ArticlePloS one2014
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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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.
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Who cites it
22 citing papers in PubMed, 35 citations in OpenAlex.
- Cis- and trans-action of the cold-induced lncRNAs, SVALKA and SVALNA, regulate CBF1 and CBF3 in Arabidopsis.EMBO reports · 2025Article
- Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis.The Plant cell · 2024Article
- AdvancingPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology.GigaScience · 2024Article
- The non-coding RNA SVALKA locus produces a cis-natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures.Plant communications · 2023Article
- TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes.BMC bioinformatics · 2021Article
- Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence.Nature communications · 2021Article
- Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.Nature communications · 2020Article
- Organismal benefits of transcription speed control at gene boundaries.EMBO reports · 2020Article
- Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis.Nucleic acids research · 2020Article
- Article
- Bioinformatic analysis of Chinese hamster ovary host cell protein lipases.AIChE journal. American Institute of Chemical Engineers · 2018Article
- Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles.BMC genomics · 2018Article
- Improved annotation with de novo transcriptome assembly in four social amoeba species.BMC genomics · 2017Article
- Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder.Frontiers in molecular neuroscience · 2017Article
- Genome-wide dynamics of alternative polyadenylation in rice.Genome research · 2016Article
- How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?RNA (New York, N.Y.) · 2016Article
- Article
- Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.BMC genomics · 2015Article
- In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq.PloS one · 2015Article
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
Abstract
The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3' untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3' polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1) gene and 3' UTR re-annotation (including extension of one 3' UTR by 5.9 kb); (2) disentangling of gene expression in complex regions; (3) clearer interpretation of small RNA expression and (4) identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental data.
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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.