Monitoring Novel Functional Elements in the Bovine Genome Applying RNAseq

The functional annotation of the bovine genome is still poor compared to that of model organisms or human. However, deep transcriptome sequencing by RNAseq now offers the tool for a precise and truly holistic identification of novel, previously unknown functionally relevant loci in the genome. Our study monitored the transcriptome of whole blood leucocytes in response to an antiviral vaccination and also the transcriptome of differentially pigmented skin in cattle with a homozygous spotted background. To this end, we applied multiplexed, paired-end RNAseq experiments on an Illumina Genome Analyzer GAIIx. After quality control and alignment to the bovine genome, 85.1 – 89% of all reads mapped to the bovine genome corresponding to 57.8 - 75.2 Mill reads per sample. Transcript assembly identified 13,086 novel skin transcripts previously unknown in the bovine genome. Among these, 37 % were classified as potential long noncoding RNA (lncRNA). This category of transcripts is gaining interest as important regulatory component of mechanisms involved in e.g chromatin modification or epigenetic regulation. Data analysis of the whole blood transcriptome in response to vaccination highlighted a novel, cytokine-like locus. The respective transcript has no homology to any other gene described in any species, but is the most differentially expressed element in response to antiviral vaccination. Due to its predicted structural feature, it is assumed to be associated to the GM-CSF family. Comparative sequence analysis of the homologous genomic regions in other mammals, e.g. human, suggests that this locus might have been lost in other species.