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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.
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.
Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.
TLDR
A large-scale survey for SNPs was examined by a combination of gel-based sequencing and high-density variation-detection DNA chips, and a genetic map was constructed showing the location of 2227 candidate SNPs.
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.
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.
Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing a novel RNA–binding protein gene
TLDR
The region contains a single–copy gene, DAZ (Deleted in AZoospermia), which is transcribed in the adult testis and appears to encode an RNA binding protein, and the possibility that DAZ is AZF should now be explored.
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.
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.
Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing a novel RNA-binding protein gene
TLDR
The authors have detected deletions of portions of the Y chromosome long arm in 12 of 89 men with azoospermia (no spermatozoa in their semen), and found no evidence of YRRM genes, recently proposed as AZF candidates in the AZF region.
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.
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