{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T03:22:28Z","timestamp":1789874548395,"version":"4.0.1"},"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T00:00:00Z","timestamp":1771459200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62172273"],"award-info":[{"award-number":["62172273"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["24510714300"],"award-info":[{"award-number":["24510714300"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Municipal Science and Technology Major Project, China","award":["2021SHZDZX0102"],"award-info":[{"award-number":["2021SHZDZX0102"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>PIWI proteins maintain genome integrity by piRNA-guided cleavage of complementary RNA targets. While Cleave-N\u2019-Seq (CNS-seq) has advanced our understanding of PIWI targeting logic through quantitative mapping of cleavage rates and pairing rules, its labor-intensive workflows hinder systematic exploration of sequence determinants. Here, we present PAIRNet, a deep learning framework that predicts PIWI-mediated RNA cleavage rates by explicitly modeling guide-target interactions. Recognizing that interaction geometry, not just sequence, dictates cleavage efficiency, PAIRNet integrates biochemical insights with computational innovation: it encodes pairing states, mismatch types, insertions, and deletions alongside learnable positional embeddings to quantify spatial dependencies; employs a hybrid CNN-Transformer architecture prioritizing duplex dynamics over static sequence features to resolve both local catalytic motifs (e.g., contiguous base-pairing at g10\u2013g11) and distal structural perturbations; and incorporates interpretability modules (saliency maps, counterfactual analysis) to link interaction patterns to biochemical insights and uncover position-specific cleavage rules. Validated across four PIWI-guide datasets, PAIRNet consistently ranks among the top two performers in all experimental conditions, achieving the most pronounced relative improvements in PCC, 34.7% for MILI and 14.6% for MIWI, over second-ranking methods. Critically, PAIRNet recapitulates key biological principles\u2014stringent complementarity at catalytic residues (g10\u2013g11) and tolerance for 3\u2019 mismatches\u2014aligning with structural studies of PIWI dynamics. By bridging biochemical precision with computational scalability, PAIRNet establishes a roadmap for designing high-specificity piRNA silencing tools while accelerating mechanistic studies of RNA-guided genome defense.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013936","type":"journal-article","created":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T18:31:11Z","timestamp":1771525871000},"page":"e1013936","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["PAIRNet: Predicting PIWI cleavage specificity via position-aware RNA interaction modeling"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6604-0564","authenticated-orcid":true,"given":"Lin","family":"Zeng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenzhen","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enzhi","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6270-0449","authenticated-orcid":true,"given":"Shikui","family":"Tu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,2,19]]},"reference":[{"issue":"6","key":"pcbi.1013936.ref001","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.cell.2007.01.043","article-title":"Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila","volume":"128","author":"J Brennecke","year":"2007","journal-title":"Cell."},{"key":"pcbi.1013936.ref002","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1146\/annurev.cellbio.24.110707.175327","article-title":"The biogenesis and function of PIWI proteins and piRNAs: progress and prospect","volume":"25","author":"T Thomson","year":"2009","journal-title":"Annu Rev Cell Dev Biol."},{"issue":"5818","key":"pcbi.1013936.ref003","doi-asserted-by":"crossref","first-page":"1587","DOI":"10.1126\/science.1140494","article-title":"A slicer-mediated mechanism for repeat-associated siRNA 5\u2019 end formation in Drosophila","volume":"315","author":"LS Gunawardane","year":"2007","journal-title":"Science."},{"issue":"7376","key":"pcbi.1013936.ref004","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/nature10672","article-title":"Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing","volume":"480","author":"M Reuter","year":"2011","journal-title":"Nature."