scholarly journals Comparative analysis of DNA repeats and identification of a Fesreba centromeric element in fescues and ryegrasses

2020 ◽  
Author(s):  
Jana Zwyrtková ◽  
Alžběta Němečková ◽  
Jana Čížková ◽  
Kateřina Holušová ◽  
Veronika Kapustová ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Grass Species ◽  
Striking Difference ◽  
Dna Repeats ◽  
Copy Numbers ◽  
Genome Wide ◽  
Speed Up

Abstract Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up development of cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass ( Lolium ) species and diploid and hexaploid fescues ( Festuca ) species. In this work we characterized repetitive DNA sequences and their contribution to genome size in seven fescue and ryegrass species. Results Partial genome sequences were produced by Illumina technology and used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed most striking difference in copy numbers in nuclear genomes between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative analysis of repeatome in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. The element was abundant in centromeric regions of the fescues and ryegrasses and may have a role in function of their centromeres.

scholarly journals Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses

2020 ◽  
Author(s):  
Jana Zwyrtková ◽  
Alžběta Němečková ◽  
Jana Čížková ◽  
Kateřina Holušová ◽  
Veronika Kapustová ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Grass Species ◽  
Dna Repeats ◽  
Biotic And Abiotic Stresses ◽  
Centromere Function ◽  
Genome Wide ◽  
Speed Up ◽  
Partial Genome

Abstract Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up the development of new cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species ( Lolium spp.) and diploid and hexaploid fescue species ( Festuca spp.). In this work we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species, as well as one fescue and two ryegrass cultivars. Results Partial genome sequences produced by Illumina technology were used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative repeatome analysis in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. A new LTR element Fesreba was identified and found abundant in centromeric regions of the fescues and ryegrasses. It may have a role in the function of their centromeres.

scholarly journals Epigenetic Deregulation of Telomere-Related Genes in Newly Diagnosed Multiple Myeloma Patients

Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6348
Author(s):  
Samrat Roy Choudhury ◽  
Cody Ashby ◽  
Fenghuang Zhan ◽  
Frits van Rhee
Keyword(s):  
Dna Methylation ◽  
Multiple Myeloma ◽  
Dna Sequences ◽  
Critical Length ◽  
Newly Diagnosed ◽  
Genome Wide ◽  
Healthy Donors ◽  
Binding Factor ◽  
G Quadruplex

High-risk Multiple Myeloma (MM) patients were found to maintain telomere length (TL), below the margin of short critical length, consistent with proactive overexpression of telomerase. Previously, DNA methylation has been shown as a determinant of telomere-related gene (TRG) expression and TL to assess risk in different types of cancer. We mapped genome-wide DNA methylation in a cohort of newly diagnosed MM (NDMM; n = 53) patients of major molecular subgroups, compared to age-matched healthy donors (n = 4). Differential methylation and expression at TRG-loci were analyzed in combination with overlapping chromatin marks and underlying DNA-sequences. We observed a strong correlation (R2 ≥ 0.5) between DNA methylation and expression amongst selective TRGs, such that demethylation at the promoters of DDX1 and TERF1 were associated to their oncogenic upregulation, while demethylation at the bodies of two key tumor suppressors ZNF208 and RAP1A led to downregulation of the genes. We demonstrated that TRG expression may be controlled by DNA methylation alone or in cooperation with chromatin modifications or CCCTC-binding factor at the regulatory regions. Additionally, we showed that hypomethylated DMRs of TRGs in NDMM are stabilized with G-quadruplex forming sequences, suggesting a crucial role of these epigenetically vulnerable loci in MM pathogenesis. We have identified a panel of five TRGs, which are epigenetically deregulated in NDMM patients and may serve as early detection biomarkers or therapeutic targets in the disease.

Verteilung und enzymatische Hypermethylierung invers repetitiver DNA-Sequenzen in verschiedenen Mäuse-und menschlichen Zellen / Distribution and Enzymic Hypermethylation of Inverted DNA Repeats in Different Murine and Human Cells

1979 ◽  
Vol 34 (7-8) ◽  
pp. 558-564 ◽  
Author(s):  
Thomas L. J. Boehm ◽  
Dusan Drahovsky
Keyword(s):  
Dna Sequences ◽  
Mammalian Cells ◽  
Nuclear Dna ◽  
Repetitive Sequences ◽  
Specific Class ◽  
Dna Repeats ◽  
Quantitative Analyses ◽  
Chang Cells ◽  
P815 Mouse

Abstract A specific class of DNA sequences, the inverted repetitive sequences, forms a double-stranded structure within a single linear polynucleotide chain in denatured DNA. The reassociation process is unimolecular and occurs very fast. Quantitative analyses have shown that these sequences com-E rise about 4-5% of the nuclear DNA of various mammalian cells (P815 mouse mastocytoma, Hela, L cells, Raji and Chang cells, and human embryonic hepatocytes) and are interspersed within sequences of other degrees of repetitiveness.After labeling the cells with L-[Metnyl-3H]methionine and [14C]deoxycytidine, relative rates of enzymic DNA methylation were computed on the basis of 3H and 14C radioactivities found in py­ rimidine residues of the nuclear DNA. The results indicate that DNA of inverted repetitive sequences is methylated to a level about 50% higher than the ordinary repetitive sequences and to about 300% higher than the unique and intermediary sequences.The biological function of the inverted repeats as well as the role of their enzymic hypermethyl­ ation is unknown.

scholarly journals Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mohanad A. Ibrahim ◽  
Badr M. Al-Shomrani ◽  
Mathew Simenc ◽  
Sultan N. Alharbi ◽  
Fahad H. Alqahtani ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Transposable Elements ◽  
Genome Evolution ◽  
De Novo ◽  
Endogenous Retroviruses ◽  
Similar Proportion ◽  
Copy Numbers ◽  
Genome Wide ◽  
Vicugna Pacos ◽  
A Genome

Abstract Background Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available. Results We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies (https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline). Annotation results indicated a similar proportion of each genomes comprising TEs (35–36%). Class I LTR retrotransposons comprised 16–20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1–2% of each genome. Conclusions The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.

