Chromosome Research

, Volume 18, Issue 4, pp 419–430 | Cite as

AZFc region of the Y chromosome shows singular structural organization

  • Sanjay Premi
  • Jyoti Srivastava
  • Jörg Thomas Epplen
  • Sher AliEmail author


Owing to clonal inheritance, haploid status and lack of recombination, structural polymorphism in the human Y chromosome is more prevalent than that in the remaining parts of the genome. We studied structural organization of the AZFc region, assessed microdeletions therein and studied copy number variation (CNV) of several candidate genes in 750 Indian males. FISH mapping of 13 Y-specific BAC/cosmid clones uncovered a hitherto unreported AZFc configuration showing inter-DAZ gene sequence onto the Yp instead of Yq region. Such inter-DAZ gene arrangements were also detected in five German males (European Y). In 40–50% males, partial u3 and one of the green amplicons, g1, g2 or g3 was present on the Yp in addition to Yq, suggesting an alteration in the IR3 region. Among other AZFc candidates, complete TTY3 and partial CDY1 BAC sequences were detected on the proximal 5p and distal 15q regions, respectively, in both the sexes. However, primers deduced from these clones showed male specific amplification of TTY3 and CDY1 exons suggesting (re)organization of their flanking sequences between Y and autosomes. Importantly, ∼5% males showed CNV of various Y-linked genes, and ∼3%, random microdeletions across the AZF region. Present study demonstrates hitherto unreported singular structural organization with respect to DAZ, TTY3 and CDY1 genes highlighting organizational complexities of the human Y chromosome in the global context.


Structural polymorphism Copy number variation AZFc configuration Autosomal homologies 



Azoospermia factor


Bacterial artificial chromosome


Basic protein on Y


Chromodomain protein on Y


Chromodomain protein, Y-like


Copy number polymorphism


Copy number variations


Children's Hospital Oakland Research Institute


Chondroitin sulfate proteoglycan 4-like, Y-linked pseudogene 1


Cycle threshold


Deleted in azoospermia


Deleted in azoospermia-like


Dead (aspartate-glutamate-alanine-aspartate) box polypeptide 3, Y-linked


Fluorescence in situ hybridization


Golgi auto antigen, golgin subfamily a, 2-like, Y-linked


Human retro-viral sequences


Male specific region on Y chromosome


Non-allelic homologous recombination


Natural background radiation


National Institute of Immunology Ethical and Biosafety Committees


Non-recombining region of the Y


Polymerase chain reaction


PTPN13-like, Y-linked


Single nucleotide variants


Sex determining region on Y chromosome


Sequence tagged sites


Testis specific transcripts, Y-linked


Ubiquitin specific peptidase 9 on Y


Ubiquitously transcribed tetra-tricopeptide repeat gene, Y-linked


Variable charge, Y-linked


Whole chromosome painting


XK, Kell blood group complex subunit-related, Y-linked


Yeast artificial chromosome


Zinc finger protein, X-linked


Zinc finger protein, Y-linked



This work was supported by a DBT Grant No. BT/PR8476/AAQ/01/315/2006 to SA and a core grant from the Department of Biotechnology, Govt. of India to the National Institute of Immunology, New Delhi. Senior Research Fellowship from the Council of Scientific and Industrial Research, New Delhi to SP and Equipment donation from the Alexander Von Humboldt Foundation, Bonn, Germany to SA are gratefully acknowledged. We thank Dr. Sangeeta Thatai and Shri Khem Singh Negi for technical assistance.

Supplementary material

10577_2010_9123_MOESM1_ESM.doc (46 kb)
Supplementary Table 1 Details of the BAC and cosmid clones used as probes for FISH and PCR primers used for the authentication of the corresponding clones. (DOC 46 kb)
10577_2010_9123_MOESM2_ESM.doc (26 kb)
Supplementary Table 2 List of Y chromosome specific STS markers (DOC 25 kb)
10577_2010_9123_MOESM3_ESM.doc (47 kb)
Supplementary Table 3 List of SNVs and STSs used to ascertain the intactness of the DAZ genes and AZFc region. “+” denotes the presence of signal in the males analyzed (DOC 47 kb)
10577_2010_9123_Fig7_ESM.jpg (96 kb)
Supplementary Figure 1

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Supplementary Figure 2

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Supplementary Figure 3

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Supplementary Figure 4

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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Sanjay Premi
    • 1
  • Jyoti Srivastava
    • 1
  • Jörg Thomas Epplen
    • 1
    • 2
  • Sher Ali
    • 1
    Email author
  1. 1.Molecular Genetics LaboratoryNational Institute of ImmunologyNew DelhiIndia
  2. 2.Abteilung HumangenetikMA/5/142, Ruhr UniversitäteBochumGermany

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