ArticleNucleic acids research2015
Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- A method of comprehensive sequencing analysis of the small RNA fragmentome (RiboMarker).RNA (New York, N.Y.) · 2026Article
- RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution.bioRxiv : the preprint server for biology · 2025Article
- RNA modifications, alternative splicing and circular RNA landscape in the mouse brain: inosine and beyond.Scientific reports · 2025Article
- Efficient circRNA Detection Using the Processive Reverse Transcriptase uMRT.Bio-protocol · 2025Article
- Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq.RNA (New York, N.Y.) · 2024Article
- Advances in methods for tRNA sequencing and quantification.Trends in genetics : TIG · 2024Review
- Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.Nature biotechnology · 2021Article
- Simultaneous processing and degradation of mitochondrial RNAs revealed by circularized RNA sequencing.Nucleic acids research · 2017Article
- Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner.Nucleic acids research · 2017Article
- Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells.RNA (New York, N.Y.) · 2016Article
- RNA polymerase II pausing as a context-dependent reader of the genome.Biochemistry and cell biology = Biochimie et biologie cellulaire · 2016Review
- Regulation of mammalian transcription and splicing by Nuclear RNAi.Nucleic acids research · 2016Review
- CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite.RNA (New York, N.Y.) · 2016Article
- Design and bioinformatics analysis of genome-wide CLIP experiments.Nucleic acids research · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived from cultured human cells after crosslinking and immunoprecipitation (CLIP). Here, we report a method for obtaining strand-specific small RNA libraries for RNA sequencing that requires picograms of RNA. We employ an intramolecular circularization step that increases the efficiency of library preparation and avoids the need for intermolecular ligations of adaptor sequences. Other key features include random priming for full-length cDNA synthesis and gel-free library purification. Using our method, we generated CLIP-Seq libraries from nuclear RNA that had been UV-crosslinked and immunoprecipitated with anti-Argonaute 2 (Ago2) antibody. Computational protocols were developed to enable analysis of raw sequencing data and we observe substantial differences between recognition by Ago2 of RNA species in the nucleus relative to the cytoplasm. This RNA self-circularization approach to RNA sequencing (RC-Seq) allows data to be obtained using small amounts of input RNA that cannot be sequenced by standard methods.
Indexed as
Identifiers
What OpenQuestion holds
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.