{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T11:08:20Z","timestamp":1788952100121,"version":"build-2803163510"},"reference-count":62,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Hong Kong Research Grants Council","award":["GRF 17318422"],"award-info":[{"award-number":["GRF 17318422"]}]},{"name":"Hong Kong Research Grants Council","award":["17308925"],"award-info":[{"award-number":["17308925"]}]},{"name":"Laboratory for Synthetic Chemistry and Chemical Biology"},{"DOI":"10.13039\/501100003452","name":"Innovation and Technology Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003452","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Chromatin-associated RNAs (caRNAs) play critical roles in regulating chromatin organization and transcription, underscoring the importance of their study. Proximity labeling has emerged as a promising and versatile technique for profiling caRNAs with high spatiotemporal resolution. While being a powerful technique, traditional proximity labeling methods depend on complex, high-input enrichment protocols, which significantly limit their wide practical application. Here, we developed a straightforward, enrichment-free caRNA profiling strategy: proximity crosslinking-induced RNA depletion sequencing (PCRD-seq). This approach leverages the proximity crosslinking between chromatin and its surrounding RNAs induced by singlet oxygen generated by HoeDBF, a photosensitizer targeting chromatin region. The proximity crosslinking hinders the release of caRNAs during routine TRIzol extraction, consequently leading to a specific depletion of these RNAs. This method was successfully applied to investigate the role of U1 small nuclear RNA (snRNA) in RNA chromatin retention and the differences in chromatin-associated transcriptomes between two ovarian cancer cell lines with opposite metastatic capability. Moreover, our PCRD-seq exhibits potential in profiling nuclear lamina-associated RNAs, which paves the way for its application to profile RNAs associated with other chromatin subdomains. The minimal cell input and simple workflow render PCRD-seq a transformative tool for wide applications.<\/jats:p>","DOI":"10.1093\/nar\/gkag853","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T11:53:02Z","timestamp":1787140382000},"source":"Crossref","is-referenced-by-count":0,"title":["PCRD-seq: proximity crosslinking-induced RNA depletion sequencing for low-input chromatin-associated transcriptome profiling"],"prefix":"10.1093","volume":"54","author":[{"given":"Jinghua","family":"Han","sequence":"first","affiliation":[{"name":"Department of Chemistry, The University of Hong Kong , Hong Kong, SAR, 999077 ,","place":["China"]},{"name":"Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories , Hong Kong, SAR, 999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Chemistry, The University of Hong Kong , Hong 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999077 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice S T","family":"Wong","sequence":"additional","affiliation":[{"name":"Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories , Hong Kong, SAR, 999077 ,","place":["China"]},{"name":"School of Biological Sciences, The University of Hong Kong , Hong Kong, SAR ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0438-449X","authenticated-orcid":false,"given":"Ying","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Chemistry, The University of Hong Kong , Hong Kong, SAR, 999077 ,","place":["China"]},{"name":"Laboratory for Synthetic Chemistry and Chemical Biology Limited, New Territories , Hong Kong, SAR, 999077 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