Variability and evolution of highly repeated DNA sequences in the genus Beta

Genome ◽  
1993 ◽  
Vol 36 (6) ◽  
pp. 1074-1079 ◽  
Author(s):  
T. Schmidt ◽  
J. S. Heslop-Harrison
Keyword(s):  
Dna Sequences ◽  
Satellite Dna ◽  
Polyacrylamide Gel Electrophoresis ◽  
Type I ◽  
Dna Repeats ◽  
Repeated Dna ◽  
Copy Numbers ◽  
Wild Beet ◽  
Lower Variability

Satellite DNA from wild beet species was separated from restriction endonuclease digested genomic DNA by polyacrylamide gel electrophoresis. Two nonhomologous HaeIII satellite DNA repeats were cloned from the wild beet Beta trigyna. The type I repeat is 140–149 bp long and AT rich, while the type II is 162 bp in size and GC rich. A third repetitive HaeIII element cloned from the related wild beet B. corolliflora was shown to be organized as a HinfI satellite DNA family in the cultivated beet B. vulgaris ssp. vulgaris and the wild beet B. vulgaris ssp. maritima. This type III satellite monomer is 149 bp long and contains a high number of short direct subrepeats. The monomer was found in different genomic organizations and copy numbers in all sections of the genus Beta indicating an amplification early in the phylogeny. The HaeIII repeats from B. trigyna are characterized by a lower variability and form long tandem arrays in the genomes of Corollinae species. The investigation of the distribution of all three sequence families provided data that may contribute to the solution of taxonomic problems of the genus Beta and be useful in the characterization of hybrids and derived lines with alien wild beet chromosomes.Key words: satellite DNA, Beta vulgaris, Beta corolliflora, Beta trigyna, evolution, repetitive DNA.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

The Role of the Zakat System during the Colonial-period in Malaysia and Uzbekistan: A Comparative Analysis

2017 ◽  
Vol 04 ◽  
pp. 40-54
Author(s):  
Avazbek Ganiyev Oybekovich ◽  
◽  
Hassan Shakeel Shah ◽  
Mohammad Ayaz ◽  
◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Colonial Period

Role of Transcriptional Read-Through in PRE Activity in Drosophila melanogaster

Acta Naturae ◽  
2016 ◽  
Vol 8 (2) ◽  
pp. 79-86 ◽  
Author(s):  
P. V. Elizar’ev ◽  
D. V. Lomaev ◽  
D. A. Chetverina ◽  
P. G. Georgiev ◽  
M. M. Erokhin
Keyword(s):  
Dna Sequences ◽  
Cell Types ◽  
Transcription Terminator ◽  
Response Elements ◽  
Polycomb Response Elements ◽  
The Individual ◽  
Multicellular Organisms ◽  
Different Cell Types ◽  
Main Factor

Maintenance of the individual patterns of gene expression in different cell types is required for the differentiation and development of multicellular organisms. Expression of many genes is controlled by Polycomb (PcG) and Trithorax (TrxG) group proteins that act through association with chromatin. PcG/TrxG are assembled on the DNA sequences termed PREs (Polycomb Response Elements), the activity of which can be modulated and switched from repression to activation. In this study, we analyzed the influence of transcriptional read-through on PRE activity switch mediated by the yeast activator GAL4. We show that a transcription terminator inserted between the promoter and PRE doesnt prevent switching of PRE activity from repression to activation. We demonstrate that, independently of PRE orientation, high levels of transcription fail to dislodge PcG/TrxG proteins from PRE in the absence of a terminator. Thus, transcription is not the main factor required for PRE activity switch.

The role of graining in ensuring food security

2020 ◽  
pp. 75-79
Author(s):  
R. M. Gambarova
Keyword(s):  
Food Security ◽  
Comparative Analysis ◽  
Systems Approach ◽  
Point Of View ◽  
Government Support ◽  
Grain Production ◽  
The Government ◽  
Favorable Conditions ◽  
Grain Farms

Relevance. Grain is the key to strategic products to ensure food security. From this point of view, the creation of large grain farms is a matter for the country's selfsufficiency and it leading to a decrease in financial expense for import. Creation of such farms creates an abundance of productivity from the area and leads to obtaining increased reproductive seeds. The main policy of the government is to minimize dependency from import, create abundance of food and create favorable conditions for export potential.The purpose of the study: the development of grain production in order to ensure food security of the country and strengthen government support for this industry.Methods: comparative analysis, systems approach.Results. As shown in the research, if we pay attention to the activities of private entrepreneurship in the country, we can see result of the implementation of agrarian reforms after which various types of farms have been created in republic.The role of privateentrepreneurshipinthedevelopmentofproduction is great. Тhe article outlines the sowing area, production, productivity, import, export of grain and the level of selfsufficiency in this country from 2015 till 2017.

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