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Schematic representation of the Y chromosome showing different regions/genes involved in spermatogenesis and Y-linked copy number variations. A) AZoospermia Factor (AZF)a, AZFb, and AZFc regions are located on the long arm of the Y chromosome (Yq) with an overlap between AZFb and AZFc; the TSPY1 gene is present on the short arm of the Y chromosome (Yp) arranged in a tandemly repeated array. B) AZFc region showing the location of multicopy genes and transcription units in the reference sequence (Y hapogroup R). The arrows with the same motifs represent repeated homologous sequences, which may undergo NAHR. C) The "b2/b4" deletion (complete AZFc deletion) removing all AZFc genes is depicted. Three alternative breakpoints for gr/gr deletion(s) are shown which all remove half of the AZFc gene content. An example of partial AZFc duplication (gr/gr) is shown (similarly to the gr/gr deletion, different breakpoints may give origin to different types of gr/gr duplications). 

Schematic representation of the Y chromosome showing different regions/genes involved in spermatogenesis and Y-linked copy number variations. A) AZoospermia Factor (AZF)a, AZFb, and AZFc regions are located on the long arm of the Y chromosome (Yq) with an overlap between AZFb and AZFc; the TSPY1 gene is present on the short arm of the Y chromosome (Yp) arranged in a tandemly repeated array. B) AZFc region showing the location of multicopy genes and transcription units in the reference sequence (Y hapogroup R). The arrows with the same motifs represent repeated homologous sequences, which may undergo NAHR. C) The "b2/b4" deletion (complete AZFc deletion) removing all AZFc genes is depicted. Three alternative breakpoints for gr/gr deletion(s) are shown which all remove half of the AZFc gene content. An example of partial AZFc duplication (gr/gr) is shown (similarly to the gr/gr deletion, different breakpoints may give origin to different types of gr/gr duplications). 

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Since the first definition of the AZoospermia Factor (AZF) regions, the Y chromosome has become an important target for studies aimed to identify genetic factors involved in male infertility. This chromosome is enriched with genes expressed exclusively or prevalently in the testis and their absence or reduction of their dosage is associated with sp...

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... microdeletions: the AZF deletions Microdeletions of the Y chromosome are the most frequent known genetic cause of spermatogenic failure in infertile men, second only to the Klinefelter syndrome (5). The first association between azoospermia (absence of spermato- zoa in the ejaculate) and microscopically detectable dele- tions of the long arm of the Y chromosome (Yq) has been demonstrated by Tiepolo and Zuffardi, in 1976 (6). They proposed the existence of a spermatogenesis factor, the AZF, encoded by a gene on distal Yq. With the develop- ment of molecular genetic tools it became possible to cir- cumscribe the AZF region, in which microdeletions arise, and to highlight a certain deletion pattern with 3 recurrent- ly deleted sub-regions in proximal, middle and distal Yq11, designated AZFa, AZFb and AZFc, respectively (7,8) (Fig. ...