},{"issue":"7376","key":"pcbi.1013936.ref005","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nature10547","article-title":"The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements","volume":"480","author":"S De Fazio","year":"2011","journal-title":"Nature."},{"key":"pcbi.1013936.ref006","article-title":"The tiny, conserved zinc-finger protein GTSF1 helps PIWI proteins achieve their full catalytic potential","author":"A Arif","year":"2021","journal-title":"arXiv preprint"},{"issue":"2","key":"pcbi.1013936.ref007","article-title":"The piRNA size matters","volume":"11","author":"J Liu","year":"2023","journal-title":"Natl Sci Rev."},{"issue":"1","key":"pcbi.1013936.ref008","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1186\/s12964-024-01724-5","article-title":"piRNA associates with immune diseases","volume":"22","author":"M Jiang","year":"2024","journal-title":"Cell Commun Signal."},{"issue":"3","key":"pcbi.1013936.ref009","article-title":"The piRNA response to retroviral invasion of the Koala Genome","volume":"179","author":"T Yu","year":"2019","journal-title":"Cell."},{"issue":"6","key":"pcbi.1013936.ref010","doi-asserted-by":"crossref","DOI":"10.1002\/wrna.1555","article-title":"PIWI pathway against viruses in insects","volume":"10","author":"A Kolliopoulou","year":"2019","journal-title":"Wiley Interdiscip Rev RNA."},{"issue":"1","key":"pcbi.1013936.ref011","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cell.2018.03.006","article-title":"Metazoan MicroRNAs","volume":"173","author":"DP Bartel","year":"2018","journal-title":"Cell."},{"issue":"4","key":"pcbi.1013936.ref012","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.cell.2005.08.044","article-title":"Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes","volume":"123","author":"C Matranga","year":"2005","journal-title":"Cell."},{"issue":"9","key":"pcbi.1013936.ref013","doi-asserted-by":"crossref","first-page":"953","DOI":"10.1038\/nsmb.1630","article-title":"Structural determinants of miRNAs for RISC loading and slicer-independent unwinding","volume":"16","author":"T Kawamata","year":"2009","journal-title":"Nat Struct Mol Biol."},{"issue":"7969","key":"pcbi.1013936.ref014","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1038\/s41586-023-06257-4","article-title":"Relaxed targeting rules help PIWI proteins silence transposons","volume":"619","author":"I Gainetdinov","year":"2023","journal-title":"Nature."},{"issue":"4","key":"pcbi.1013936.ref015","doi-asserted-by":"crossref","DOI":"10.1016\/j.molcel.2019.06.012","article-title":"High-throughput analysis reveals rules for target RNA binding and cleavage by AGO2","volume":"75","author":"WR Becker","year":"2019","journal-title":"Mol Cell."},{"issue":"7923","key":"pcbi.1013936.ref016","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/s41586-022-05009-0","article-title":"GTSF1 accelerates target RNA cleavage by PIWI-clade argonaute proteins","volume":"608","author":"A Arif","year":"2022","journal-title":"Nature."},{"issue":"6472","key":"pcbi.1013936.ref017","doi-asserted-by":"crossref","DOI":"10.1126\/science.aav1741","article-title":"The biochemical basis of microRNA targeting efficacy","volume":"366","author":"SE McGeary","year":"2019","journal-title":"Science."},{"issue":"1","key":"pcbi.1013936.ref018","doi-asserted-by":"crossref","first-page":"115166","DOI":"10.1016\/j.celrep.2024.115166","article-title":"The structural basis for RNA slicing by human Argonaute2","volume":"44","author":"AA Mohamed","year":"2025","journal-title":"Cell Rep."},{"issue":"6","key":"pcbi.1013936.ref019","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/s41576-022-00567-5","article-title":"High-throughput biochemistry in RNA sequence space: predicting structure and function","volume":"24","author":"E Marklund","year":"2023","journal-title":"Nat Rev Genet."},{"issue":"11","key":"pcbi.1013936.ref020","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1109\/5.726791","article-title":"Gradient-based learning applied to document recognition","volume":"86","author":"Y Lecun","year":"1998","journal-title":"Proc IEEE."},{"key":"pcbi.1013936.ref021","article-title":"Attention is all you need","volume":"30","author":"A Vaswani","year":"2017","journal-title":"Advances in neural information processing systems."