ArticlePLoS genetics2019
Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 33 citations in OpenAlex.
- Pervasive Positive Selection on X-linked Ampliconic Genes in Primates.Genome biology and evolution · 2026Article
- Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.bioRxiv : the preprint server for biology · 2026Article
- Signatures of sex ratio distortion in humans.bioRxiv : the preprint server for biology · 2026Article
- ZNF280AY: a pseudogene on the ovine Y chromosome and its copy number variation associated with testicular size in Hu sheep.Journal of animal science · 2025Article
- Multiple strategies were adopted to optimize the enzymatic characteristics and improve the expression of bovine chymosin BtChy inFrontiers in microbiology · 2025Article
- Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness.Nature genetics · 2025Article
- Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content.Nature communications · 2024Article
- Genome-Wide Analysis Reveals Copy Number Variant GeneAnimals : an open access journal from MDPI · 2024Article
- Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China's Native Pig Breeds via Whole-Genome Resequencing.International journal of molecular sciences · 2024Article
- Transcript Isoform Diversity of Y Chromosome Ampliconic Genes of Great Apes Uncovered Using Long Reads and Telomere-to-Telomere Reference Genome Assemblies.bioRxiv : the preprint server for biology · 2024Article
- The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content.Research square · 2024Article
- Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.Genome biology and evolution · 2023Article
- Genome-wide identification of candidate copy number polymorphism genes associated with complex traits of Tibetan-sheep.Scientific reports · 2023Article
- The complete sequence of a human Y chromosome.Nature · 2023Article
- Testis-Specific Protein Y-Encoded (TSPY) Is Required for Male Early Embryo Development inInternational journal of molecular sciences · 2023Article
- Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups.G3 (Bethesda, Md.) · 2022Article
- Article
- Copy number variation of ZNF280BY across eight sheep breeds and its association with testicular size of Hu sheep.Journal of animal science · 2022Article
- Stage-specific disruption of X chromosome expression during spermatogenesis in sterile house mouse hybrids.G3 (Bethesda, Md.) · 2022Article
- Genome-Wide Detection of Copy Number Variations and Evaluation of Candidate Copy Number Polymorphism Genes Associated With Complex Traits of Pigs.Frontiers in veterinary science · 2022Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The Y chromosome harbors nine multi-copy ampliconic gene families expressed exclusively in testis. The gene copies within each family are >99% identical to each other, which poses a major challenge in evaluating their copy number. Recent studies demonstrated high variation in Y ampliconic gene copy number among humans. However, how this variation affects expression levels in human testis remains understudied. Here we developed a novel computational tool Ampliconic Copy Number Estimator (AmpliCoNE) that utilizes read sequencing depth information to estimate Y ampliconic gene copy number per family. We applied this tool to whole-genome sequencing data of 149 men with matched testis expression data whose samples are part of the Genotype-Tissue Expression (GTEx) project. We found that the Y ampliconic gene families with low copy number in humans were deleted or pseudogenized in non-human great apes, suggesting relaxation of functional constraints. Among the Y ampliconic gene families, higher copy number leads to higher expression. Within the Y ampliconic gene families, copy number does not influence gene expression, rather a high tolerance for variation in gene expression was observed in testis of presumably healthy men. No differences in gene expression levels were found among major Y haplogroups. Age positively correlated with expression levels of the HSFY and PRY gene families in the African subhaplogroup E1b, but not in the European subhaplogroups R1b and I1. We also found that expression of five Y ampliconic gene families is coordinated with that of their non-Y (i.e. X or autosomal) homologs. Indeed, five ampliconic gene families had consistently lower expression levels when compared to their non-Y homologs suggesting dosage regulation, while the HSFY family had higher expression levels than its X homolog and thus lacked dosage regulation.
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