1. Sequencing the mouse y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes.

    Cell 159(4):800 (2014) PMID 25417157 PMCID PMC4260969

    We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y chromosomes are heterochromatic and gene poor, the mouse MSY is 99.9% euchromatic and contains about 700 protein-coding genes. Only 2% of th...
  2. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes.

    Cell 159(4):800 (2014) PMID 25417157 PMCID PMC4260969

    We sequenced the MSY (male-specific region of the Y chromosome) of the C57BL/6J strain of the laboratory mouse Mus musculus. In contrast to theories that Y chromosomes are heterochromatic and gene poor, the mouse MSY is 99.9% euchromatic and contains about 700 protein-coding genes. Only 2% of th...
  3. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators.

    Nature 508(7497):494 (2014) PMID 24759411 PMCID PMC4139287

    The human X and Y chromosomes evolved from an ordinary pair of autosomes, but millions of years ago genetic decay ravaged the Y chromosome, and only three per cent of its ancestral genes survived. We reconstructed the evolution of the Y chromosome across eight mammals to identify biases in gene ...
  4. No bull: upholding community standards in public sharing of biological datasets.

    PNAS 110(46):E4277 (2013) PMID 24173037 PMCID PMC3831999

  5. Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms

    Genomics 102(4):257 (2013)

    Amplicons – large, nearly identical repeats in direct or inverted orientation – are abundant in the male-specific region of the human Y chromosome (MSY) and provide targets for intrachromosomal non-allelic homologous recombination (NAHR). Thus far, NAHR events resulting in deletions, d...
  6. Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms.

    Genomics 102(4):257 (2013) PMID 23643616 PMCID PMC3785290

    Amplicons--large, nearly identical repeats in direct or inverted orientation--are abundant in the male-specific region of the human Y chromosome (MSY) and provide targets for intrachromosomal non-allelic homologous recombination (NAHR). Thus far, NAHR events resulting in deletions, duplications,...
  7. Independent specialization of the human and mouse X chromosomes for the male germ line.

    Nature Genetics 45(9):1083 (2013) PMID 23872635 PMCID PMC3758364

    We compared the human and mouse X chromosomes to systematically test Ohno's law, which states that the gene content of X chromosomes is conserved across placental mammals. First, we improved the accuracy of the human X-chromosome reference sequence through single-haplotype sequencing of amplicon...
  8. Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes.

    Bioessays 34(12):1035 (2012) PMID 23055411 PMCID PMC3581811

    Studies of Y chromosome evolution often emphasize gene loss, but this loss has been counterbalanced by addition of new genes. The DAZ genes, which are critical to human spermatogenesis, were acquired by the Y chromosome in the ancestor of Old World monkeys and apes. We and our colleagues recentl...
  9. AZFcDeletions and Spermatogenic Failure: A Population-Based Survey of 20,000 Y Chromosomes

    The American Journal of Human Genetics 91(5):890 (2012)

    Deletions involving the Y chromosome’s AZFc region are the most common known genetic cause of severe spermatogenic failure (SSF). Six recurrent interstitial deletions affecting the region have been reported, but their population genetics are largely unexplored. We assessed the deletion...
  10. AZFc deletions and spermatogenic failure: a population-based survey of 20,000 Y chromosomes.

    The American Journal of Human Genetics 91(5):890 (2012) PMID 23103232 PMCID PMC3487143

    Deletions involving the Y chromosome's AZFc region are the most common known genetic cause of severe spermatogenic failure (SSF). Six recurrent interstitial deletions affecting the region have been reported, but their population genetics are largely unexplored. We assessed the deletions' prevale...
  11. Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes.

    Nature 483(7387):82 (2012) PMID 22367542 PMCID PMC3292678

    The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200-300 million years. The human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes' genes owing to genetic decay. This evolutionary decay was driven by a series...
  12. Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition.

    Nature 466(7306):612 (2010) PMID 20622855 PMCID PMC2943333

    In birds, as in mammals, one pair of chromosomes differs between the sexes. In birds, males are ZZ and females ZW. In mammals, males are XY and females XX. Like the mammalian XY pair, the avian ZW pair is believed to have evolved from autosomes, with most change occurring in the chromosomes foun...
  13. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.

    Nature 463(7280):536 (2010) PMID 20072128 PMCID PMC3653425

    The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome. Little is known about the recent evolution of the Y chromosome because only t...
  14. Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection

    The American Journal of Human Genetics 85(6):923 (2009)

    Y-linked single-nucleotide polymorphisms (SNPs) have served as powerful tools for reconstructing the worldwide genealogy of human Y chromosomes and for illuminating patrilineal relationships among modern human populations. However, there has been no systematic, worldwide survey of sequ...
  15. Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection.

    The American Journal of Human Genetics 85(6):923 (2009) PMID 20004767 PMCID PMC2790577

    Y-linked single-nucleotide polymorphisms (SNPs) have served as powerful tools for reconstructing the worldwide genealogy of human Y chromosomes and for illuminating patrilineal relationships among modern human populations. However, there has been no systematic, worldwide survey of sequence varia...
  16. Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes.

    Cell 138(5):855 (2009) PMID 19737515 PMCID PMC3616640

    Massive palindromes in the human Y chromosome harbor mirror-image gene pairs essential for spermatogenesis. During evolution, these gene pairs have been maintained by intrapalindrome, arm-to-arm recombination. The mechanism of intrapalindrome recombination and risk of harmful effects are unknown...
  17. Isodicentric Y Chromosomes and Sex Disorders as Byproducts of Homologous Recombination that Maintains Palindromes

    Cell 138(5):855 (2009)

    Massive palindromes in the human Y chromosome harbor mirror-image gene pairs essential for spermatogenesis. During evolution, these gene pairs have been maintained by intrapalindrome, arm-to-arm recombination. The mechanism of intrapalindrome recombination and risk of harmful effects are un...
  18. MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome.

    Nucleic Acids Research 36(Database issue):D809 (2008) PMID 17965095 PMCID PMC2238960

    Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer. Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisel...
  19. Ubl4b, an X-derived retrogene, is specifically expressed in post-meiotic germ cells in mammals

    Gene Expression Patterns 7(1):131 (2007)

    Post-translational modification by ubiquitin and ubiquitin-related proteins plays critical roles in protein degradation and in regulation of essential cellular processes. In mammals, transcription grinds to a halt during late spermiogenesis due to compaction of the spermatid genome, which c...
  20. Ubl4b, an X-derived retrogene, is specifically expressed in post-meiotic germ cells in mammals.

    Gene Expression Patterns 7(1-2):131 (2007) PMID 16872915 PMCID PMC1647293

    Post-translational modification by ubiquitin and ubiquitin-related proteins plays critical roles in protein degradation and in regulation of essential cellular processes. In mammals, transcription grinds to a halt during late spermiogenesis due to compaction of the spermatid genome, which create...