The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Thiol-linked alkylation for the metabolic sequencing of RNA
Open accessPreprint — published as 10.1038/nmeth.4435 · Paper page
Abstract
Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady-state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), an orthogonal chemistry-based epitranscriptomics-sequencing technology that uncovers 4-thiouridine (s 4 U)-incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM-seq enables rapid access to RNA polymerase II-dependent gene expression dynamics in the context of total RNA. When applied to mouse embryonic stem cells, SLAM-seq provides global and transcript-specific insights into pluripotency-associated gene expression. We validated the method by showing that the RNA-polymerase II-dependent transcriptional output scales with Oct4/Sox2/Nanog-defined enhancer activity; and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N 6 -methyladenosine. SLAM-seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective, and scalable manner. One Sentence Summary: Chemical nucleotide-analog derivatization provides global insights into transcriptional and post-transcriptional gene regulation
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“Note, that the ability to determine de novo synthesized transcripts will depend on (1) the s(4)U uptake kinetics of the chosen cellular system, (2) the overall transcriptional activity of the cell type and (3) the library sequencing depth.”
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Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm
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Metadata
- Authors
- Herzog, V. A., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, T. R., Wlotzka, W., von Haeseler, A., Zuber, J., & Ameres, S. L.
- Affiliations
- Institute of Molecular Biotechnology (AT)
- Research Institute of Molecular Pathology (AT)
- Max Perutz Labs (AT)
- Corresponding author
- Ameres, Stefan L.
- ORCID
- Venue
- Nature Methods
- Publisher
- openRxiv
- Published
- 2017-08-17
- Volume
- 14
- Issue
- 12
- Pages
- 1198-1204
- ISSN
- 1548-7091 (ISSN-L)
- PMC
- PMC5712218
- OpenAlex
- W2759506905
- Cited by
- 622
- References
- 66
- Citations by year
- 2026: 80 · 2025: 79 · 2024: 117 · 2023: 84 · 2022: 71 · 2021: 73 · 2020: 52 · 2019: 44 · 2018: 21 · 2017: 1
- FWCI
- 13.19
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Österreichischen Akademie der Wissenschaften
- Austrian Science Fund (W12-7-B09, Y-733-B22 START, F4322)
- Wirtschaftsagentur Wien
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- SLAM-seq, RNA turnover, RNA metabolism, RNA polymerase II transcription, gene expression dynamics, microRNA, N6-methyladenosine, post-transcriptional regulation, mouse embryonic stem cells, enhancer activity
- MeSH terms
- Alkylation, RNA, RNA Polymerase II, RNA Processing, Post-Transcriptional, Sulfhydryl Compounds, Thiouridine, Gene Expression Profiling, Gene Regulatory Networks, Embryonic Stem Cells, High-Throughput Screening Assays, High-Throughput Nucleotide Sequencing
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