Copy number variation-based polymorphism in a new pseudoautosomal region 3 (PAR3) of a human X-chromosome-transposed region (XTR) in the Y chromosome

  title={Copy number variation-based polymorphism in a new pseudoautosomal region 3 (PAR3) of a human X-chromosome-transposed region (XTR) in the Y chromosome},
  author={Avinash M. Veerappa and Prakash Padakannaya and Nallur B. Ramachandra},
  journal={Functional \& Integrative Genomics},
A 3.5-Mb region of the X chromosome underwent duplication and transposition to the Y chromosome ~5–6 Mya. This X-transposed-region (XTR) originated at Xq21.3 and was inserted at Yp11.2. The two locations have 98.78 % homology and a high concentration of tandem repeats. In whole-genome scans of ten large families with dyslexic members, we identified transposed blocks comprising >102 kb of the Yp11.2 region in its homologous region at Xq21.3 in three females from three different families… 

Genetic Diversity on the Human X Chromosome Does Not Support a Strict Pseudoautosomal Boundary

Unlike the autosomes, recombination between the X chromosome and the Y chromosome is often thought to be constrained to two small pseudoautosomal regions (PARs) at the tips of each sex chromosome.

The fragile Y hypothesis: Y chromosome aneuploidy as a selective pressure in sex chromosome and meiotic mechanism evolution

Increased rates of Y aneuploidy may impose positive selection for gene movement off the Y and translocations and fusions which expand the recombining region, raising doubt about the prospects for long‐term retention of the human Y‐chromosome despite recent evidence for stable gene content in older non‐recombining regions.

Recombination between heterologous human acrocentric chromosomes

The ubiquity of signals of heterologous recombination seen in the HPRC draft pangenome’s acrocentric assemblies suggests that this phenomenon is a basic feature of human cellular biology, providing sequence and population-based confirmation of hypotheses first developed cytogenetically fifty years ago.

The Eutherian Pseudoautosomal Region

The pseudoautosomal region (PAR) is a unique segment of sequence homology between differentiated sex chromosomes where recombination occurs during meiosis, of evolutionary, genetic and biomedical significance and a ‘research hotspot' in eutherian genomes.

Global patterns of large copy number variations in the human genome reveal complexity in chromosome organization.

This study unraveled the force of independent evolutionary dynamics on genome organization and complexity across chromosomes and populations.

Major sex differences in allele frequencies for X chromosome variants in the 1000 Genomes Project data

An unexpectedly high proportion of SNPs on the X chromosome in the 1000 Genomes Project phase 3 data were identified with significant sex differences in minor allele frequencies (sdMAF), and it was consistent between the five super-populations.

Genetics of the human Y chromosome and its association with male infertility

Screening for Yq microdeletions would aid the clinician in determining the cause of male infertility and decide a rational management strategy for the patient, as these deletions are transmitted to 100% of male offspring born through assisted reproduction, testing of Yq deletions will allow the couples to make an informed choice regarding the perpetuation ofmale infertility in future generations.

Genome‐wide copy number scan identifies disruption of PCDH11X in developmental dyslexia

PCDH11X, expressed in brain is implicated in cell–cell communication, verbal ability, cerebral asymmetry, and dendritic synaptic plasticity, may be regarded as a new candidate gene for dyslexia.

“Aligning RNA-Seq reads to a sex chromosome complement informed reference genome increases ability to detect sex differences in gene expression”

It is found that using a reference genome with the sex chromosome complement of the sample resulted in higher measurements of X-linked gene transcription for both male and female samples and more differentially expressed genes on the X and Y chromosomes.

Sex chromosome loss and the pseudoautosomal region genes in hematological malignancies

With the widespread detection of loss of a sex chromosome in different hematological malignances, the elucidation of the role of pseudoautosomal region genes in the development and progression of these diseases would be invaluable to the field.



The Human Pseudoautosomal Region (PAR): Origin, Function and Future.

The present review summarizes the current understanding of the evolution of PAR and provides up-to-date information about individual genes residing in this region.

Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y.

The persistence and expansion of deletion lineages, together with direct phenotypic evidence, suggests that absence of these genes has no major deleterious effects, and a mechanism of non-allelic homologous recombination is supported.

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

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.

Maintenance of X- and Y-inactivation of the pseudoautosomal (PAR2) gene SPRY3 is independent from DNA methylation and associated to multiple layers of epigenetic modifications.

It is reported that the silencing of the second repressed PAR2 gene, SPRY3, appears to be independent of DNA methylation, which suggests genes without CpG islands may be less prone to reactivation than previously thought and that genes with CPG islands require promoter methylation as an additional layer of repression.

The DNA sequence of the human X chromosome

This analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome.

Gene duplications as a recurrent theme in the evolution of the human pseudoautosomal region 1: isolation of the gene ASMTL.

The data presented suggest that exon duplication and exon shuffling as well as gene fusion may represent common characteristics in the pseudoautosomal region.

Normal and abnormal interchanges between the human X and Y chromosomes.

The high recombination activity of the pseudoautosomal region at male meiosis sometimes results in unequal crossover which can generate various sex-reversal syndromes.

The human pseudoautosomal regions: a review for genetic epidemiologists

Two intervals of sequence identity at the tips of X and Y chromosomes, the human pseudoautosomal regions PAR1 and PAR2, have drawn interest from researchers in human genetics, cytogenetics, and

Abundant gene conversion between arms of palindromes in human and ape Y chromosomes

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.

Accelerated evolution of Protocadherin11X/Y: A candidate gene‐pair for cerebral asymmetry and language

  • N. WilliamsJ. CloseM. GiouzeliT. Crow
  • Biology
    American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics
  • 2006
The evolutionary sequence of events together with the prior case for an X‐Y homologous gene suggests that this gene‐pair is a candidate for the evolution of hominid‐specific characteristics including the sexual dimorphism of cerebral asymmetry, a putative correlate of language.