scholarly journals Copy number variations of five Y chromosome genes in donkeys

2017 ◽  
Vol 60 (4) ◽  
pp. 391-397 ◽  
Author(s):  
Haoyuan Han ◽  
Xiaocheng Zhao ◽  
Xiaoting Xia ◽  
Hong Chen ◽  
Chuzhao Lei ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Single Copy ◽  
Copy Number Variations ◽  
Sperm Production ◽  
Specific Transcript ◽  
Normal Sperm ◽  
Copy Numbers ◽  
Qpcr Method ◽  
Male Sex

Abstract. In mammals, the Y chromosome plays a pivotal role in male sex determination and is essential for normal sperm production. A number of studies were conducted on Y chromosome genes of various species and identified single-copy and multi-copy genes. However, limited studies about donkey Y chromosome genes have been done. In this study, 263 male samples from 13 Chinese donkey breeds were collected to analyze the copy number variations (CNVs) of five Y chromosome genes using the quantitative PCR (qPCR) method. These five genes (cullin 4 B Y (CUL4BY), equus testis-specific transcript y1 (ETSTY1), equus testis-specific transcript y4 (ETSTY4), equus testis-specific transcript Y 5 (ETSTY5), and sex-determining region Y (SRY) were identified as multi-copy, whose median copy numbers (MCNs) were 5, 45, 2, and 2, and 13 with CNV ranges of 1–57, 1–227, 1–37, 1–86 and 1–152, respectively. The CNVs of these five genes were shared in different breeds. Compared to previous studies, the copy numbers of five genes showed some distinct consequences in this study. In particular, the well-known single-copy SRY gene showed CNVs in donkeys. Our results provided genetic variations of donkey Y chromosome genes.

scholarly journals Eight Y chromosome genes show copy number variations in horses

2018 ◽  
Vol 61 (3) ◽  
pp. 263-270
Author(s):  
Haoyuan Han ◽  
Xin Zhang ◽  
Xiaocheng Zhao ◽  
Xiaoting Xia ◽  
Chuzhao Lei ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Distribution Patterns ◽  
Single Copy ◽  
Copy Number Variations ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Specific Transcript ◽  
Copy Numbers ◽  
The Impact

Abstract. Copy number variations (CNVs), which represent a significant source of genetic diversity on the Y chromosome in mammals, have been shown to be associated with the development of many complex phenotypes, such as reproduction and male fertility. The occurrence of CNVs has been confirmed on the Y chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y chromosome (ECAY) genes are largely unknown. To demonstrate the copy number variations of Y chromosome genes in horses, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of the eukaryotic translation initiation factor 1A Y (EIF1AY), equine testis-specific transcript on Y 1 (ETSTY1), equine testis-specific transcript on Y 4 (ETSTY4), equine testis-specific transcript on Y 5 (ETSTY5), equine transcript Y4 (ETY4), ubiquitin activating enzyme Y (UBE1Y), sex determining region Y (SRY), and inverted repeat 2 Y (YIR2) across 14 Chinese domestic horse breeds in this study. Our results revealed that these eight genes were multi-copy; furthermore, some of the well acknowledged single-copy genes such as SRY and EIF1AY were found to be multi-copy in this research. The median copy numbers (MCNs) varied among different breeds for the same gene. The CNVs of Y chromosome genes showed different distribution patterns among Chinese horse breeds, indicating the impact of natural selection on copy numbers. Our results will provide fundamental information for future functional studies.

scholarly journals Copy Number Variations of Four Y-Linked Genes in Swamp Buffaloes

Animals ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 31
Author(s):  
Ting Sun ◽  
Quratulain Hanif ◽  
Hong Chen ◽  
Chuzhao Lei ◽  
Ruihua Dang
Keyword(s):  
Y Chromosome ◽  
Copy Number ◽  
Water Buffalo ◽  
Single Copy ◽  
Copy Number Variations ◽  
Tetratricopeptide Repeat ◽  
Dead Box ◽  
Complex Phenotypes ◽  
Swamp Buffaloes ◽  
Number Variation

