scholarly journals Rich polymorphic variants of alpha satellite 34mer higher order repeats in hg38 assembly of human chromosome Y

2019 ◽  
Author(s):  
Ines Vlahović ◽  
Matko Glunčić ◽  
Vladimir Paar
Keyword(s):  
Cell Division ◽  
Y Chromosome ◽  
Tandem Repeats ◽  
Genomic Sequence ◽  
Higher Order ◽  
Alpha Satellite ◽  
Satellite Dnas ◽  
Polymorphic Variants ◽  
Human Y Chromosome

AbstractA challenging problem in human population genetics is related to the unique role of human Y chromosome, with properties that distinguish humans from other species. Centromeres in primate genomes are constituted of tandem repeats of ∼ 171 bp alpha satellite monomers, commonly organized into higher order repats (HORs). Because of gaps in DNA sequencing, HOR regions as genomic “black holes” have been understudied in spite of crucial importance. Only recently the sequencing of more complete satellite DNAs becomes accessible. In human Y chromosome the largest alpha satellite higher order repeat unit 34/36mer was found, but its polymorphic variants were not investigated. Here, we study the human Y chromosome centromeric genomic sequence from hg38 assembly using our novel ALPHAsub algorithm for simple identification of alpha satellite arrays and robust GRM algorithm for HOR identification in repeat sequences. We determine the monomer alignment scheme for alpha satellite HOR array based on canonical 34mer HOR, discovering a wealth of novel polymorphic variants which include the HOR-type monomer duplications, monomer deletions/insertions or rearrangements and non-HOR insertions.Author SummaryThe centromere is important for segregation of chromosomes during cell division in eukaryotes. Its destabilization results in chromosomal missegregation, aneuploidy, hallmarks of cancers and birth defects. In primate genomes centromeres contain tandem repeats of ∼ 171 bp alpha satellite DNA, commonly organized into higher order repeats (HORs). In this work, we used our bioinformatics algorithms to study the human Y chromosome centromeric genomic sequence and we discover a wealth of novel polymorphic variants which include the HOR-type monomer duplications, monomer deletions/insertions or rearrangements and non-HOR insertions. These results could help to understand the role of alpha satellites and alpha HOR structures in centromeric organization and function, in particular their role in creating a functional kinetochore that is crucial for chromosome segregation during cell division.

scholarly journals Variation in Short Tandem Repeats Is Deeply Structured by Genetic Background on the Human Y Chromosome

1999 ◽  
Vol 65 (6) ◽  
pp. 1623-1638 ◽  
Author(s):  
Elena Bosch ◽  
Francesc Calafell ◽  
Fabrício R. Santos ◽  
Anna Pérez-Lezaun ◽  
David Comas ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Genetic Background ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Human Y Chromosome ◽  
Short Tandem

Human Y-chromosome short tandem repeats: A tale of acculturation and migrations as mechanisms for the diffusion of agriculture in the Balkan Peninsula

2010 ◽  
Vol 142 (3) ◽  
pp. 380-390 ◽  
Author(s):  
Sheyla Mirabal ◽  
Tatjana Varljen ◽  
Tenzin Gayden ◽  
Maria Regueiro ◽  
Slavica Vujovic ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Balkan Peninsula ◽  
Human Y Chromosome ◽  
Short Tandem

scholarly journals The Role of Satellite DNAs in Genome Architecture and Sex Chromosome Evolution in Crambidae Moths

2021 ◽  
Vol 12 ◽  
Author(s):  
Diogo C. Cabral-de-Mello ◽  
Magda Zrzavá ◽  
Svatava Kubíčková ◽  
Pedro Rendón ◽  
František Marec
Keyword(s):  
Sex Chromosomes ◽  
Ostrinia Nubilalis ◽  
Tandem Repeats ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Satellite Dnas ◽  
Telomere Function ◽  
Eukaryotic Genomes

Tandem repeats are important parts of eukaryotic genomes being crucial e.g., for centromere and telomere function and chromatin modulation. In Lepidoptera, knowledge of tandem repeats is very limited despite the growing number of sequenced genomes. Here we introduce seven new satellite DNAs (satDNAs), which more than doubles the number of currently known lepidopteran satDNAs. The satDNAs were identified in genomes of three species of Crambidae moths, namely Ostrinia nubilalis, Cydalima perspectalis, and Diatraea postlineella, using graph-based computational pipeline RepeatExplorer. These repeats varied in their abundance and showed high variability within and between species, although some degree of conservation was noted. The satDNAs showed a scattered distribution, often on both autosomes and sex chromosomes, with the exception of both satellites in D. postlineella, in which the satDNAs were located at a single autosomal locus. Three satDNAs were abundant on the W chromosomes of O. nubilalis and C. perspectalis, thus contributing to their differentiation from the Z chromosomes. To provide background for the in situ localization of the satDNAs, we performed a detailed cytogenetic analysis of the karyotypes of all three species. This comparative analysis revealed differences in chromosome number, number and location of rDNA clusters, and molecular differentiation of sex chromosomes.

