{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T06:03:05Z","timestamp":1789624985439,"version":"build-2803163510"},"reference-count":58,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370707"],"award-info":[{"award-number":["32370707"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070655"],"award-info":[{"award-number":["32070655"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Plant Cell &amp;amp; Environment"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    In addition to microRNAs (miRNAs), some small interfering RNAs (siRNAs) such as\n                    <jats:italic>trans<\/jats:italic>\n                    \u2010acting siRNAs are also associated with ARGONAUTE 1 (AGO1) for target cleavage in plants. Efficient identification of the AGO1\u2010enriched small RNAs (sRNAs) and their targets became a challenging task. Here, we emphasized the utility of RIP (RNA immunoprecipitation) sequencing in probing the above issue. By analyzing the AGO1\u2010RIP\u2010sRNA\u2010seq data, 42\u2009991, 22\u2009516, 34\u2009555, and 19\u2009754 AGO1\u2010enriched sRNAs were identified from flowers, leaves, roots, and seedlings of\n                    <jats:italic>Arabidopsis<\/jats:italic>\n                    , respectively. RIP\u2010RNA\u2010seq of DCL1 and HYL1 enabled us to discover 14 miRNA precursor candidates encoding the AGO1\u2010enriched sRNAs. Second, to reduce the false positive rate of small RNA binding site (SBS) predictions, we focused on the SBSs covered by the AGO1 RIP peaks representing the transcriptome\u2010wide binding regions of this protein. Degradome\u2010based cleavage site mapping enabled us to identify the targetomes of the AGO1\u2010enriched sRNAs in distinct samples. Notably, a great portion of the sRNA\u2013target pairs detected in the wild\u2010type seedlings were absent in the\n                    <jats:italic>ago1<\/jats:italic>\n                    mutants. The high AGO1 dependency demonstrated the reliability of our workflow for sRNA target identification. Moreover, GO (Gene Ontology) term enrichment analysis showed that the ecotype\u2010 and organ\u2010specific targetomes were functionally related to environmental response and organ development, respectively. Finally, some of the AGO1\u2010enriched sRNAs showed great potential of regulating specific long non\u2010coding RNAs. Together, by employing RIP\u2010seq, our study provided a promising workflow for identification of the AGO1\u2010enriched sRNomes and their targetomes in plants.\n                  <\/jats:p>","DOI":"10.1111\/pce.70893","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T05:21:41Z","timestamp":1789622501000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification of the ARGONAUTE 1\u2010Enriched sRNomes and Targetomes by Integrated RIP\u2010Seq Data Analysis in\n                    <i>Arabidopsis thaliana<\/i>"],"prefix":"10.1111","author":[{"given":"Zhifang","family":"Jiang","sequence":"first","affiliation":[{"name":"College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zedi","family":"Feng","sequence":"additional","affiliation":[{"name":"College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiling","family":"Dong","sequence":"additional","affiliation":[{"name":"College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Yao","sequence":"additional","affiliation":[{"name":"College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxia","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Pharmacy Hangzhou Normal University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4654-0622","authenticated-orcid":false,"given":"Yijun","family":"Meng","sequence":"additional","affiliation":[{"name":"College of Life and Environmental Sciences Hangzhou Normal University Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"issue":"12","key":"e_1_2_9_2_1","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1038\/ng1478","article-title":"Evolution of microRNA Genes by Inverted Duplication of Target Gene Sequences in Arabidopsis thaliana","volume":"36","author":"Allen E.","year":"2004","journal-title":"Nature Genetics"},{"issue":"12","key":"e_1_2_9_3_1","doi-asserted-by":"crossref","first-page":"4010","DOI":"10.1093\/nar\/gkp272","article-title":"Comprehensive Prediction of Novel microRNA Targets in Arabidopsis thaliana","volume":"37","author":"Alves\u2010Junior L.","year":"2009","journal-title":"Nucleic Acids Research"},{"issue":"15","key":"e_1_2_9_4_1","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger A. 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G.","year":"2026","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_9_6_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4939-7165-7_1","article-title":"Plant ARGONAUTEs: Features, Functions, and Unknowns","volume":"1640","author":"Carbonell A.","year":"2017","journal-title":"Methods in Molecular Biology"},{"issue":"9","key":"e_1_2_9_7_1","doi-asserted-by":"crossref","first-page":"3613","DOI":"10.1105\/tpc.112.099945","article-title":"Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer\u2010Defective Mutants","volume":"24","author":"Carbonell A.","year":"2012","journal-title":"Plant Cell"},{"issue":"9","key":"e_1_2_9_8_1","doi-asserted-by":"crossref","first-page":"3318","DOI":"10.1073\/pnas.0611119104","article-title":"Bioinformatic Prediction and Experimental Validation of a microRNA\u2010Directed Tandem trans\u2010Acting siRNA Cascade in Arabidopsis","volume":"104","author":"Chen H. 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