ArticleCurrent protocols in molecular biology2017
A Detailed Protocol for Subcellular RNA Sequencing (subRNA-seq).
Article in Current protocols in molecular biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 50 citations in OpenAlex.
- APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.Nature protocols · 2026Review
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- mRNALocator-imb: an imbalance-tolerant ensemble framework integrating random forest and transformer for mRNA subcellular localization prediction.Frontiers in genetics · 2026Article
- Ovarian tumor cells gain competitive advantage by actively reducing the cellular fitness of microenvironment cells.Nature biotechnology · 2025Article
- NPM1 mislocalization mediated by RNA Pol I inhibition alters chromatin landscape.bioRxiv : the preprint server for biology · 2025Article
- Long-read Sequencing of Nascent RNA from Budding and Fission Yeasts.bioRxiv : the preprint server for biology · 2025Article
- Stabilizing a mammalian RNA thermometer confers neuroprotection in subarachnoid hemorrhage.Nature communications · 2025Article
- Article
- The PRMT5-splicing axis is a critical oncogenic vulnerability that regulates detained intron splicing.iScience · 2025Article
- Nanosilicates promote angiogenesis through activation of ROS-mediated WNT/β-catenin pathway.Science advances · 2025Article
- The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells.Nucleic acids research · 2025Article
- CytoLNCpred-a computational method for predicting cytoplasm associated long non-coding RNAs in 15 cell-lines.Frontiers in bioinformatics · 2025Article
- Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.Molecular cell · 2024Article
- Spatial omics advances for in situ RNA biology.Molecular cell · 2024Review
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- Control of endothelial cell function and arteriogenesis by MEG3:EZH2 epigenetic regulation of integrin expression.Molecular therapy. Nucleic acids · 2024Article
- Article
- TOP1 and R-loops facilitate transcriptional DSBs at hypertranscribed cancer driver genes.iScience · 2024Article
- ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins.Nature communications · 2023Article
- SINEUP non-coding RNA activity depends on specific N6-methyladenosine nucleotides.Molecular therapy. Nucleic acids · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
In eukaryotic cells, RNAs at various maturation and processing levels are distributed across cellular compartments. The standard approach to determine transcript abundance and identity in vivo is RNA sequencing (RNA-seq). RNA-seq relies on RNA isolation from whole-cell lysates and thus mainly captures fully processed, stable, and more abundant cytoplasmic RNAs over nascent, unstable, and nuclear RNAs. Here, we provide a step-by-step protocol for subcellular RNA-seq (subRNA-seq). subRNA-seq allows the quantitative measurement of RNA polymerase II-generated RNAs from the chromatin, nucleoplasm, and cytoplasm of mammalian cells. This approach relies on cell fractionation prior to RNA isolation and sequencing library preparation. High-throughput sequencing of the subcellular RNAs can then be used to reveal the identity, abundance, and subcellular distribution of transcripts, thus providing insights into RNA processing and maturation. Deep sequencing of the chromatin-associated RNAs further offers the opportunity to study nascent RNAs. Subcellular RNA-seq libraries are obtained within 5 days. © 2017 by John Wiley & Sons, Inc.
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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.