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Primer3 on the WWW for general users and for biologist programmers.
TLDR
This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs. Expand
The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes
TLDR
The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length, and is a mosaic of heterochromatic sequences and three classes of euchromatics sequences: X-transposed, X-degenerate and ampliconic. Expand
Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection
TLDR
It is suggested that the existence of this deletion as a polymorphism reflects a balance between haploid selection, which culls gr/gr-deleted Y chromosomes from the population, and homologous recombination, which continues to generate newgr/gr deletions. Expand
Abundant gene conversion between arms of palindromes in human and ape Y chromosomes
TLDR
It is concluded that during recent evolution, an average of approximately 600 nucleotides per newborn male have undergone Y–Y gene conversion, which has had an important role in the evolution of multi-copy testis gene families in the MSY. Expand
Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure.
TLDR
The discovery of breakpoint hotspots suggest that factors in addition to homology underlie these deletions, which are the largest of all human interstitial deletions for which deletion junctions and complete intervening sequence are available. Expand
Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators
TLDR
It is proposed that beyond its roles in testis determination and spermatogenesis, the Y chromosome is essential for male viability, and has unappreciated roles in Turner’s syndrome and in phenotypic differences between the sexes in health and disease. Expand
The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men
TLDR
The complete nucleotide sequence of AZFc was determined by identifying and distinguishing between near-identical amplicons (massive repeat units) using an iterative mapping–sequencing process. Expand
High mutation rates have driven extensive structural polymorphism among human Y chromosomes
TLDR
High mutation rates have driven extensive structural polymorphism among human Y chromosomes and limited variation in the copy number of Y-linked genes is found, which raises the possibility of selective constraints. Expand
Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content
TLDR
It is suggested that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, ‘genetic hitchhiking’ effects in the absence of meiotic crossing over, frequent ectopic recombination within theMSY, and species differences in mating behaviour. Expand
The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned
TLDR
Sequence analysis indicates that the Y–chromosomal DAZ cluster arose during primate evolution by transposing the autosomal gene to the Y, amplifying and pruning exons within the transposed gene and amplifying the modified gene. Expand
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