. Gallant‐Behm, Justin N. Siemian, David Tran, Matthew L. Rook, Chunhua Yang, Kokulapalan Wimalanathan, Hryhoriy Bohdanovych Zhoba, Alex Prinzen, Mingwei Li, Taylor Lynch et al. · 2026 · Pain
  22. The clade-specific target recognition mechanisms of plant RISCs
    Hiro‐oki Iwakawa · 2024 · Nucleic Acids Research
  23. Mathematical model of RNA-directed DNA methylation predicts tuning of negative feedback required for stable maintenance
    Renee Dale, Rebecca A. Mosher · 2024 · Open Biology
  24. Biochemical principles of miRNA targeting in flies
    Joel Vega‐Badillo, Phillip D. Zamore, Karina Jouravleva · 2026 · Nature Communications
  25. From transient recognition to efficient silencing: a RISCky business
    François Major · 2020 · Nature Structural & Molecular Biology
  26. A tweak and a peek: How Cas9 pries open double-stranded DNA to check its sequence
    Selma Sinan, Rick Russell · 2022 · Nature Structural & Molecular Biology
  27. Structural basis for differential targeting properties of small RNAs in plants and animals
    Yao Xiao, Ian J. MacRae · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  28. Target complementarity in cnidarians supports a common origin for animal and plant microRNAs
    Yael Admoni, Arie Fridrich, Talya Razin, Miguel Salinas‐Saavedra, Michal Rabani, Uri Frank A, Yehu Moran · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  29. AGO2 slicing restrains RTL1 to prevent vascular defects and lethal neonatal muscle failure
    Manish Kumar, Andréa Gutierrez Maria, Aurelia Moses, Mahendra Prajapat, Jenna Clements, Moe Kitazawa, Hirosuke Shiura, Kei Fukuda, Joana Alves Vidigal · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  30. A High-Throughput Platform for Rapid Adaptation of DNA Aptamers to SARS-CoV-2 Evolution
    Yujie He, Zhenglin Yang, Yu-An Kuo, Yuting Wu, Diego Fonseca-Albert, Kyle K Le, Jeffrey G Guo, Yanxing Wang, Anh-Thu Nguyen, Yuan-I Chen et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  31. Gene expression in sight
    Stijn Sonneveld · 2021
  32. Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in vivo in CNS
    Faith Conroy, Rachael Miller, Julia F. Alterman, Matthew R. Hassler, Dimas Echeverria, Bruno M.D.C. Godinho, Emily G. Knox, Ellen Sapp, Jaquelyn Sousa, Ken Yamada et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  33. Asymmetric trichotomous data partitioning enables development of predictive machine learning models using limited siRNA efficacy datasets
    Kathryn R. Monopoli, Dmitry Korkin, Anastasia Khvorova · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  34. Relative specificity as an important consideration in the big data era
    Xiaoxiao Zhang, Yan Zeng · 2022 · Frontiers in Genetics
  35. Small regulatory RNAs: from bench to bedside – a keystone symposia meeting report
    Soo Mi Lee, Michael T. Winters, Iván Martínez, Frank John Slack · 2023 · RNA Biology
  36. Expression, not sequence, distinguishes miR-238 from its miR-239ab sister miRNAs in promoting longevity in Caenorhabditis elegans
    Laura B. Chipman, San Luc, Ian A. Nicastro, Jesse J. Hulahan, Delaney C. Dann, Devavrat M. Bodas, Amy E. Pasquinelli · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  37. Additional file 1 of Long non-coding RNAs HERH-1 and HERH-4 facilitate cyclin A2 expression and accelerate cell cycle progression in advanced hepatocellular carcinoma
    Tao Liu, Shi, Qiao, Yang, Lei, Shusen Wang, Hongli Song, Zhenglu Wang, Xinnv Xu, Hongsheng Liu, Hong Zheng, Zhongyang Shen · 2021 · Figshare
  38. Additional file 2 of CRISPR guides induce gene silencing in plants in the absence of Cas
    Veerendra Kumar Sharma, Sandeep Marla, Wenguang Zheng, Divya Mishra, Jun T. Huang, Wei Zhang, Geoffrey P. Morris, David E. Cook · 2022 · Figshare
  39. A Dose-Response Model for Accurate Detection and Quantification of Transcriptome-Wide Gene Knockdown for Oligonucleotide-Based Medicines
    David Pekker, Steven Kuntz, Monica McArthur, Timothy Shaw, Sara Yanke, Swagatam Mukhopadhyay · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Modeling RNA duplex dynamics with Gibbs sampling enhances base-pair prediction accuracy and reveals structural activity profiles
    Simon Chasles, François Major · 2025 · NAR Genomics and Bioinformatics
  41. Radiation Modifies Let-7 miRNA Binding to AGO2 Independent of Changes in Transcription to Influence Tumor Cell Radiosensitivity
    Taqveema Ali, Charlotte Degorre, Philip J. Tofilon · 2025 · International Journal of Molecular Sciences
  42. Additional file 3 of CRISPR guides induce gene silencing in plants in the absence of Cas