Hypothesis: a Y-chromosomal gene causes gonadoblastoma in dysgenetic gonads

Development ◽  
1987 ◽  
Vol 101 (Supplement) ◽  
pp. 151-155 ◽  
Author(s):  
David C. Page
Keyword(s):  
Y Chromosome ◽  
Dna Hybridization ◽  
Physiological Function ◽  
Hybridization Analysis ◽  
Chromosomal Gene ◽  
Normal Males ◽  
Part Model ◽  
Human Y Chromosome

The role of the human Y chromosome in the etiology of gonadoblastoma, a gonadal neoplasm, is considered and a two-part model is presented. According to this hypothesis: (1) There is a gene on the Y chromosome that strongly predisposes dysgenetic gonads to develop gonadoblastomas (Page, 1986) and (2) this postulated GBY gene (GonadoBlastoma locus on Y chromosome) has some physiological function in normal males. GBY may, for example, function in or prior to spermatogenesis in normal testes. Y-DNA hybridization analysis of individuals with gonadoblastoma and partial deletions of the Y chromosome should be of use in testing this proposal. To date, such studies suggest that GBY maps to the region that includes deletion intervals 4B to 7, i.e. it is located near the centromere or on the long arm of the Y chromosome.

II. Distribution of DNA base sequences Sequence organization of the human Y chromosome

1978 ◽  
Vol 283 (997) ◽  
pp. 329-329
Keyword(s):  
Y Chromosome ◽  
Dna Hybridization ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Male And Female ◽  
Sequence Organization ◽  
Dna Base ◽  
Base Sequences ◽  
Specific Sequences ◽  
Human Y Chromosome

A comparison of restriction patterns of human male and female DNA after digestion with Hae III reveals two bands which are present only in male DNA and which are produced by cleavage of repetitive sequences found only on the human Y chromosome (Cooke 1976). Repetitive Y specific sequences can also be detected by exhaustive DNA/DNA hybridization (Kunkel, Smith & Boyer 1976). When DNA from one of these repetitive sequences is isolated as a fragment 3300 bases long from a Hae III digest of male DNA this material can be used as a probe for related sequences in male and female DNA. In both male and female DNA there is DNA which does not contain Hae III sites, which is complementary to this sequence and probably represents related tandem repeats. However, in male DNA fragments which are multiples of 3300 bases long are present showing that this sequence is tandemly repeated.

scholarly journals The Human Y Chromosome: The Biological Role of a “Functional Wasteland”

2001 ◽  
Vol 1 (1) ◽  
pp. 18-24 ◽  
Author(s):  
Lluís Quintana-Murci ◽  
Marc Fellous
Keyword(s):  
Y Chromosome ◽  
Male Fertility ◽  
Its Sequence ◽  
Distinguishing Characteristic ◽  
Biological Functions ◽  
Sry Gene ◽  
Male Phenotype ◽  
Mammalian Embryos ◽  
Human Y Chromosome

“Functional wasteland,” “Nonrecombining desert” and “Gene-poor chromosome” are only some examples of the different definitions given to the Y chromosome in the last decade. In comparison to the other chromosomes, the Y is poor in genes, being more than 50% of its sequence composed of repeated elements. Moreover, the Y genes are in continuous decay probably due to the lack of recombination of this chromosome. But the human Y chromosome, at the same time, plays a central role in human biology. The presence or absence of this chromosome determines gonadal sex. Thus, mammalian embryos with a Y chromosome develop testes, while those without it develop ovaries (Polani [38]). What is responsible for the male phenotype is the testis-determining SRY gene (Sinclair [52]) which remains the most distinguishing characteristic of this chromosome. In addition to SRY, the presence of other genes with important functions has been reported, including a region associated to Turner estigmata, a gene related to the development of gonadoblastoma and, most important, genes related to germ cell development and maintenance and then, related with male fertility (Lahn and Page [31]). This paper reviews the structure and the biological functions of this peculiar chromosome.

Genetic Testing of Language Replacement Hypothesis in Southwest Asia

2006 ◽  
Vol 10 (2) ◽  
pp. 191-208
Author(s):  
Levon Yepiskoposian ◽  
Armine Khudoyan ◽  
Ashot Harutyunian
Keyword(s):  
Y Chromosome ◽  
Tandem Repeats ◽  
Genetic Distances ◽  
Structured Populations ◽  
South Caucasus ◽  
The Caucasus ◽  
Unique Event ◽  
Sampling Procedures ◽  
Human Y Chromosome ◽  
Short Tandem

AbstractThe regions of the Caucasus, Anatolia, and the Near East represent an extremely important area with respect to ancient population migration and expansion, and the spread of the Caucasian, Indo-European, Afro-Asiatic, and Altaic languages. We examined genetic variation within and between 12 ethno-territorial populations belonging to four major language families by using six microsatellites, or short tandem repeats (STR) and 12 Unique Event Polymorphism (UEP) loci mapped to the non-recombining portion of the human Y-chromosome. The applied set of markers did not unconditionally support the language replacement hypothesis for the populations under consideration. Moreover, regarding the South Caucasus and Anatolia, our results showed greater genetic distances between the populations from different language families, and close genetic affinity for the populations from the same language group—in this case, for the Turkophone ethnic units. The results point to the importance of appropriate Y-chromosome sampling procedures in geographically structured populations and to the necessity of using a relevant set of markers that provides best discrimination of populations with different genetic histories.