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... AZFc region consists almost entirely of repetitive se- quence blocks called 'amplicons' which are arranged in direct and/or inverted repeats (12,21). The region con- tains multicopy genes expressed specifically in the testis and their dosage may vary according to different types of rearrangements. The first AZFc candidate gene isolated from the AZFc re- gion on the long arm of the human Y chromosome was DAZ (Deleted in AZoospermia), which is specifically tran- scribed in the adult testis (22). The DAZ gene belongs to a gene family consisting of 3 members: BOULE on chro- mosome 2, DAZ-Like (DAZL) on chromosome 3 and DAZ, on the Yq. Members of this gene family are expressed exclusively in germ cells and encode testis-specific RNA- binding proteins that contain a highly conserved RNA- Recognition Motif (RRM) and a unique DAZ repeat (23). With regard to the reference sequence (corresponding to a Y chromosome belonging to haplogroup R), DAZ is present on the Y chromosome in 4 copies (DAZ1, DAZ2, DAZ3, and DAZ4). The AZFc region also harbors CDY1, present in 2 copies (CDY1a and CDY1b). CDY protein products have been identified as histone acetyltrans- ferases with a strong preference for histone 4 (24), thus are likely to be involved in both spermatogenic histone replacement and DNA transcription. Other genes in- volved in AZFc deletions are BPY2, the function of which is still unknown, and 5 transcription units TTTY3, TTTY4, TTTY17, CSPG4LY, and GOLGA2LY. Due to its structure, the AZFc region is particularly sus- ceptible to NAHR events which may cause the formation of both partial deletions or duplications and therefore al- ter the AZFc gene dosage (Fig. 2). Although a number of different partial AZFc deletions have been described, only one of them resulted to be clinically relevant. This is the "gr/gr" deletion, named after the fluorescent probes ("green" and "red") used when it was detected for the first time (21). It removes half of the AZFc gene content, including two DAZ copies, one CDY1 copy, and one BPY2 copy. The clinical significance of the gr/gr deletion has been the object of a long debate. Controversies are mainly related to a number of selection biases (lack of ethnic/geographic matching of cases and controls; inap- propriate selection of infertile and control men) and methodological issues (lack of confirmation of gene loss) (25)(26)(27). Moreover, another potential confounding factor derives from the fact that the frequency and phenotypic expression may vary among different ethnic groups, on the basis of the Y chromosome background; for exam- ple, in specific Y haplogroups, such as D2b, Q3, and Q1, common in Japan and certain areas of China, the dele- tion is fixed and apparently does not have any negative effect on spermatogenesis (28,29). The presence of gr/gr deletion in Caucasian normozoospermic controls (al- though at a significantly lower frequency) prompted us to evaluate whether the Y background could influence the phenotypic variability in Caucasians, as well (30). It has been previously described that the loss of DAZ1/DAZ2 and CDY1 is prevalent (or even specific) in carriers with impaired sperm production (31-33) while it was hypothesized that the restoration of normal AZFc gene dosage in case of gr/gr deletion followed by b2/b4 duplication may explain the lack of effect on sperm count ...
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... the last years, Y-linked CNV analyses have been extended to the short arm of the Y chromosome which contains a TSPY1 gene array with variable number of TSPY1 copies (46, 47 and references therein). The TSPY1 belongs to a protein superfamily comprising SET and NAP, which are activating factors of the replication pro- cess. Indeed, TSPY1 is abundantly expressed in early stages of tumorigenesis in gonadoblastoma and could be potentially involved in other human cancers (48). Ex- pression analysis in the testis indicates the involvement of the TSPY1 in spermatogenesis as a pro-proliferative fac- tor (48). In fact, TSPY1 is mainly expressed in gono- cytes/pre-spermatogonia of embryonic testis and in sper- matogonia and spermatocytes at meiotic prophase I in adult testis. A role in early fetal germ cells development has also been addressed by Schoner et al. (49) who pro- vided evidence of TSPY1 ability to partially rescue sper- matogenesis and fertility in transgenic Kit W-v /Kit W-v mice. TSPY1 is unusual in being arranged in a tandem array of 20.4 Kb of repeated units, bearing a single active TSPY1 copy each (Fig. 2). Although copy number varies among individuals within a range of 11 to 76 (26,46,50,51), the majority of men (about 65% of the Italian population) re- main within a restricted interval (21 to 35 copies) (46). The evolutionary conservation of multiple TSPY1 copies on the Y chromosome of other mammals as well as the above mentioned limited variation in copy number in hu- mans suggest that a minimum TSPY1 copy number is like- ly to be maintained through selection (52). Only few stud- ies have focused on the eventual TSPY1 influence on spermatogenesis and frustratingly they all reached 3 dif- ferent conclusions, probably due to study design biases (46, 50, 51). Indeed, crucial for a reliable analysis is the TSPY1 CNV susceptibility to stratification biases. As a matter of fact, significantly different means of TSPY1 copy number were found among different Y haplogroups (46,53), highlighting the importance of Y haplogroups-match- ing between cases and controls. The only available study to date in which cases and controls were matched for Y hgr distribution has been performed in the Italian popu- lation by our group. The method used for the detection of TSPY1 copy number was validated against pulsed-field gel electrophoresis (the gold standard method) (46). The initially published study population has been recently en- larged and previous results confirmed i.e. a significantly lower TSPY1 copy number in 212 infertile men with ab- normal sperm parameters compared to 168 normo- zoospermic subjects (28.5±7.9 vs 32.6±10.1, respective- ly; p<0.001) has been found. The relevance of TSPY1 CNV in spermatogenesis is also attested by the positive correlation observed with sperm count both in infertile and normozoospermic subjects (Fig. 3). In the light of these findings, low TSPY1 copy number can be regarded as a new genetic risk factor for male infertility with po- tential clinical consequences and should be taken into consideration in the context of a multigenic approach to idiopathic ...

