ArticlePloS one2016
Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- FLYNC: a machine-learning-driven framework for discovering long noncoding RNAs inNAR genomics and bioinformatics · 2026Article
- Analyzing the transcriptomic diversity in isolated mature adipocytes from the major fat depots in rainbow trout (Oncorhynchus mykiss).BMC genomics · 2026Article
- Why the lipid deposition in the muscle fibers and myosepta is selective in triploid rainbow trout? A lncRNA‒mRNA study.BMC genomics · 2025Article
- The Regulatory Role of LncRNAs in Modulating Autophagy and Drug Resistance in Non-Small-Cell Lung Cancer: Focus on Targeted Therapeutic Approaches.Biomolecules · 2025Review
- Autophagy-related lncRNAs and exosomal lncRNAs in colorectal cancer: focusing on lncRNA-targeted strategies.Cancer cell international · 2024Review
- A cloud-based training module for efficient de novo transcriptome assembly using Nextflow and Google cloud.Briefings in bioinformatics · 2024Article
- Genome-Wide Identification and Involvement in Response to Biotic and Abiotic Stresses of lncRNAs in Turbot (International journal of molecular sciences · 2023Article
- Article
- Genome-wide identification and characterization of tissue specific long non-coding RNAs and circular RNAs in common carp (Frontiers in genetics · 2023Article
- Coding and Noncoding Genes Involved in Atrophy and Compensatory Muscle Growth in Nile Tilapia.Cells · 2022Article
- The Emerging Role of Long Non-Coding RNAs in Esophageal Cancer: Functions in Tumorigenesis and Clinical Implications.Frontiers in pharmacology · 2022Review
- The Emerging Roles of the β-Secretase BACE1 and the Long Non-coding RNA BACE1-AS in Human Diseases: A Focus on Neurodegenerative Diseases and Cancer.Frontiers in aging neuroscience · 2022Review
- Genome-wide identification of antisense lncRNAs and their association with susceptibility toFrontiers in immunology · 2022Article
- Non-Coding RNAs: Novel Players in Insulin Resistance and Related Diseases.International journal of molecular sciences · 2021Review
- The emerging regulatory roles of noncoding RNAs in immune function of fish: MicroRNAs versus long noncoding RNAs.Molecular genetics and genomics : MGG · 2021Review
- LncRNA: A Potential Research Direction in Intestinal Barrier Function.Digestive diseases and sciences · 2021Review
- Systematic and computational identification of Androctonus crassicauda long non-coding RNAs.Scientific reports · 2021Article
- De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives.International journal of molecular sciences · 2021Article
- PacBio Iso-Seq Improves the Rainbow Trout Genome Annotation and Identifies Alternative Splicing Associated With Economically Important Phenotypes.Frontiers in genetics · 2021Article
- Regulation of Hippo, TGFβ/SMAD, Wnt/Frontiers in oncology · 2021Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200 nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.
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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.