    Veerendra Kumar Sharma, Sandeep Marla, Zheng, Wenguang, Mishra, Divya, Huang, Jun, Zhang, Wei, Morris, Geoffrey Preston, David E. Cook · 2022 · Figshare
  43. Additional file 1 of CRISPR guides induce gene silencing in plants in the absence of Cas
    Veerendra Kumar Sharma, Sandeep Marla, Zheng, Wenguang, Mishra, Divya, Huang, Jun, Zhang, Wei, Morris, Geoffrey Preston, David E. Cook · 2022 · Figshare
  44. Additional file 2 of Long non-coding RNAs HERH-1 and HERH-4 facilitate cyclin A2 expression and accelerate cell cycle progression in advanced hepatocellular carcinoma
    Liu, Tao, Shi, Qiao, Yang, Lei, Wang, Shusen, Song, Hongli, Wang, Zhenglu, Xu, Xinnv, Liu, Hongsheng, Hong Zheng, Shen, Zhongyang · 2021 · Figshare
  45. Programmed Manipulation of RNA Targets By Human Argonaute 2
    Robert F. Lusi, Salvador Moncayo von Hase, Corey Model, Steven M. Banik · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  46. RIMap-RISC: a transcriptome-wide database of structurally modeled human microRNA interactions
    Simon Chasles, Zakary Gaillard-Duchassin, Jordan Quenneville, Mélanie Lemaire, Étienne Gagnon, François Major · 2026 · Genome biology
  47. A novel proteasome-ribosome axis regulated by endogenous siRNAs in oocytes governs maternal-to-zygotic transition
    Junchao Xue, Lin Zeng, Xuejia Li, Shuxian Liu, Lili Li, Zhenzhen Li, Congjing Wang, Xuanxuan Guo, Di Rao, Ran Huo et al. · 2026 · Vita
  48. The Cepeda Framework: A Modular, Safety-First Preclinical Architecture for Testing Coordinated Multi-Hallmark Rejuvenation Hypotheses in Biological Aging
    CÉSAR JULIÁN OROZCO CEPEDA, FTC Scientific Group, Co-Investigator (Computational Analysis) · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  49. Identification and functional characterization of proteins involved in the regulation of viral microRNAs biogenesis
    Antoine Creugny · 2019 · theses.fr (ABES)
  50. Variation génétique et plasmatique des microARNs : impact sur les paramètres biologiques de l’hémostase
    Florian Thibord · 2019 · theses.fr (ABES)
  51. Study of mechanisms regulating the biogenesis of microRNAs expressed by Kaposi’s sarcoma-associated herpesvirus
    Monika Vilimova · 2022 · theses.fr (ABES)
  52. Rational Design and Screening of Chemically Modified Anti-SARS-CoV-2 siRNA
    Zihui Cheng, Ying Cai, Enhua Zhang, Yong Cheng, Yizhe Li, Xiaojuan Zhang, Guochun Liang, Mengying Hou, Can Wang, Tianwen Hu et al. · 2026 · ACS Infectious Diseases
  53. Understanding the biological limits of hybridization-dependent siRNA off-target interactions
    Luca Penso-Dolfin, Judith Hauptmann, Nina Was, Vivien Hehne, Marie Wickström Lindholm, Eliot Morrison · 2026 · Molecular Therapy — Nucleic Acids
  54. Spatiotemporal Control of microRNA –Target Interactions
    Linh T. T. Le · 2026 · Wiley Interdisciplinary Reviews - RNA
  55. Central guide–target pairing activates human Argonaute2 by uncoupling the N-PAZ and MID–PIWI lobes
    Huaqun Zhang, Andrew Savidge, GeunYoung Sim, Mi Seul Park, Audrey C. Kehling, Vishal Annasaheb Adhav, Kotaro Nakanishi · 2026 · Proceedings of the National Academy of Sciences
  56. A cuffed CRISPR guide RNA for microRNA activity-dependent genome editing
    Arman Adel, Yutaro Shuto, Shunsuke Kawasaki, Yonggang Lu, Hiroki Ono, Satoshi N. Omura, Ryoya Nakagawa, Alima Suleimenova, Meghan Robinson, Tabea L. Stephan et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  57. High-Throughput On-Chip Screening Enables Rapid Adaptation of DNA Aptamers to SARS-CoV-2 Evolution
    Yujie He, Zhenglin Yang, Yu-An Kuo, Yuting Wu, Diego Fonseca-Albert, Kyle K Le, Jeffrey Guo, Yanxing Wang, Anh-Thu Nguyen, Yuan‐I Chen et al. · 2026 · ACS Nano
  58. ‘Guide and Prejudice’— How Argonautes recognize targets across domains of life
    Jack P. K. Bravo · 2026 · FEBS Letters
  59. Elucidating the Requirements for microRNA-Mediated Upregulation Enables Reengineering of Upregulatory Sites
    Helia Dehghan Harati, Thusini Uggalla Arachchige, Xinghai Liu, Lara K. Mahal · 2026 · ACS Chemical Biology
  60. Therapeutic oligonucleotides as genetic medicines: The current state and future perspective
    Bruno M.D.C. Godinho, Chantal M. Ferguson, Annemieke M Aartsma-Rus · 2026 · Cell Reports Medicine
  61. Adhesion gateway: decoding mechanobiological cues for cytoskeletal reconfiguration
    Gangotry Mukhopadhyay, V. Karthick, D. Inbakandan, Prathap Somu, Jeyaraj Iyyappan, Ravi Mani · 2026 · Molecular Biology Reports
  62. Engineered human Argonaute 2 for targeted C-to-U RNA base editing
    Robert F. Lusi, Salvador Moncayo von Hase, Corey Model, Steven M. Banik · 2026 · Nature Biotechnology
  63. Human Argonaute 2 is a programmable targeting domain for RNA editing
    2026 · Nature Biotechnology