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... In addition, modern genetic tolls allow the identification of minor DNA alterations. On the long arm of the Y chromosome, for instance, the azoospermia factor (AZF) regions have multiple genes associated with fertility [5], that are susceptible to microdeletion and/ or microduplication due to their ampliconic sequences organized as palindromes prone to nonallelic homologous recombination [6]. ...
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... However, as a diagnostic limitation, the G-banded karyotype does not allow the identi cation of minor DNA alterations. On the long arm of the Y chromosome, for instance, the azoospermia factor (AZF) regions have multiple genes associated with fertility [4] that are susceptible to microdeletion and/or microduplication due to their ampliconic sequences organized as palindromes prone to nonallelic homologous recombination [5]. ...
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Objectives Male infertility accounts for approximately 30% of cases of reproductive failure. The characterization of genetic variants using cytogenomic techniques is essential for the adequate clinical management of these patients. We aimed to conduct a cytogenetic investigation of numerical and structural rearrangements and a genomic study of Y chromosome microdeletions/microduplications in infertile men derived from a single centre with over 14 years of experience. Results We evaluated 151 infertile men in a transversal study using peripheral blood karyotypes and 15 patients with normal karyotypes through genomic investigation by multiplex ligation-dependent probe amplification (MLPA) or polymerase chain reaction of sequence-tagged sites (PCR-STS) techniques. Out of the 151 patients evaluated by karyotype, 13 presented chromosomal abnormalities: 2 had numerical alterations, and 11 had structural chromosomal rearrangements. PCR-STS detected a BPY2 gene region and RBMY2DP pseudogene region microdeletion in one patient. MLPA analysis allowed the identification of one patient with CDY2B_1 and CDY2B_2 probe duplications (CDY2B gene) and one patient with BPY2_1, BPY2_2, and BPY2_4 probe duplications (BPY2 gene).
... Another cause of genome instability is CNVs-a phenomenon characterized by the presence of repeated genome sections with the number of repeats in the genome varying between individuals. A classic and simple example of CNVs related to male infertility is microdeletions in the AZF locus of the Y chromosome [32][33][34]. The nature of the Y chromosome AZF regions, rich in repetitive sequences, makes it prone to frequent rearrangements, often leading to full or partial AZF deletions [35,36]. ...
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... 29 A proposed mechanism for the disparate outcomes associated with deletions of AZFa, AZFb, AZFc, AZFbc, and AZFabc focuses on the importance of the DAZ gene, which is a copy number variant (CNV) located in four nearly identical copies in the AZFc reference sequence (DAZ1, DAZ2, DAZ3, and DAZ4). 30,31 While it is understood that most genes contained within AZF are critical to successful spermatogenesis, it is believed that two additional, analogous copies of the DAZ gene, known as DAZL (Daz-Like), are located on the autosomal chromosome 3, in addition to its copies contained in AZFc. Unlike the other YCMs discussed, when AZFc alone is absent, it is proposed that the autosomal gene copies of DAZL can serve to "rescue" spermatogenesis and therefore facilitate the production of rare sperm required for retrieval via mTESE. ...
