ArticleNucleic acids research2010
RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed, 48 citations in OpenAlex.
- Insights into the human cDNA: A descriptive study using library screening in yeast.Journal, genetic engineering & biotechnology · 2024Article
- The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.Frontiers in molecular biosciences · 2021Review
- Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA.Nucleic acids research · 2020Article
- Identifying the Translatome of Mouse NEBD-Stage Oocytes via SSP-Profiling; A Novel Polysome Fractionation Method.International journal of molecular sciences · 2020Article
- Comparative transcriptomics in Leishmania braziliensis: disclosing differential gene expression of coding and putative noncoding RNAs across developmental stages.RNA biology · 2019Article
- Two genetic codes: Repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives.Communicative & integrative biology · 2017Article
- Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.Bioinformatics (Oxford, England) · 2015Article
- Generation of a neuro-specific microarray reveals novel differentially expressed noncoding RNAs in mouse models for neurodegenerative diseases.RNA (New York, N.Y.) · 2014Article
- BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.Bioinformatics (Oxford, England) · 2014Article
- Characterization of the human ESC transcriptome by hybrid sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Article
- Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs.BioEssays : news and reviews in molecular, cellular and developmental biology · 2013Review
- Profiling and identification of small rDNA-derived RNAs and their potential biological functions.PloS one · 2013Article
- Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation.Nucleic acids research · 2012Article
- Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis.Nucleic acids research · 2012Article
- RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs.Nucleic acids research · 2012Article
- Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.Journal of nucleic acids · 2012Article
- Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression.Nucleic acids research · 2011Article
- Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures.BMC bioinformatics · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Up to 450,000 non-coding RNAs (ncRNAs) have been predicted to be transcribed from the human genome. However, it still has to be elucidated which of these transcripts represent functional ncRNAs. Since all functional ncRNAs in Eukarya form ribonucleo-protein particles (RNPs), we generated specialized cDNA libraries from size-fractionated RNPs and validated the presence of selected ncRNAs within RNPs by glycerol gradient centrifugation. As a proof of concept, we applied the RNP method to human Hela cells or total mouse brain, and subjected cDNA libraries, generated from the two model systems, to deep-sequencing. Bioinformatical analysis of cDNA sequences revealed several hundred ncRNP candidates. Thereby, ncRNAs candidates were mainly located in intergenic as well as intronic regions of the genome, with a significant overrepresentation of intron-derived ncRNA sequences. Additionally, a number of ncRNAs mapped to repetitive sequences. Thus, our RNP approach provides an efficient way to identify new functional small ncRNA candidates, involved in RNP formation.
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.