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Michi Miura
Department Kawasaki Medical School Kawasaki Medical School, Department of Microbiology, Position Instructor |
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| Article types | 原著 |
| Language | English |
| Peer review | Peer reviewed |
| Title | CUT&RUN detects distinct DNA footprints of RNA polymerase II near the transcription start sites. |
| Journal | Formal name：Chromosome Research Abbreviation：Chromosome Res ISSN code：15736849/09673849 |
| Domestic / Foregin | Foregin |
| Volume, Issue, Page | 28(3-4),pp.381-393 |
| Author and coauthor | Miura Michi, Chen Honglin |
| Authorship | Lead author,Corresponding author |
| Publication date | 2020/12 |
| Summary | CUT&RUN is a powerful tool to study protein-DNA interactions in vivo. DNA fragments cleaved by the targeted micrococcal nuclease identify the footprints of DNA-binding proteins on the chromatin. We performed CUT&RUN on human lung carcinoma cell line A549 maintained in a multi-well cell culture plate to profile RNA polymerase II. Long (> 270 bp) DNA fragments released by CUT&RUN corresponded to the bimodal peak around the transcription start sites, as previously seen with chromatin immunoprecipitation. However, we found that short (< 120 bp) fragments identify a well-defined peak localised at the transcription start sites. This distinct DNA footprint of short fragments, which constituted only about 5% of the total reads, suggests the transient positioning of RNA polymerase II before promoter-proximal pausing, which has not been detected in the physiological settings by standard chromatin immunoprecipitation. We showed that the positioning of the large-size-class DNA footprints around the short-fragment peak was associated with the directionality of transcription, demonstrating the biological significance of distinct CUT&RUN footprints of RNA polymerase II. |
| DOI | 10.1007/s10577-020-09643-0 |
| PMID | 33070289 |