Copy number variation (CNV), a significant source of genetic diversity in the mammalian Y chromosome, is associated with the development of many complex phenotypes, such as spermatogenesis and male fertility. The contribution of Y-linked CNVs has been studied in various species, however, water buffalo has not been explored in this area and the genetic information still remains unknown. The aim of the current study was to investigate the CNVs of four Y-linked genes, including, sex determining Region of Y-Chromosome (SRY), ubiquitously transcribed tetratricopeptide repeat gene protein on the chromosome Y (UTY), DEAD-box helicase 3 Y-linked (DDX3Y, also known as DBY), and oral-facial-digital syndrome 1 Y-linked (OFD1Y) in 254 swamp buffaloes from 15 populations distributed across China, Vietnam, and Laos using quantitative real-time PCR (qPCR). Our results revealed the prevalence of a single-copy UTY gene in buffaloes. The DBY and OFD1Y represented CNVs among and within different buffalo breeds. The SRY showed CNVs only in Vietnamese and Laotian buffaloes. In conclusion, this study indicated that DBY, OFD1Y, and SRY showed CNVs, while the UTY was a single-copy gene in swamp buffaloes.

scholarly journals The Y chromosome-linked copy number variations and male fertility

2011 ◽  
Vol 34 (5) ◽  
pp. 376-382 ◽  
Author(s):  
C. Krausz ◽  
C. Chianese ◽  
C. Giachini ◽  
E. Guarducci ◽  
I. Laface ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Male Fertility ◽  
Copy Number ◽  
Copy Number Variations

scholarly journals Copy Number Variations of CEP63, FOSL2 and PAQR6 Serve as Novel Signatures for the Prognosis of Bladder Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhao Cai ◽  
Huang Chen ◽  
Jingqiao Bai ◽  
Yang Zheng ◽  
Jianhui Ma ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Prognostic Factors ◽  
High Risk ◽  
Copy Number ◽  
Copy Number Variations ◽  
Invasive Bladder Cancer ◽  
Gene Copy ◽  
Muscle Invasive Bladder Cancer ◽  
Copy Numbers ◽  
Muscle Invasive

BackgroundFinding effective prognostic signatures is of great urgency due to the high risk of recurrence and progression of bladder cancer (BC). Although a lot of genetic alterations are involved in the carcinogenesis, none of them were referred in the current risk group stratifications. In this study, we aimed to find significant copy number variations (CNVs) to predict prognosis for BC patients.MethodsCNVs with high aberration frequencies in BC were explored by array-based comparative genomic hybridization in 65 tumor samples. Candidates were validated in independent groups of BC tumor samples (n=219) and urine samples (n=123). 3D digital PCR was applied for detecting accurate gene copy numbers in BC urine. In order to explore the prognostic value of candidate CNVs, all enrolled patients were followed up for the disease-free survival (DFS). Cox proportional hazards regression analysis was performed to find the independent prognostic factors for DFS.ResultsCNVs of CEP63, FOSL2 and PAQR6 with high aberration frequencies (67.7%, 56.9% and 60.0%, respectively) were found in BC tumors. Copy numbers of CEP63, FOSL2 and PAQR6 were gained in 219 tumor samples. CNVs of CEP63 and FOSL2 were correlated with advanced tumor stage and high grade. Retrospective analysis (median follow-up time: 69 months) revealed that CNVs of CEP63 and FOSL2 were independent prognostic factors for DFS of non-muscle-invasive bladder cancer (NMIBC) patients, while CNVs of FOSL2 and PAQR6 were independent prognostic factors for DFS of muscle-invasive bladder cancer (MIBC) patients. Models for predicting DFS were constructed based on CNVs of three genes. Patients with high prognostic indexes tended to have poor DFS. Prognostic index can also help to identify those with worse outcomes among high risk NMIBC patients. Copy number gains of CEP63 and FOSL2 in urine were found to be significantly correlated with poor DFS of NMIBC patients.ConclusionsCNVs of CEP63, FOSL2 and PAQR6 were capable of predicting DFS and may serve as promising signatures for prognosis of BC.

scholarly journals High levels of copy number variation of ampliconic genes across major human Y haplogroups

2017 ◽  
Author(s):  
Danling Ye ◽  
Arslan Zaidi ◽  
Marta Tomaszkiewicz ◽  
Corey Liebowitz ◽  
Michael DeGiorgio ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Y Chromosome ◽  
Copy Number ◽  
Gene Copy Number ◽  
Gene Families ◽  
Digital Pcr ◽  
Gene Copy ◽  
Copy Numbers ◽  
Number Variation ◽  
Gene Copy Numbers

