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Y Chromosome

Y Structure Y Evolution
    The human Y chromosome has now been sequenced and published in the June 19, 2003 issue of Nature. The article explains the evolution of the Y chromosome at genetic level. It also serves to illustrate the structure of a chromosome in general. The followings is an attempt to summarize the main features in the article.

    Y Chromosome Structure and Evolution:

Figure 01 Y Chromosome Structure [large image]

Figure 02 Y Chromosome Evolution
[view large image]

  • Cytogeneticists use stains to distinguish chromosomes. Dark-staining genetic material, called heterochromatin, is more tightly coiled and has more repetitive DNA sequences than the lighter-staining euchromatin. Heterochromatin hugs the centromere and is present at the tips (telomeres). It is interspersed with euchromatin along the rest of the chromosome. The largest constriction is the centromere, which divides the medium size chromosome into a short arm (p) and a long arm (q). For short chromosome, the centromere locates near one end, while the long chromosome has an approximately centralized centromere. It is thought that heterochromatin only maintains the chromosome's structural integrity, all the active genes are located in the euchromatin (see Figure 11-33 and Figure 01).
  • Figure 01 shows that structure of the Y chromosome with each sub-structure represented by different colour. The short pseudoautosomal regions (~5%) are located at both ends. They are the only portions that are still identical to the corresponding regions of the X chromosome, reflecting the frequent exchange of DNA between these regions (crossover) that occurs during sperm production. Prioritization in the Human Genome Project had led to the sequencing for the heterochromatic regions of the Y and other chromosomes being set aside to be dealt with later, if ever.


  • Figure 02 is the evolutionary map of the MSY. At the bottom is the euchromatic region of the MSY as shown in Figure 01 (b). Coloured rectangles extending above this schematic depict the estimated male-specific ages of the corresponding segments of the modern MSY. These ages are plotted on the logarithmic scale (a). It is found that the difference in X-Y gene pairs occurred in a stepwise fashion along the length of the X chromosome, in four "evolutionary strata". This suggested that at least four events had punctuated human sex chromosome evolution. These processes are represented by the four Groups in (b). Column (c) indicates the chromosomes from which the X-transposed or ampliconic sequences apparently arose through transposition during evolution. Column (d) shows the MSY genes that apparently arose at the indicated times. Column (e) shows the approximate times of divergence between the human and certain other vertebrate lineages.
  • Three regions in MSY called AZFa, b, and c, are recognized to be vital for sperm development. Deletions of any of these regions will cause spermatogenic failure. AZFa includes the USP9Y and DBY genes (see Table 11-02), while AZFb and AZFc occupy about 1/3 of the MSY toward the end of the long arm section.
  • MSY Sequence Class Gene Symbol Gene Name # of Copies Tissue Expression X-linked
    Homologue
    X-transposed TGIF2LY TGF(beta)-induced transcription factor 1 testis TGIF2LX
    PCDH11Y Protocadherin 11 Y 1 Fetal brain, brain PCDH11X
    Total     2    
    X-degererate SRY Sex determining region Y 1 Mostly testis SOX3
    RPS4Y1 Ribosomal protein S4 Y isoform 1 1 Ubiquitous RPS4X
    ZFY Zinc finger Y 1 Ubiquitous ZFY
    AMELY Amelogenin Y 1 Teeth AMELX
    TBL1Y Transducin(beta)-like 1 protein Y 1 Fetal brain, prostate TBL1X
    PRKY Protein kinase Y 1 Ubiquitous PRKX
    USP9Y Ubiqutin-specific protease 9 Y 1 Ubiquitous USP9X
    DBY Dead box Y 1 Ubiquitous DBX
    UTY Ubiquitous TPR motif Y 1 Ubiquitous UTX
    TMSB4Y Thymosin(beta)-4 Y 1 Ubiquitous TMSB4X
    NLGN4Y Neuroligin 4 isoform Y 1 Brain, prostate, testis NLGN4X
    CYorf15A Chromosome Y open reading frame 15A 1 Ubiquitous CXorf15
    CYorf15B Chromosome Y open reading frame 15B 1 Ubiquitous CXorf15
    SMCY SMC(mouse) homologue, Y 1 Ubiquitous SMCX
    EIF1AY Translation initiation factor 1A Y 1 Ubiquitous EIF1AX
    RPS4Y2 Ribosomal protein S4 Y isoform 2 1 Ubiquitous RPS4X
    Total     16    
    Ampliconic TSPY Testis-specific protein Y ~35 Testis  
    VCY Variable charge Y 2 Testis VCX
    XKRY XK related Y 2 Testis  
    CDY Chromodomain Y 4 Testis  
    HSFY Heat shock transcription factor Y 2 Testis  
    RBMY RNA-binding motif Y 6 Testis RBMX
    PRY PTP-BL related Y 2 Testis  
    BPY2 Basic protein Y 2 3 Testis  
    DAZ Deleted in azoospermia 4 Testis  
    Total     ~60    
    Grand total     ~78    

    Table 01 MSY Genes and Gene Families

    Sequencing of the MSY in chimpanzee has been completed in early 2010. By comparing some regions of the Y chromosome with those from human, it is found that there is rapid evolution during the past 6 million years. The chimpanzee MSY contains twice as
    Chimpanzee Y Chromosome many massive palindromes, yet it has lost large fraction of the MSY protein-coding genes (such as the X-transposed shown in Figure 06) in the last common ancestor. It is suggested that the extraordinary divergence was driven by 4 factors:
    1. The prominent role of the MSY in sperm production.
    2. Genetic hitchhiking effects in the absence of meiotic crossing over.
    3. Frequent ectopic recombination within the MSY.
    4. Species differences in mating behavior.

    Figure 06 Chimpanzee MSY [view large image]

    The report concludes that although genetic decay may be the principal dynamic in the evolution of newly emergent Y chromosomes, wholesale renovation is the paramount theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs.