ArticleNucleic acids research2020
Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 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
28 citing papers in PubMed, 44 citations in OpenAlex.
- Loss of U11/U12 spliceosome geneLife science alliance · 2026Article
- The adhesion GPCR ADGRV1 controls glutamate homeostasis in hippocampal astrocytes supporting neurons.Acta neuropathologica communications · 2026Article
- Characterization of Mitochondrial Double-Stranded RNA Levels in Non-Small Cell Lung Carcinoma.Cancer research communications · 2026Article
- SnoBIRD: a tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes.Nucleic acids research · 2025Article
- Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential.Genome biology · 2025Article
- Review
- Small Nucleolar RNAs in Head and Neck Squamous Cell Carcinomas.Journal of dental research · 2025Review
- Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq.RNA (New York, N.Y.) · 2024Article
- Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster.Nucleic acids research · 2024Article
- Precision run-on sequencing (PRO-seq) for microbiome transcriptomics.Nature microbiology · 2024Article
- Genome annotation: From human genetics to biodiversity genomics.Cell genomics · 2023Review
- Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences.Genome biology · 2023Article
- A genome-wide landscape of mRNAs, lncRNAs, circRNAs and miRNAs during intramuscular adipogenesis in cattle.BMC genomics · 2022Article
- A chromosome-level genome of the booklouse, Liposcelis brunnea, provides insight into louse evolution and environmental stress adaptation.GigaScience · 2022Article
- MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts.BMC bioinformatics · 2022Article
- TGIRT-seq Protocol for the Comprehensive Profiling of Coding and Non-coding RNA Biotypes in Cellular, Extracellular Vesicle, and Plasma RNAs.Bio-protocol · 2021Article
- circCORO1C promotes the proliferation and metastasis of hepatocellular carcinoma by enhancing the expression of PD-L1 through NF-κB pathway.Journal of clinical laboratory analysis · 2021Article
- Low-bias ncRNA libraries using ordered two-template relay: Serial template jumping by a modified retroelement reverse transcriptase.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Systematic Identification and Functional Validation of New snoRNAs in Human Muscle Progenitors.Non-coding RNA · 2021Article
- Annotation of snoRNA abundance across human tissues reveals complex snoRNA-host gene relationships.Genome biology · 2021Article
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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 111 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new snoRNA and tRNA-like genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distorts the perceived architecture of the human transcriptome.
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.