Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species
| Autor: | Hans H. Cheng, Ian F Korf, Juan F. Medrano, Alison L. Van Eenennaam, Colin Kern, Huaijun Zhou, Pablo J. Ross, Ying Wang, Mary E. Delany, James L. Chitwood, Catherine W. Ernst |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Male lcsh:QH426-470 Swine Bioinformatics lcsh:Biotechnology ved/biology.organism_classification_rank.species Computational biology Biology Proteomics Genome Medical and Health Sciences 03 medical and health sciences 0302 clinical medicine lcsh:TP248.13-248.65 Information and Computing Sciences Genetics Animals Epigenetics Model organism Gene Domestic Regulation of gene expression ved/biology Gene Expression Profiling Human Genome High-Throughput Nucleotide Sequencing Molecular Sequence Annotation Biological Sciences Long non-coding RNA Gene regulation lcsh:Genetics 030104 developmental biology Gene Expression Regulation Organ Specificity Animals Domestic 030220 oncology & carcinogenesis Long non-coding RNAs RNA RNA Long Noncoding Cattle Long Noncoding Generic health relevance DNA microarray Chickens Biotechnology |
| Zdroj: | BMC genomics, vol 19, iss 1 BMC Genomics, Vol 19, Iss 1, Pp 1-14 (2018) |
| Popis: | Background Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs identified lncRNAs in specific developmental stages or differentially expressed under specific conditions in a limited number of tissues, more comprehensive identification of lncRNAs in these species is needed. The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs. As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs. Results Comprehensive lncRNA annotations for the chicken, cattle, and pig genomes were generated by utilizing RNA-seq from eight tissue types from two biological replicates per species at the adult developmental stage. A total of 9393 lncRNAs in chickens, 7235 lncRNAs in cattle, and 14,429 lncRNAs in pigs were identified. Including novel isoforms and lncRNAs from novel loci, 5288 novel lncRNAs were identified in chickens, 3732 in cattle, and 4870 in pigs. These transcripts match previously known patterns of lncRNAs, such as generally lower expression levels than mRNAs and higher tissue specificity. An analysis of lncRNA conservation across species identified a set of conserved lncRNAs with potential functions associated with chromatin structure and gene regulation. Tissue-specific lncRNAs were identified. Genes proximal to tissue-specific lncRNAs were enriched for GO terms associated with the tissue of origin, such as leukocyte activation in spleen. Conclusions LncRNAs were identified in three important farm animal species using eight tissues from adult individuals. About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species. While lncRNAs are less conserved than protein-coding genes, a set of positionally conserved lncRNAs were identified among chickens, cattle, and pigs with potential functions related to chromatin structure and gene regulation. Tissue-specific lncRNAs have potential regulatory functions on genes enriched for tissue-specific GO terms. Future work will include epigenetic data from ChIP-seq experiments to further refine these annotations. |
| Databáze: | OpenAIRE |
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