Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing
Open accessAbstract
Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5'splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated with Pol II CTD phosphorylated on the serine 5 position (S5P), which is accumulated over downstream exons. Also, depletion of termination factors substantially reduces Pol II pausing at gene ends, leading to termination defects. Notably, termination factors play an additional promoter role by restricting non-productive RNA synthesis in a Pol II CTD S2P-specific manner. Our results suggest that CTD phosphorylation patterns established for yeast transcription are significantly different in mammals. Taken together, mNET-seq provides dynamic and detailed snapshots of the complex events underlying transcription in mammals.
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Higher RNA Pol II accumulation has been reported at spliced exons, as compared to skipped exons.
“Moreover, higher RNA Pol II accumulation has been reported at spliced exons, as compared to skipped exons (Kwak et al, 2013; Mayer et al, 2015; Nojima et al, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Nojima et al, 2015
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- Authors
- Nojima, T., Gomes, T., Grosso, A. R. F., Kimura, H., Dye, M. J., Dhir, S., Carmo-Fonseca, M., & Proudfoot, N. J.
- Affiliations
- University of Oxford (GB)
- University of Lisbon (PT)
- Corresponding author
- Proudfoot, Nicholas J.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-04
- Volume
- 161
- Issue
- 3
- Pages
- 526-540
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4410947
- OpenAlex
- W2076825429
- Cited by
- 562
- References
- 63
- Citations by year
- 2026: 23 · 2025: 28 · 2024: 52 · 2023: 50 · 2022: 57 · 2021: 67 · 2020: 65 · 2019: 57 · 2018: 49 · 2017: 51 · 2016: 45 · 2015: 16
- FWCI
- 23.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
- Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
- Funders
- KANAE foundation
- JSPS
- JST CREST
- Wellcome Trust (091805/Z/10/Z)
- ERC (339270)
- Fundação Ciência e Tecnologia, Portugal
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- nascent RNA, RNA polymerase II, CTD phosphorylation, RNA processing, splicing, spliceosome, transcription termination, termination factors, promoter activity, elongation, single-nucleotide resolution
- MeSH terms
- HeLa Cells, Humans, Phosphorylation, RNA Polymerase II, RNA Processing, Post-Transcriptional, Transcription, Genetic, Genome, Human, Sequence Analysis, RNA, Protein Structure, Tertiary, MicroRNAs
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