Structure of a hypervariable tandemly repeated DNA sequence on the short arm of the human Y chromosome

Tyler‐Smith, Chris; Taylor, Lesley A.; Müller, Ulrich

doi:10.1016/0022-2836(88)90110-6

Cited by 94 publications

(75 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In a separate study, we found high incidence of TSPY copy loss in the blood of men who had prostate cancer compared with men who did not have prostate cancer. Previous reports have suggested that the average copy number of TSPY in a normal population is about 27 to 40 copies (30,31). In our study, TSPY copy number distribution in prostate tumor and blood samples averaged around 20 to 30 copies.…”

Section: Discussionsupporting

confidence: 51%

See 1 more Smart Citation

Detection of Recurrent Copy Number Loss at Yp11.2 Involving TSPY Gene Cluster in Prostate Cancer Using Array-Based Comparative Genomic Hybridization

Vijayakumar¹,

Hall²,

Reveles³

et al. 2006

Cancer Research

View full text Add to dashboard Cite

show abstract

Section: Discussionsupporting

confidence: 51%

“…We speculate that the TSPY gene cluster located close to the centromere on Yp has the potential to undergo genomic rearrangement through homologous recombination. Each TSPY gene is contained within a 20.4-kb repeat tandemly repeated into one long array at Yp11.2 (31). There is >99% sequence similarity between these repeats.…”

Section: Discussionmentioning

confidence: 99%

Detection of Recurrent Copy Number Loss at Yp11.2 Involving TSPY Gene Cluster in Prostate Cancer Using Array-Based Comparative Genomic Hybridization

Vijayakumar¹,

Hall²,

Reveles³

et al. 2006

Cancer Research

View full text Add to dashboard Cite

show abstract

“…This analysis revealed that 80.2% (444,601/554,625 bp) of the pericentromeric sequence was composed of segmental duplications. In addition, 73.8% (409,187 bp) and 5.3% (29,289 (Tyler-Smith 1987). The overlap sizes of the clones are as follows: RP1-85D24 ↔ RP11-131M06 71,279 bp; RP11-131M06 ↔ RP11-886I11 33,248 bp; RP11-886I11 ↔ RP11-295P22 10,705 bp.…”

Section: Segmental Duplications In the Pericentromeric Yq11 Regionmentioning

confidence: 99%

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

et al. 2005

View full text Add to dashboard Cite

Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those embedded within euchromatin. We identified and analyzed a euchromatic island within the pericentromeric repeats of the human Y chromosome. This 450-kb island, although not recalcitrant to subcloning and present in 100 tested males from different ethnic origins, was not detected and is not contained within the published Y chromosomal sequence. The entire 450-kb interval is almost completely duplicated and consists predominantly of interchromosomal rather than intrachromosomal duplication events that are usually prevalent on the Y chromosome. We defined the modular structure of this interval and detected a total of 128 underlying pairwise alignments (Ն90% and Ն1 kb in length) to various autosomal pericentromeric and ancestral pericentromeric regions. We also analyzed the putative gene content of this region by a combination of in silico gene prediction and paralogy analysis. We can show that even in this exceptionally duplicated region of the Y chromosome, eight putative genes with open reading frames reside, including fusion transcripts formed by the splicing of exons from two different duplication modules as well as members of the homeobox gene family DUX.

show abstract

“…We obtained copy numbers consistent with that in the reference human genome for all but two gene families (Supplemental Table S12)-RBMY and TSPY. For these two families, intraspecific variability in family size was noted previously (Tyler-Smith et al 1988;Giachini et al 2009;. Next, we examined the size of ampliconic gene families for 14 wild-born gorillas.…”

Section: Ampliconic Genesmentioning

confidence: 99%

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

et al. 2016

View full text Add to dashboard Cite

The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short-and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.

show abstract

Structure of a hypervariable tandemly repeated DNA sequence on the short arm of the human Y chromosome

Cited by 94 publications

References 38 publications

Detection of Recurrent Copy Number Loss at Yp11.2 Involving TSPY Gene Cluster in Prostate Cancer Using Array-Based Comparative Genomic Hybridization

Detection of Recurrent Copy Number Loss at Yp11.2 Involving TSPY Gene Cluster in Prostate Cancer Using Array-Based Comparative Genomic Hybridization

Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Contact Info

Product

Resources

About