The Heterochromatic Region of the Bovine Y Chromosome Is Gene-Rich

The mammalian Y chromosome is largely heterochromatic because of the existence of the male-specific repetitive sequences. The Y has been considered a genetic wasteland for a long time until the sequencing of the human Y chromosome (HSAY) that contains only 78 genes and 78 non-coding (nc) RNAs. Our studies of the bovine Y chromosome (BTAY) revealed that the heterochromatic region of BTAY is gene-rich. The BTAY male-specific region (MSY) is ~40 Mb, 80% of which are ampliconic sequences (traditionally referred as heterochromatic region). The majority (96%) of the ampliconic sequences shares intra-chromosomal similarities ≥99% with elaborate arrays of inverted repeats (IRs). Each IR (~420 Kb) represents a repetitive unit, which was repeated up to ~80 times on BTAY. Four major gene families, HSFY, TSPY, ZNF280AY, and ZNF280BY, were identified within each repetitive unit, with a total gene copy number of 190, 157, 79, 230, respectively, in the MSY region. Therefore, the gene density (20.1 genes/Mb) of the heterochromatic region of BTAY is significantly higher than that of the bovine X chromosome (9.4) and the genome average (7.7). A deep-sequencing of testis-expressed BTAY transcripts further identified over 300 novel transcription units (TUs), largely ncRNAs, which are all amplified in the heterochromatic region up to 80-320 copies. In addition, almost all the BTAY genes/TUs are active at the transcriptional level in the bovine testis, reflecting a high transcriptional activity and suggesting a role in spermatogenesis and male fertility.