},{"issue":"8053","key":"pcbi.1013936.ref022","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1038\/s41586-024-08438-1","article-title":"Structural insights into RNA cleavage by PIWI argonaute","volume":"639","author":"Z Li","year":"2025","journal-title":"Nature."},{"issue":"7875","key":"pcbi.1013936.ref023","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41586-021-03856-x","article-title":"Structural basis for piRNA targeting","volume":"597","author":"TA Anzelon","year":"2021","journal-title":"Nature."},{"issue":"7923","key":"pcbi.1013936.ref024","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/s41586-022-05009-0","article-title":"GTSF1 accelerates target RNA cleavage by PIWI-clade argonaute proteins","volume":"608","author":"A Arif","year":"2022","journal-title":"Nature."},{"issue":"7","key":"pcbi.1013936.ref025","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1038\/s41588-020-0657-7","article-title":"The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility","volume":"52","author":"P-H Wu","year":"2020","journal-title":"Nat Genet."},{"key":"pcbi.1013936.ref026","doi-asserted-by":"crossref","unstructured":"XGBoost CTG. A scalable tree boosting system. In: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016. p. 785\u201394.","DOI":"10.1145\/2939672.2939785"},{"issue":"1","key":"pcbi.1013936.ref027","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"L Breiman","year":"2001","journal-title":"Machine Learning."},{"issue":"6088","key":"pcbi.1013936.ref028","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/323533a0","article-title":"Learning representations by back-propagating errors","volume":"323","author":"DE Rumelhart","year":"1986","journal-title":"Nature."},{"issue":"5","key":"pcbi.1013936.ref029","doi-asserted-by":"crossref","DOI":"10.1214\/aos\/1013203451","article-title":"Greedy function approximation: a gradient boosting machine.","volume":"29","author":"JH Friedman","year":"2001","journal-title":"Ann Statist."},{"key":"pcbi.1013936.ref030","doi-asserted-by":"crossref","unstructured":"Bishop CM. Neural networks for pattern recognition. Oxford University Press; 1995.","DOI":"10.1093\/oso\/9780198538493.001.0001"},{"issue":"1","key":"pcbi.1013936.ref031","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1109\/TIT.1967.1053964","article-title":"Nearest neighbor pattern classification","volume":"13","author":"T Cover","year":"1967","journal-title":"IEEE Trans Inform Theory."},{"issue":"1","key":"pcbi.1013936.ref032","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1080\/00401706.1970.10488634","article-title":"Ridge regression: biased estimation for nonorthogonal problems","volume":"12","author":"AE Hoerl","year":"1970","journal-title":"Technometrics."},{"issue":"2","key":"pcbi.1013936.ref033","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1023\/A:1018054314350","article-title":"Bagging predictors","volume":"24","author":"L Breiman","year":"1996","journal-title":"Mach Learn."},{"issue":"1","key":"pcbi.1013936.ref034","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1006\/jcss.1997.1504","article-title":"A decision-theoretic generalization of on-line learning and an application to boosting","volume":"55","author":"Y Freund","year":"1997","journal-title":"Journal of Computer and System Sciences."},{"issue":"1","key":"pcbi.1013936.ref035","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/s10994-006-6226-1","article-title":"Extremely randomized trees","volume":"63","author":"P Geurts","year":"2006","journal-title":"Mach Learn."},{"issue":"8","key":"pcbi.1013936.ref036","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1038\/s41594-024-01287-6","article-title":"Mammalian PIWI-piRNA-target complexes reveal features for broad and efficient target silencing","volume":"31","author":"Z Li","year":"2024","journal-title":"Nat Struct Mol Biol."},{"issue":"17","key":"pcbi.1013936.ref037","article-title":"A conserved PIWI silencing complex detects piRNA-target engagement","volume":"85","author":"D De","year":"2025","journal-title":"Mol Cell."}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013936","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T18:31:18Z","timestamp":1771525878000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013936"}},"subtitle":[],"editor":[{"given":"Nir","family":"Ben-Tal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,2,19]]},"references-count":37,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1013936","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,19]]}}}