ArticlePloS one2015
A catalogue of novel bovine long noncoding RNA across 18 tissues.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 89 citations in OpenAlex.
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- Identification and Classification of Long Non-Coding RNAs in the Mammary Gland of the Holstein Cow.International journal of molecular sciences · 2023Article
- Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review.International journal of molecular sciences · 2023Review
- Comprehensive transcriptomic analysis of long non-coding RNAs in bovine ovarian follicles and early embryos.PloS one · 2023Review
- Differential expression of long non-coding RNAs underVirulence · 2022Article
- Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases.Pathogens (Basel, Switzerland) · 2022Review
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- LncRNAs in domesticated animals: from dog to livestock species.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Transcriptome Sequencing to Identify Important Genes and lncRNAs Regulating Abdominal Fat Deposition in Ducks.Animals : an open access journal from MDPI · 2022Article
- Mammary epithelial cell transcriptome reveals potential roles of lncRNAs in regulating milk synthesis pathways in Jersey and Kashmiri cattle.BMC genomics · 2022Article
- Identification of Long Noncoding RNAs Involved in Eyelid Pigmentation of Hereford Cattle.Frontiers in genetics · 2022Article
- Identification of Potential Long Non-Coding RNA Candidates that Contribute to Triple-Negative Breast Cancer in Humans through Computational Approach.International journal of molecular sciences · 2021Article
- Emerging Role of MicroRNA-200 Family in Dentistry.Non-coding RNA · 2021Review
- A novel lncRNA promotes myogenesis of bovine skeletal muscle satellite cells via PFN1-RhoA/Rac1.Journal of cellular and molecular medicine · 2021Article
- Identification and co-expression analysis of long noncoding RNAs and mRNAs involved in the deposition of intramuscular fat in Aohan fine-wool sheep.BMC genomics · 2021Article
- Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression.Frontiers in veterinary science · 2021Article
- PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long non-coding RNA (lncRNA) have been implicated in diverse biological roles including gene regulation and genomic imprinting. Identifying lncRNA in bovine across many differing tissue would contribute to the current repertoire of bovine lncRNA, and help further improve our understanding of the evolutionary importance and constraints of these transcripts. Additionally, it could aid in identifying sites in the genome outside of protein coding genes where mutations could contribute to variation in complex traits. This is particularly important in bovine as genomic predictions are increasingly used in genetic improvement for milk and meat production. Our aim was to identify and annotate novel long non coding RNA transcripts in the bovine genome captured from RNA Sequencing (RNA-Seq) data across 18 tissues, sampled in triplicate from a single cow. To address the main challenge in identifying lncRNA, namely distinguishing lncRNA transcripts from unannotated genes and protein coding genes, a lncRNA identification pipeline with a number of filtering steps was developed. A total of 9,778 transcripts passed the filtering pipeline. The bovine lncRNA catalogue includes MALAT1 and HOTAIR, both of which have been well described in human and mouse genomes. We attempted to validate the lncRNA in libraries from three additional cows. 726 (87.47%) liver and 1,668 (55.27%) blood class 3 lncRNA were validated with stranded liver and blood libraries respectively. Additionally, this study identified a large number of novel unknown transcripts in the bovine genome with high protein coding potential, illustrating a clear need for better annotations of protein coding genes.
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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.