ArticleNature protocols2021
Revealing nascent RNA processing dynamics with nano-COP.
Article in Nature protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 48 citations in OpenAlex.
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Improving calls of differentially transcribed enhancers and their upstream regulators.Bioinformatics advances · 2026Article
- Polyadenylation landscape of in vivo long-term potentiation in the rat brain.RNA (New York, N.Y.) · 2025Article
- mRNA initiation and termination are spatially coordinated.Science (New York, N.Y.) · 2025Article
- Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts.bioRxiv : the preprint server for biology · 2025Article
- Improving confidence of differential transcription calls in enhancers.bioRxiv : the preprint server for biology · 2025Article
- scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection.Nature communications · 2025Article
- Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination.Nature communications · 2025Article
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.Genome research · 2025Article
- Mapping snoRNA-target RNA interactions in an RNA-binding protein-dependent manner with chimeric eCLIP.Genome biology · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing.bioRxiv : the preprint server for biology · 2024Article
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- Co-transcriptional gene regulation in eukaryotes and prokaryotes.Nature reviews. Molecular cell biology · 2024Review
- A kinetic dichotomy between mitochondrial and nuclear gene expression processes.Molecular cell · 2024Article
- A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis.bioRxiv : the preprint server for biology · 2023Article
- High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription.Nature communications · 2023Article
- Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts.Nature structural & molecular biology · 2023Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
During maturation, eukaryotic precursor RNAs undergo processing events including intron splicing, 3'-end cleavage, and polyadenylation. Here we describe nanopore analysis of co-transcriptional processing (nano-COP), a method for probing the timing and patterns of RNA processing. An extension of native elongating transcript sequencing, which quantifies transcription genome-wide through short-read sequencing of nascent RNA 3' ends, nano-COP uses long-read nascent RNA sequencing to observe global patterns of RNA processing. First, nascent RNA is stringently purified through a combination of 4-thiouridine metabolic labeling and cellular fractionation. In contrast to cDNA or short-read-based approaches relying on reverse transcription or amplification, the sample is sequenced directly through nanopores to reveal the native context of nascent RNA. nano-COP identifies both active transcription sites and splice isoforms of single RNA molecules during synthesis, providing insight into patterns of intron removal and the physical coupling between transcription and splicing. The nano-COP protocol yields data within 3 d.
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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.