ArticleNature protocols2016
Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide.
Article in Nature protocols, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it, 118 citations in OpenAlex.
- Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs.Molecular cell · 2017Pooled it
- Cohesin acts as a transcriptional gatekeeper by restraining pause-release to promote processive elongation.Nature communications · 2026Article
- Regulation of RNA transcript elongation in metazoans and its relevance to disease.Nature reviews. Molecular cell biology · 2026Review
- Site-specific DNA double-strand break induces local transcription in cis and protein expression.Communications biology · 2026Article
- Phosphorylation of SF3B1 by CDK11 orchestrates spliceosome activation via SNIP1-dependent RES complex recruitment.Nature communications · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- IWS1 positions downstream DNA to globally stimulate Pol II elongation.Nature communications · 2025Article
- Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition.Nature structural & molecular biology · 2025Article
- Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.Molecular cell · 2025Article
- Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.Nucleic acids research · 2025Article
- RNA Polymerase II Activity Control of Gene Expression and Involvement in Disease.Journal of molecular biology · 2025Review
- Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.bioRxiv : the preprint server for biology · 2024Article
- Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation.Nature communications · 2024Article
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- Nuclear export is a limiting factor in eukaryotic mRNA metabolism.PLoS computational biology · 2024Article
- DNA G-Quadruplex Is a Transcriptional Control Device That Regulates Memory.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2024Article
- Blood transcriptome differentiates clinical clusters for asthma.The World Allergy Organization journal · 2024Article
- Internal and external normalization of nascent RNA sequencing run-on experiments.BMC bioinformatics · 2024Article
- PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.Nature communications · 2023Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The transcription cycle of RNA polymerase II (Pol II) correlates with changes to the phosphorylation state of its large subunit C-terminal domain (CTD). We recently developed Native Elongation Transcript sequencing using mammalian cells (mNET-seq), which generates single-nucleotide-resolution genome-wide profiles of nascent RNA and co-transcriptional RNA processing that are associated with different CTD phosphorylation states. Here we provide a detailed protocol for mNET-seq. First, Pol II elongation complexes are isolated with specific phospho-CTD antibodies from chromatin solubilized by micrococcal nuclease digestion. Next, RNA derived from within the Pol II complex is size fractionated and Illumina sequenced. Using mNET-seq, we have previously shown that Pol II pauses at both ends of protein-coding genes but with different CTD phosphorylation patterns, and we have also detected phosphorylation at serine 5 (Ser5-P) CTD-specific splicing intermediates and Pol II accumulation over co-transcriptionally spliced exons. With moderate biochemical and bioinformatic skills, mNET-seq can be completed in ∼6 d, not including sequencing and data analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.