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... New high-throughput methods have been instrumental for analysing multiple DNA molecules in parallel in large cohort studies. Indeed, NGS, such as WES (whole exome sequencing) and WGS (whole genome sequencing), allow also detecting single nucleotide variants (SNVs) and copy number variations (CNVs) potentially related to male infertility phenotypes [3,[20][21][22][23][24][25][26][27]. Whilst WES offers a global view of coding regions, it does not identify variants in non-coding regions, such as promoters, enhancer regions and untranslated region (UTR). ...
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... The results of several genome-wide association studies (GWAS) indicate no overlapping SNVs (Aston & Carrell, 2009;Aston, Krausz, Laface, Ruiz-Castane, & Carrell, 2010;Hu et al., 2014;Sato et al., 2015;Zhao et al., 2012). Several studies have investigated the CNV load in different male infertility scenarios (Tuttelmann et al., 2011;Krausz et al., 2011;Lopes et al., 2013;Lo Giacco et al., 2014). Well-known CNV relate to the Y chromosome, including AZF microdeletions, which may lead to loss of essential genes for spermatogenesis (Krausz & Riera-Escamilla, 2018). ...
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... In support of some functional constraints is the observation that the loss or partial deletion of Y ampliconic gene copies is linked to infertility in humans. For example, TSPY copy number was linked to both infertility [11] and sperm count [11][12][13]. The long arm of the human Y chromosome includes three azoospermia factor regions (AZFa, AZFb, and AZFc), which cover most of the ampliconic genes families and are active during different phases of spermatogenesis [14]. ...
... The long arm of the human Y chromosome includes three azoospermia factor regions (AZFa, AZFb, and AZFc), which cover most of the ampliconic genes families and are active during different phases of spermatogenesis [14]. Complete or partial deletion of these regions is linked to azoospermia and arrest of spermatogenesis [2,12,[14][15][16]. Presumably, copy number decrease linked with infertility is accompanied by a reduction in gene expression of the affected Y ampliconic gene families, however this is yet to be demonstrated. ...
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... Linear R 2 values are reported in the figure, both P < 0.001. Developments in genomic technologies led to the discovery of numerous CNVs in infertile men (Krausz et al., 2011;T€ uttelmann et al., 2011). Therefore, it is now well accepted that changes in DNA content, in conjunction with other genetic or environmental factors, may compromise fertility by altering spermatogenesis or sperm function. ...
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Background Copy number variations (CNVs) play an important role in the onset of several diseases, and recently research focused on the relationship between these structural variants and diseases of the reproductive tract, including male infertility and cryptorchidism. Objectives To evaluate the contribution of copy number variations of E2F1 gene to idiopathic male infertility and the factors influencing expression of this gene. Materials and Methods We performed a retrospective study on 540 subjects recruited from September 2014 to February 2015. TaqMan CNV assay was used to analyze E2F1 CNV. Real‐time PCR was used to assess E2F1 and HSP70 expression level in heat stressed and transfected cells with three E2F1 copies. Results We found a significant difference in the frequency of altered E2F1 copies in patients (12/343, 3.5%) compared with controls (0/197) (p = 0.005). Six patients with E2F1 CNV had history of cryptorchidism, but the prevalence between men with idiopathic infertility (6/243, 2.5%) and infertile men with history of cryptorchidism (6/100, 6.0%) was not statistically different (p = 0.1). E2F1 expression increased under heat stress conditions, especially in cells carrying more copies of gene and this was associated with increased expression of HSP70. Discussion Our data suggest that an abnormal E2F1 expression caused by multiple copies of E2F1 gene predisposes to the onset of infertility and that the risk further increases if subjects with altered E2F1 copies have stressful conditions, such as heat stress or history of cryptorchidism. Conclusion This study shows a link between E2F1 CNV and male infertility, suggesting that the increased risk of spermatogenic impairment associated with higher E2F1 copies might be due to higher susceptibility to stressful conditions.