AbstractDue to its highly repetitive nature, the human male-specific Y chromosome remains understudied. It is important to investigate variation on the Y chromosome to understand its evolution and contribution to phenotypic variation, including infertility. Approximately 20% of the human Y chromosome consists of ampliconic regions which include nine multi-copy gene families. These gene families are expressed exclusively in testes and usually implicated in spermatogenesis. Here, to gain a better understanding of the role of the Y chromosome in human evolution and in determining sexually dimorphic traits, we studied ampliconic gene copy number variation in 100 males representing ten major Y haplogroups world-wide. Copy number was estimated with droplet digital PCR. In contrast to low nucleotide diversity observed on the Y in previous studies, here we show that ampliconic gene copy number diversity is very high. A total of 98 copy-number-based haplotypes were observed among 100 individuals, and haplotypes were sometimes shared by males from very different haplogroups, suggesting homoplasies. The resulting haplotypes did not cluster according to major Y haplogroups. Overall, only three gene families (DATZ, RBMY, TSPY) showed significant differences in copy number among major Y haplogroups, and the haplogroup of an individual could not be predicted based on his ampliconic gene copy numbers. Finally, we found a significant correlation between copy number variation and individual’s height (for three gene families), but not between the former and facial masculinity/femininity. Our results suggest rapid evolution of ampliconic gene copy numbers on the human Y, and we discuss its causes.

scholarly journals The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 40 ◽  
Author(s):  
Fabrizio Signore ◽  
Caterina Gulìa ◽  
Raffaella Votino ◽  
Vincenzo De Leo ◽  
Simona Zaami ◽  
...  
Keyword(s):  
Male Infertility ◽  
Y Chromosome ◽  
Copy Number ◽  
Significant Proportion ◽  
Copy Number Variations ◽  
World Health ◽  
Idiopathic Male Infertility ◽  
Negative Results ◽  
Pubmed Database ◽  
Structural Anomalies

The World Health Organization (WHO) defines infertility as the inability of a sexually active, non-contracepting couple to achieve spontaneous pregnancy within one year. Statistics show that the two sexes are equally at risk. Several causes may be responsible for male infertility; however, in 30–40% of cases a diagnosis of idiopathic male infertility is made in men with normal urogenital anatomy, no history of familial fertility-related diseases and a normal panel of values as for endocrine, genetic and biochemical markers. Idiopathic male infertility may be the result of gene/environment interactions, genetic and epigenetic abnormalities. Numerical and structural anomalies of the Y chromosome represent a minor yet significant proportion and are the topic discussed in this review. We searched the PubMed database and major search engines for reports about Y-linked male infertility. We present cases of Y-linked male infertility in terms of (i) anomalies of the Y chromosome structure/number; (ii) Y chromosome misbehavior in a normal genetic background; (iii) Y chromosome copy number variations (CNVs). We discuss possible explanations of male infertility caused by mutations, lower or higher number of copies of otherwise wild type, Y-linked sequences. Despite Y chromosome structural anomalies are not a major cause of male infertility, in case of negative results and of normal DNA sequencing of the ascertained genes causing infertility and mapping on this chromosome, we recommend an analysis of the karyotype integrity in all cases of idiopathic fertility impairment, with an emphasis on the structure and number of this chromosome.

scholarly journals Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome

2019 ◽  
Vol 28 (16) ◽  
pp. 2785-2798 ◽  
Author(s):  
Wentao Shi ◽  
Sandra Louzada ◽  
Marina Grigorova ◽  
Andrea Massaia ◽  
Elena Arciero ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Y Chromosome ◽  
Sperm Motility ◽  
Copy Number ◽  
Population Variation ◽  
Gene Copy ◽  
Copy Numbers ◽  
Fish Samples ◽  
Number Variation ◽  
Fibre Fish

Abstract Human RBMY1 genes are located in four variable-sized clusters on the Y chromosome, expressed in male germ cells and possibly associated with sperm motility. We have re-investigated the mutational background and evolutionary history of the RBMY1 copy number distribution in worldwide samples and its relevance to sperm parameters in an Estonian cohort of idiopathic male factor infertility subjects. We estimated approximate RBMY1 copy numbers in 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by multicolour fibre-FISH. These fibre-FISH samples provided accurate calibration standards for the entire panel and led to detailed insights into population variation and mutational mechanisms. RBMY1 copy number worldwide ranged from 3 to 13 with a mode of 8. The two larger proximal clusters were the most variable, and additional duplications, deletions and inversions were detected. Placing the copy number estimates onto the published Y-SNP-based phylogeny of the same samples suggested a minimum of 562 mutational changes, translating to a mutation rate of 2.20 × 10−3 (95% CI 1.94 × 10−3 to 2.48 × 10−3) per father-to-son Y-transmission, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increased or decreased copy number, but possible copy number stabilizing selection. An analysis of RBMY1 copy numbers among 376 infertility subjects failed to replicate a previously reported association with sperm motility and showed no significant effect on sperm count and concentration, serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and testosterone levels or testicular and semen volume. These results provide the first in-depth insights into the structural rearrangements underlying RBMY1 copy number variation across diverse human lineages.

