ArticleNature structural & molecular biology2011
Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.
Article in Nature structural & molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 197 papers.
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Who cites it
197 citing papers in PubMed, 336 citations in OpenAlex.
- Cohesin acts as a transcriptional gatekeeper by restraining pause-release to promote processive elongation.Nature communications · 2026Article
- StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts.Nature methods · 2026Article
- Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells.bioRxiv : the preprint server for biology · 2026Article
- Predicting trajectories of illness using RNA velocity of whole blood.Nature communications · 2026Observational
- Prolonged Sample Storage Reshapes the mInternational journal of molecular sciences · 2026Article
- Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib.Science advances · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Co-transcriptional gene regulation in plants.aBIOTECH · 2026Review
- Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment.NAR cancer · 2025Article
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- Impact of commercial RNA extraction methods on the recovery of human RNA sequence data from archival fixed tissues.BioTechniques · 2025Article
- Laser-capture microdissection for spatial transcriptomics of immunohistochemically detected neurons.The Journal of biological chemistry · 2025Article
- Deciphering HIV-1 Transcription Initiation and Elongation from Single-Molecule Imaging Data.Research (Washington, D.C.) · 2025Article
- Decoding protein-RNA interactions using CLIP-based methodologies.Nature reviews. Genetics · 2024Review
- Post-transcriptional regulation supports the homeostatic expression of mature RNA.Briefings in bioinformatics · 2024Article
- NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs.Genome biology · 2024Article
- A single workflow for multi-species blood transcriptomics.BMC genomics · 2024Article
- KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing.bioRxiv : the preprint server for biology · 2024Article
- The 3D Genome in Brain Development: An Exploration of Molecular Mechanisms and Experimental Methods.Neuroscience insights · 2024Review
- Hitting the brakes on transcription to extend lifespan.Trends in genetics : TIG · 2023Article
137 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptome sequencing allows for analysis of mature RNAs at base pair resolution. Here we show that RNA-seq can also be used for studying nascent RNAs undergoing transcription. We sequenced total RNA from human brain and liver and found a large fraction of reads (up to 40%) within introns. Intronic RNAs were abundant in brain tissue, particularly for genes involved in axonal growth and synaptic transmission. Moreover, we detected significant differences in intronic RNA levels between fetal and adult brains. We show that the pattern of intronic sequence read coverage is explained by nascent transcription in combination with co-transcriptional splicing. Further analysis of co-transcriptional splicing indicates a correlation between slowly removed introns and alternative splicing. Our data show that sequencing of total RNA provides unique insight into the transcriptional processes in the cell, with particular importance for normal brain development.
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