Association of genetic polymorphism of cytokines and antioxidant enzymes with the development of asbestosis

2020 ◽  
Vol 60 (12) ◽  
pp. 898-903
Author(s):  
Lyudmila P. Kuzmina ◽  
Anastasiya G. Khotuleva ◽  
Evgeniy V. Kovalevsky ◽  
Nikolay N. Anokhin ◽  
Iraklij M. Tskhomariya
Keyword(s):  
Antioxidant Enzymes ◽  
Genetic Polymorphism ◽  
Genetic Predisposition ◽  
Risk Groups ◽  
Dust Exposure ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Gstp1 Gene ◽  
Polymorphic Variants

Introduction. Various industries widely use chrysotile asbestos, which determines the relevance of research aimed at the prevention of asbestos-related diseases. It is promising to assess the role of specific genes, which products are potentially involved in the development and regulation of certain links in the pathogenesis of asbestosis, forming a genetic predisposition to the disease. The study aims to analyze the presence of associations of genetic polymorphism of cytokines and antioxidant enzymes with asbestosis development. Materials and methods. Groups were formed for examination among employees of OJSC "Uralasbest" with an established diagnosis of asbestosis and without lung diseases. For each person included in the study, dust exposure doses were calculated considering the percentage of time spent at the workplace during the shift for the entire work time. Genotyping of single nucleotide polymorphisms of cytokines IL1b (rs16944), IL4 (rs2243250), IL6 (rs1800795), TNFα (rs1800629) and antioxidant enzymes SOD2 (rs4880), GSTP1 (rs1610011), CAT (rs1001179) was carried out. Results. The authors revealed the associations of polymorphic variants A511G IL1b gene (OR=2.457, 95% CI=1.232-4.899) and C47T SOD2 gene (OR=1.705, 95% CI=1.055-2.756) with the development of asbestosis. There was an increase in the T allele IL4 gene (C589T) frequency in persons with asbestosis at lower values of dust exposure doses (OR=2.185, 95% CI=1.057-4.514). The study showed the associations of polymorphism C589T IL4 gene and C174G IL6 gene with more severe asbestosis, polymorphism A313G GSTP1 gene with pleural lesions in asbestosis. Conclusion. Polymorphic variants of the genes of cytokines and antioxidant enzymes, the protein products directly involved in the pathogenetic mechanisms of the formation of asbestosis, contribute to forming a genetic predisposition to the development and severe course of asbestosis. Using the identified genetic markers to identify risk groups for the development and intense period of asbestos-related pathology will optimize treatment and preventive measures, considering the organism's characteristics.

Human α-satellite DNAs are not susceptible to undercondensation after 5-azacytidine treatment

1994 ◽  
Vol 65 (1-2) ◽  
pp. 92-94 ◽  
Author(s):  
J.L Fernández ◽  
V. Goyanes ◽  
C. López-Femández ◽  
J. Gosálvez
Keyword(s):  
Alpha Satellite ◽  
Satellite Dnas

scholarly journals Involvement of Very Short DNA Tandem Repeats and the Influence of the RAD52 Gene on the Occurrence of Deletions in Saccharomyces cerevisiae

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 549-557 ◽  
Author(s):  
Anne J Welcker ◽  
Jacky de Montigny ◽  
Serge Potier ◽  
Jean-Luc Souciet
Keyword(s):  
Fusion Proteins ◽  
Tandem Repeats ◽  
Chromosomal Rearrangements ◽  
Reversion Rate ◽  
Wild Type ◽  
Recombination Mechanism ◽  
Nonhomologous Recombination ◽  
Deletion Rate ◽  
Dna Tandem Repeats

Abstract Chromosomal rearrangements, such as deletions, duplications, or Ty transposition, are rare events. We devised a method to select for such events as Ura+ revertants of a particular ura2 mutant. Among 133 Ura+ revertants, 14 were identified as the result of a deletion in URA2. Of seven classes of deletions, six had very short regions of identity at their junctions (from 7 to 13 bp long). This strongly suggests a nonhomologous recombination mechanism for the formation of these deletions. The total Ura+ reversion rate was increased 4.2-fold in a rad52Δ strain compared to the wild type, and the deletion rate was significantly increased. All the deletions selected in the rad52Δ context had microhomologies at their junctions. We propose two mechanisms to explain the occurrence of these deletions and discuss the role of microhomology stretches in the formation of fusion proteins.

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