The Male-Specific Region of the Bovine Y Chromosome Is Enriched for Testis-Expressed Noncoding RNAs.

Abstract

The mammalian sex chromosomes, the X and Y, evolved from a pair of autosomes ~ 166 million years ago. Recombination suppression between these two ancestral chromosomes led to a male-specific region on the Y (MSY). Two major regions, X-degenerate and ampliconic, are usually present in MSY. The X-degenerate region contains single-copy genes evolved as a consequence of the gradual Y degeneration, whereas the ampliconic region contains multi-copy genes derived from large expansions of X-degenerate genes or genes acquired from the autosomes. Our knowledge on the gene content and its transcriptional profile of the mammalian MSY is still limited to a few species including the human, chimpanzee and rhesus monkey. The objective of this study is to investigate the transcriptional activity in the bovine MSY region based on a direct cDNA selection and Next-Generation sequencing approach. A total of ~ 6.7 million pair-end reads were obtained, ~ 3.0 million of which were aligned with the bovine MSY sequence. The Y-specific read-pairs were de novo assembled into 1438 transcripts, 260 (18%) of which comprised an open reading frame (ORF) (= 90 amino acids) and were classified as coding transcripts. The coding transcripts contain 82 novel transcripts and 178 transcripts derived from 17 protein coding genes (families), including 12 X-degenerate genes and five ampliconic gene families. Motif analysis revealed that 36 novel coding transcripts have a signature associated with either reverse transcriptase or transposase, suggesting that the transposable elements are involved in gene regulation in testes. The remaining transcripts (1177, 82%) were non-coding RNAs (ncRNAs), which are bovine (bovid)-specific and mainly ampliconic with copy numbers ranging from ~80-240. Sequence comparisons against the ncRNA databases indicated that eight ncRNAs (0.7%) had orthologs (e-value < 1e-5) in the human or mouse genome and the majority (99.3%) of the ncRNAs was novel. Two of the eight known ncRNAs belong to Piwi-interacting RNA (piRNA) and the remaining six were long ncRNA (lncRNA). A total of 50 ncRNAs were randomly selected for temporal and spatial expression profiling by RT-PCR, and the results revealed that the majority (70%) of ncRNAs were predominantly expressed across different development stages of testes, suggesting a role in testis development and spermatogenesis. We believe that the identified coding and non-coding transcripts of the bovine MSY provide an important resource to further examine the regulatory network at distinct developmental stages of spermatogenesis. This project was supported by a USDA-NIFA grant no. 2010-65205-20362 to WSL.