Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ
| العنوان: | Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ |
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| المؤلفون: | Chuan He, Tong Wu, Ruitu Lyu, Qiancheng You |
| المصدر: | Nature methods |
| سنة النشر: | 2020 |
| مصطلحات موضوعية: | Transcription, Genetic, genetic processes, DNA, Single-Stranded, RNA polymerase II, Biochemistry, DNA sequencing, Article, 03 medical and health sciences, chemistry.chemical_compound, Mice, Transcription (biology), Animals, Humans, natural sciences, Enhancer, Promoter Regions, Genetic, Molecular Biology, Polymerase, 030304 developmental biology, 0303 health sciences, Aldehydes, biology, RNA, High-Throughput Nucleotide Sequencing, Promoter, Cell Biology, Sequence Analysis, DNA, Butanones, Cell biology, Enhancer Elements, Genetic, chemistry, Gene Expression Regulation, biology.protein, DNA, Biotechnology |
| الوصف: | Transcription is a highly dynamic process that generates single-stranded DNA (ssDNA) in the genome as ‘transcription bubbles’. Here we describe a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, based on the fast and specific reaction between N3-kethoxal and guanines in ssDNA. KAS-seq allows rapid (within 5 min), sensitive and genome-wide capture and mapping of ssDNA produced by transcriptionally active RNA polymerases or other processes in situ using as few as 1,000 cells. KAS-seq enables definition of a group of enhancers that are single-stranded and enrich unique sequence motifs. These enhancers are associated with specific transcription-factor binding and exhibit more enhancer–promoter interactions than typical enhancers do. Under conditions that inhibit protein condensation, KAS-seq uncovers a rapid release of RNA polymerase II (Pol II) from a group of promoters. KAS-seq thus facilitates fast and accurate analysis of transcription dynamics and enhancer activities simultaneously in both low-input and high-throughput manner. KAS-seq applies N3-kethoxal to label guanines along single-stranded DNA in live cells, enabling characterization of ssDNA-involved transcription dynamics with as little as 1,000 cells. |
| اللغة: | English |
| تدمد: | 1548-7105 1548-7091 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::770063bd4b797da8af373b82f61e84a4Test http://europepmc.org/articles/PMC7205578Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....770063bd4b797da8af373b82f61e84a4 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15487105 15487091 |
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