Identification of long non-coding RNA in the horse transcriptome
| Autor: | Pablo J. Ross, Stephanie J. Valberg, Carrie J. Finno, Tamer A. Mansour, Erica Y. Scott, Maria Cecilia T. Penedo, C. T. Brown, Rebecca R. Bellone, James D. Murray, Michael J. Mienaltowski |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
lcsh:QH426-470 Bioinformatics lcsh:Biotechnology Equine transcriptome Computational biology Biology Genome Medical and Health Sciences Transcriptome 03 medical and health sciences Exon Databases Intergenic region Genetic Transcription (biology) lcsh:TP248.13-248.65 Information and Computing Sciences Databases Genetic Genetics Animals Horses Intergenic Sequence Analysis RNA Gene Expression Profiling Human Genome RNA Biological Sciences Long non-coding RNA lcsh:Genetics 030104 developmental biology Organ Specificity RNA Long Noncoding Long Noncoding DNA microarray Sequence Analysis Research Article Biotechnology |
| Zdroj: | BMC genomics, vol 18, iss 1 BMC Genomics, Vol 18, Iss 1, Pp 1-11 (2017) BMC Genomics |
| Popis: | Background Efforts to resolve the transcribed sequences in the equine genome have focused on protein-coding RNA. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet to be characterized in the horse. The most recent equine transcriptome based on RNA-seq from several tissues was a prime opportunity to obtain a concurrent long non-coding RNA (lncRNA) database. Results This lncRNA database has a breadth of eight tissues and a depth of over 20 million reads for select tissues, providing the deepest and most expansive equine lncRNA database. Utilizing the intergenic reads and three categories of novel genes from a previously published equine transcriptome pipeline, we better describe these groups by annotating the lncRNA candidates. These lncRNA candidates were filtered using an approach adapted from human lncRNA annotation, which removes transcripts based on size, expression, protein-coding capability and distance to the start or stop of annotated protein-coding transcripts. Conclusion Our equine lncRNA database has 20,800 transcripts that demonstrate characteristics unique to lncRNA including low expression, low exon diversity and low levels of sequence conservation. These candidate lncRNA will serve as a baseline lncRNA annotation and begin to describe the RNA-seq reads assigned to the intergenic space in the horse. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3884-2) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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