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While fragmentation of parental RNAs produces functionally diverse small RNAs, current analytical approaches are limited to abundance measures and cannot systematically quantify differential cleavage signals. Here, we present\n                    <jats:italic>qMAP<\/jats:italic>\n                    , a computational framework profiling differential fragmentation of parental RNAs from small RNA sequencing data.\n                    <jats:italic>qMAP<\/jats:italic>\n                    integrates two complementary models to identify condition-specific fragmentation patterns and includes a dedicated module to pinpoint the small RNA species driving these differences. Using\n                    <jats:italic>qMAP<\/jats:italic>\n                    , we uncover dynamic tRNA and rRNA fragmentation during mouse cell reprogramming, demonstrate the classification power of RNA fragmentation in human ulcerative colitis, develop and validate a blood-based RNA fragmentation signature of recurrent implantation failure, and identify aging-associated RNA fragmentation in sperm, which supports RNA fragmentation as a distinct regulatory dimension beyond expression\/abundance information.\n                    <jats:italic>qMAP<\/jats:italic>\n                    enables systematic exploration of the regulatory \u201cRNA fragmentome\u201d, providing a foundational tool for both mechanistic discovery and translational applications of noncanonical small RNAs.\n                  <\/jats:p>","DOI":"10.1038\/s44320-026-00237-2","type":"journal-article","created":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T17:13:25Z","timestamp":1784567605000},"page":"1626-1649","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["qMAP decodes RNA fragmentation dynamics in development and disease"],"prefix":"10.1038","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2727-9721","authenticated-orcid":false,"given":"Hukam C","family":"Rawal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiancheng","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5964-0067","authenticated-orcid":false,"given":"Xudong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6353-9589","authenticated-orcid":false,"given":"Qi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2361-1931","authenticated-orcid":false,"given":"Tong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"key":"237_CR1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-37427-7","volume":"14","author":"N Alata Jimenez","year":"2023","unstructured":"Alata Jimenez N, Castellano M, Santillan EM, Boulias K, Boan A, Arias Padilla LF, Fernandino JI, Greer EL, Tosar JP, Cochella L et al (2023) Paternal methotrexate exposure affects sperm small RNA content and causes craniofacial defects in the offspring. 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