scholarly journals Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X

2017 ◽  
Author(s):  
Barbara R Migeon ◽  
Michael A Beer ◽  
Hans T Bjornsson
Keyword(s):  
Copy Number ◽  
Partial Trisomy ◽  
Copy Number Variations ◽  
Sex Bias ◽  
X Chromosomes ◽  
Unique Region ◽  
Human Females ◽  
Specific Transcript ◽  
Embryonic Loss ◽  
Transcript Gene

To compensate for the sex difference in the number of X chromosomes, human females, like human males have only one active X. The other X chromosomes in cells of both sexes are silencedin uterobyXIST, theInactive X Specific Transcript gene, that is present on all X chromosomes. To investigate the means by which the human active X is protected from silencing byXIST, we updated the search for a key dosage sensitiveXISTrepressor using new cytogenetic data with more precise resolution. Here, based on a previously unknown sex bias in copy number variations, we identify a unique region in our genome, and propose candidate genes that lie within, as they could inactivateXIST. Unlike males, the females who duplicate this region of chromosome 19 (partial 19 trisomy) do not survive embryogenesis; this preimplantation loss of females may be one reason that more human males are born than females.

scholarly journals Meiotic effects of MSH4 copy number variation support an adaptive role for post-polyploidy gene loss

2018 ◽  
Author(s):  
Adrián Gonzalo ◽  
Marie-Odile Lucas ◽  
Catherine Marquis ◽  
Andrew Lloyd ◽  
Eric Jenczewski
Keyword(s):  
Chromosome Segregation ◽  
Meiotic Recombination ◽  
Copy Number ◽  
Gene Loss ◽  
Duplicate Gene ◽  
Single Copy ◽  
Homologous Chromosomes ◽  
Evolutionary Forces ◽  
Copy Numbers ◽  
Number Variation

ABSTRACTMany eukaryotes descend from polyploid ancestors that experienced massive duplicate gene loss. This genomic erosion is particularly strong for duplicated (meiotic) recombination genes that return to a single copy more rapidly than genome average following polyploidy. To better understand the evolutionary forces underlying duplicate loss, we analysed how varying copy numbers of MSH4, an essential meiotic recombination gene, influences crossover formation in allotetraploid Brassica napus. We show that faithful chromosome segregation and crossover frequencies between homologous chromosomes are unchanged with MSH4 duplicate loss; by contrast, crossovers between homoeologous chromosomes (which result in genomic rearrangements) decrease with reductions in MSH4 copy number. We also found that inter-homoeologue crossovers originate almost exclusively from the MSH4-dependent crossover pathway. Limiting the efficiency of this pathway by decreasing the copy number of key meiotic recombination genes could therefore contribute to adaptation to polyploidy, by promoting regular chromosome segregation and genomic stability.

scholarly journals Comprehensive Genomic And Epigenomic Analyses on Transcriptomic Regulation In Stomach Adenocarcinoma

2021 ◽  
Author(s):  
Junxing Chen ◽  
Weinan Liu ◽  
Jiabin Du ◽  
Pengcheng Wang ◽  
Jintian Wang ◽  
...  
Keyword(s):  
Copy Number ◽  
Messenger Rna ◽  
Copy Number Variations ◽  
Cancer Development ◽  
Mutation Rates ◽  
Independent Data ◽  
Omics Integration ◽  
Copy Numbers ◽  
Stomach Adenocarcinoma ◽  
Points Of View

Abstract DNA copy number variations (CNVs) and alterations in methylation (MET)-induced transcriptomic dysregulation plays an important role in promoting heterogeneous Stomach adenocarcinoma (STAD) progression. However, the association between DNA MET and CNVs, and the effect of this association during cancer development remain unknown. Altogether 313 STAD specimens had been extracted to examine DNA MET and copy numbers, and to measure messenger RNA (mRNA) expression (EXP). According to our results, copy-number-correlated (CNVcor) genes were remarkably co-regulated with MET-correlated (METcor) ones. Additionally, CNVcor and METcor genes were carried out multi-omics integration, and 3 STAD prognostic subtypes had been identified and verified using the independent data. Typically, the subtype that had higher aggressiveness was found to be associated with reduced PIK3CA, ARID1A, SPECC1, ZFHX3, KMT2D, OBSCN, ZBTB20, FSIP2, RANBP2 and TTN mutation rates, as well as increased JPH3, PLCXD3, and KCNB1 expression. Our results suggested that above mentioned genes played vital parts during invasive STAD development. And results of this comprehensive analyses on transcriptomic regulation at genomic and epigenetic levels facilitate to understand STAD pathology at various points of view, and assist in developing the effective STAD treatment.

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