Abstract
BackgroundMinisatellites are an integral part of eukaryotic genomes and show variation in the complexity of their organization. Besides their presence in non-coding regions, a small fraction of them are part of the transcriptome, possibly participating in gene regulation, expression and silencing. We studied the minisatellite (TGG)n tagged transcriptome in the water buffalo Bubalus bubalis across various tissues and the spermatozoa, and characterized the genes TSPY1 and COL6A1 discovered in the process.ResultsMinisatellite associated sequence amplification (MASA) conducted using cDNA and oligonucleotide primer (TGG)5 uncovered 38 different mRNA transcripts from somatic tissues and gonads and 15 from spermatozoa. These mRNA transcripts corresponded to several known and novel genes. The majority of the transcripts showed the highest level of expression either in the testes or spermatozoa with exception of a few showing higher expression levels in the lungs and liver. Transcript SR1, which is expressed in all the somatic tissues and gonads, was found to be similar to the Bos taurus collagen type VI alpha 1 gene (COL6A1). Similarly, SR29, a testis-specific transcript, was found to be similar to the Bos taurus testis-specific Y-encoded protein-1 representing cancer/testis antigen 78 (CT78). Subsequently, full length coding sequences (cds) of these two transcripts were obtained. Quantitative PCR (q-PCR) revealed 182-202 copies of theTSPY1 gene in water buffalo, which localized to the Y chromosome.ConclusionsThe MASA approach enabled us to identify several genes, including two of clinical significance, without screening an entire cDNA library. Genes identified with TGG repeats are not part of a specific family of proteins and instead are distributed randomly throughout the genome. Genes showing elevated expression in the testes and spermatozoa may prove to be potential candidates for in-depth characterization. Furthermore, their possible involvement in fertility or lack thereof would augment animal biotechnology.
Highlights
Satellite DNA, an integral part of eukaryotic genomes [1], present as long uninterrupted arrays, often in genetically silent heterochromatic regions [2]
Satellites are present in non-coding regions but a small fraction can be found in the transcriptome [8,9] and this subset participates in gene regulation and silencing [10,11]
Fresh water buffalo semen samples were procured from an in-vitro fertilization (IVF) center (Frozen Semen Production Center, Chak Gajaria), in Lucknow (U.P), India
Summary
Satellite DNA, an integral part of eukaryotic genomes [1], present as long uninterrupted arrays, often in genetically silent heterochromatic regions [2] These dynamic elements include transposable elements, major satellites and simple sequence repeats (SSRs) [2,3] and represent a fast-evolving part of the genome conforming to the random processes of molecular drive [4]. The presence of ITRs (internal tandem repeats) at exon-intron boundaries may give rise to novel alternatively spliced transcripts [16] Notwithstanding these observations, the precise arrangement of tandem repeats in a given species in the context of genomic organization and gene expression still remains unclear. Minisatellites are an integral part of eukaryotic genomes and show variation in the complexity of their organization Besides their presence in non-coding regions, a small fraction of them are part of the transcriptome, possibly participating in gene regulation, expression and silencing. We studied the minisatellite (TGG)n tagged transcriptome in the water buffalo Bubalus bubalis across various tissues and the spermatozoa, and characterized the genes TSPY1 and COL6A1 discovered in the process
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