The Human Genome Project has generated a blueprint for the approximately 20, 300 gene-encoded proteins potentially active in any of 230 cell types that make up the human body (human proteome). However, based on the UniProtKB/Swiss-Prot database content, about 6000 of these genes currently lack any experimental evidence at the protein level; for many others, there is very little information related to protein function, abundance, subcellular localization, and interactions. The CHROMOSOME- Centric Human Proteome Project (C-HPP) has been designed to map the entire human proteome in a systematic effort and to will enhance our understanding of human biology at the cellular level and lay a foundation for development of diagnostic, prognostic, therapeutic, and preventive medical applications. As of March 1, 2012, there are 20 international teams, including Royan Institute, focused on 18 different CHROMOSOMEs (www.chpp.org). In Iran, the current efforts are focused on mapping the proteome of human CHROMOSOME Y. The Y CHROMOSOME is unique under many aspects and comprises 95% of the CHROMOSOME’s length. It is always in the haploid state and full of repeated sequences but it is responsible for important biological roles such as sex determination and male fertility. Here, we present the most recent update of Y CHROMOSOME proteome on the platform of genomic Y sequence. Our strategy started with the definition of the proteins coded by the human Y CHROMOSOME, a list of missing/poorly characterized proteins, and proteomic profiling studies to identify those missing proteins.The project is set up to allow for a systematic exploration of the human Y CHROMOSOME proteome using antibody-based proteomics. Within this project, specific antibodies to human Y CHROMOSOME target proteins are being produced using a method involving the cloning and protein expression of protein epitope signature tags.The antibodies are subsequently validated using several approaches including siRNA. The antibodies are now being used to study expression profiles in target cell and in diseased and healthy testis samples. We also align the proteomics data set to the output of RNA-Seq and Real-Time polymerase chain reaction analysis data with defined expression thresholds. Owing to the integration of proteomic, genomic, transcriptomic, phenotypic and pathological data, novel findings are emerging from our studies.Several strategies to maximize the success of the human Y CHROMOSOME proteome project will be presented.

Denaturing High-Performance Liquid Chromatography (DHPLC) is a recently developed technique for the detection of single nucleotide polymorphisms (SNPs) and mutations. It involves the comparison between two or more DNAs as a mixture of denatured and reannealed PCR products. The methodology is based on the principle of reversed phase liquid chromatography and uses a unique DNA separation matrix. The exquisite sensitivity of the technique is determined by adjusting the oven temperature. Elution of DNA fragments is dependant on the chain length and sequence and can be predicted by computation. Under partially denaturing conditions heteroduplices formed upon mixing, denaturing, and reannealing of two, or more, CHROMOSOMEs that differ in sequence, are retained less than their corresponding homodupulices and sequence variation is recognized by the appearance of two, or more, peaks in the chromatographs. Numerous SNPs have been identified on the non-recombinant portion of the Y CHROMOSOME by using this technique. To investigate the DNA variation within Pakistan 15 Y-SNPs, an Alu insertion, a LINE1 insertion and the 12f2 deletion, mapping on the non-recombining portion of the human Y CHROMOSOME, were typed in 834 Pakistani males. The combination of these biallelic markers identified 11 stable Y chromosomal lineages or Y ‘haplogroups’ in the Pakistani population. Haplogroup frequencies were generally similar tothose in neighboring geographical areas and indicate that there was a common pool of Y lineages within Pakistan that are predominantly from West and Central Asia.

Objective: Male infertility is believed to be associated with deletions on the Y CHROMOSOME as firstly has been reported by Tiepolo and Zuffardi. The microdeletions are commonly occurring in the specific region in the CHROMOSOME Y has been called as AZF, a region that thought to contain some genes are involving in spermatogenesis (Dada et al., 2003). The AZF region is subdivided into three non-overlapping sub-regions called AZFa in the proximal portion (interval D3-D6), AZFb in the intermediate region (D13-D16) and AZFc in the distal region (D20-D22) (Foresta et al., 2001). They are strongly associated with spermatogenic defects, such as azoospermia and oligozoospermia (Ferras et al., 2004a; Foresta et al., 2005). Microdeletions in the AZF region are frequently found in patients with azoospermia. The incidence of these microdeletions has been found to vary from 3 to 55% in Yq of patients are diagnosed with infertility (Foresta et al., 1998; Vogt, 2004). Although a high percentage of infertile men with microdeletions in the Y CHROMOSOME are not able to produce children by natural mechanisms of reproduction, there can be transmission of the father’s infertility problems to his sons, when they are produced by assisted reproduction. This predisposition for infertility can include gradual alterations in spermatozoid production, so that a young man with oligozoospermia later becomes azoospermic (Kihaile et al., 2005).Materials and Methods: We examined microdeletions in the Y CHROMOSOMEs of men with azoospermia and severe oligozoospermia in Khuzestan province. Thirty-one patients with azoospermia and 47 with severe oligozoospermia were analyzed by PCR. The patients were classified according to alterations detected in three consecutive spermograms, based on the WHO technique (1999), into groups with non-obstructive azoospermia and those with severe oligozoospermia (£5 x 106 sperm/mL) and patients’ blood were collected. Genomic DNA was extracted from peripheral blood lymphocytes and microdeletion analysis was made of the regions AZFb and AZFc sequence-tagged sites. The PCR product was run by electrophoresis on a 1.5% agarose gel impregnated with ethidium bromide at 5mg/mL and visualized under UV light.Results: Among the 78 patients with azoospermia or severe oligozoospermia, 11 patients that have been diagnosed with severe oligozoospermia were positive for microdeletions, from them nine patients (21.2%) showed deletions in the AZFb region and two patients (4.2%) in the AZFc region.The ages of the azoospermic patients varied from 23 to 47 years, with a mean of 31 years. Patients with severe oligozoospermia ranged from 22 to 38 years, with a mean of 32 years.Conclusion: We conclude that microdeletions in Yq could be one of the important causes of idiopathic male infertility and our findings support previous studies.