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Satellite DNA (satellite + dna)

Distribution by Scientific Domains

Life Sciences	33%

Selected Abstracts

Satellite DNA and chromosomes in Neotropical fishes: methods, applications and perspectives

JOURNAL OF FISH BIOLOGY, Issue 5 2010
M. R. Vicari
Constitutive heterochromatin represents a substantial portion of the eukaryote genome, and it is mainly composed of tandemly repeated DNA sequences, such as satellite DNAs, which are also enriched by other dispersed repeated elements, including transposons. Studies on the organization, structure, composition and in situ localization of satellite DNAs have led to consistent advances in the understanding of the genome evolution of species, with a particular focus on heterochromatic domains, the diversification of heteromorphic sex chromosomes and the origin and maintenance of B chromosomes. Satellite DNAs can be chromosome specific or species specific, or they can characterize different species from a genus, family or even representatives of a given order. In some cases, the presence of these repeated elements in members of a single clade has enabled inferences of a phylogenetic nature. Genomic DNA restriction, using specific enzymes, is the most frequently used method for isolating satellite DNAs. Recent methods such as C0t,1 DNA and chromosome microdissection, however, have proven to be efficient alternatives for the study of this class of DNA. Neotropical ichthyofauna is extremely rich and diverse enabling multiple approaches with regard to the differentiation and evolution of the genome. Genome components of some species and genera have been isolated, mapped and correlated with possible functions and structures of the chromosomes. The 5SHindIII-DNA satellite DNA, which is specific to Hoplias malabaricus of the Erythrinidae family, has an exclusively centromeric location. The As51 satellite DNA, which is closely correlated with the genome diversification of some species from the genus Astyanax, has also been used to infer relationships between species. In the Prochilodontidae family, two repetitive DNA sequences were mapped on the chromosomes, and the SATH 1 satellite DNA is associated with the origin of heterochromatic B chromosomes in Prochilodus lineatus. Among species of the genus Characidium and the Parodontidae family, amplifications of satellite DNAs have demonstrated that these sequences are related to the differentiation of heteromorphic sex chromosomes. The possible elimination of satellite DNA units could explain the genome compaction that occurs among some species of Neotropical Tetraodontiformes. These topics are discussed in the present review, showing the importance of satellite DNA analysis in the differentiation and karyotype evolution of Actinopterygii. [source]

Molecular Characterization of a Distinct Begomovirus and its Associated Satellite DNA Molecule Infecting Sida acuta in China,

JOURNAL OF PHYTOPATHOLOGY, Issue 5 2005
Q. Xiong
Abstract Three viral isolates Hn8, Hn40 and Hn41 were obtained from Sida acuta showing yellow mosaic symptom in the Hainan province, China. Comparison of partial DNA-A sequences amplified with degenerate primers confirmed the existence of single type of Begomovirus. The complete nucleotide sequence of the DNA-A-like molecule of Hn8 was determined to be 2749 nucleotides, having a typical genetic organization of a Begomovirus. Hn8 DNA-A had the highest sequence identity (78%) with that of Ageratum yellow vein China virus-[G13] (AJ558120), and had less sequence identity with other begomoviruses. Based on the above molecular data, Hn8 was thus considered as a new Begomovirus species, for which the name Sida yellow mosaic China virus (SiYMCNV) is proposed. Satellite DNA- , molecules (Hn8- ,, Hn40- , and Hn41- ,) were found to be associated with Hn8, Hn40 and Hn41 and their complete nucleotide sequences were determined. Sequence analysis showed that Hn8- ,, Hn40- , and Hn41- , shared more than 84% nucleotide sequence identity, and they were different from other characterized DNA- ,, sharing the highest nucleotide sequence identity (47.8%) with DNA- , of Ageratum yellow vein virus. [source]

Satellite DNA and chromosomes in Neotropical fishes: methods, applications and perspectives

Solution structure of the matrix attachment region-binding domain of chicken MeCP2

FEBS JOURNAL, Issue 15 2003
Björn Heitmann
Methyl-CpG-binding protein 2 (MeCP2) is a multifunctional protein involved in chromatin organization and silencing of methylated DNA. MAR-BD, a 125-amino-acid residue domain of chicken MeCP2 (cMeCP2, originally named ARBP), is the minimal protein fragment required to recognize MAR elements and mouse satellite DNA. Here we report the solution structure of MAR-BD as determined by multidimensional heteronuclear NMR spectroscopy. The global fold of this domain is very similar to that of rat MeCP2 MBD and MBD1 MBD (the methyl-CpG-binding domains of rat MeCP2 and methyl-CpG-binding domain protein 1, respectively), exhibiting a three-stranded antiparallel ,-sheet and an ,-helix ,1. We show that the C-terminal portion of MAR-BD also contains an amphipathic helical coil, ,2/,3. The hydrophilic residues of this coil form a surface opposite the DNA interface, available for interactions with other domains of MeCP2 or other proteins. Spectroscopic studies of the complex formed by MAR-BD and a 15-bp fragment of a high-affinity binding site from mouse satellite DNA indicates that the coil is also involved in protein·DNA interactions. These studies provide a basis for discussion of the consequences of six missense mutations within the helical coil found in Rett syndrome cases. [source]

Molecular genetic characterization of Robertsonian translocations in cattle

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2001
H. Joerg
The chromosome fusion of acrocentric chromosomes, known as Robertsonian translocations, are the most common chromosome rearrangement in Bovidae. Cytogenetic studies revealed differences between the centromeres of Robertsonian translocations: the rob(1; 29) is called monocentric, whereas rob(14; 20) is a dicentric chromosome. To analyse the type of fusion, satellite sequences were hybridised to metaphase chromosomes of carriers of rob(1; 29) from different breeds and rob(14; 20) from the Simmental breed. A repeat element of the bovine 1.715 satellite was located in the centromeric regions of all 29 bovine acrocentric chromosomes. No signals were observed on either the X-,Y- or the rob(1; 29) chromosomes. In contrast, all rob(14; 20) chromosomes gave a distinct hybridisation signal. Microsatellite markers in the linkage group, originating from the fusion, revealed a characteristic allele combination for rob(1; 29) in all carriers and were able to confirm the screening of metaphases of 220 daughters of a heterozygote carrier of the rob(1; 29). The results indicate that rob(1; 29) lost parts of both centromeres and that the 1.715 satellite DNA is not necessary for the functioning of the centromere. Furthermore, rob(1; 29) appears to derive from the same mutation and is transmitted according to Mendelian law. Molekulargenetische Charakterisierung von Robertson'schen Translokationen beim Rind Die Fusion von akrozentrischen Chromosomen, bekannt als Robertson'sche Translokationen, sind die häufigsten Chromosomenveränderungen in der Rindergattung. Zytogenetische Studien zeigten Unterschiede in den Zentromeren von Robertson'schen Translokationen auf. Das Rob(1; 29) Chromosom wird als ein monozentrisches und das Rob(14/20) als ein dizentrisches Chromosom bezeichnet. Um die Fusionsarten zu analysieren, wurden Satellitensequenzen auf Metaphasenchromosomen von Trägern der Rob(1; 29) aus verschiedenen Rassen und von Trägern der Rob(14; 20) aus der Rasse der Simmentaler hybridisiert. Eine Sequenzwiederholung aus dem Rindersatelliten 1.715 wurde in den Zentromerregionen aller 29 akrozentrischer Rinderchromosomen nachgewiesen. Auf dem X, dem Y wie auch auf dem Rob(1; 29) Chromosom konnten jedoch keine Signale beobachtet werden, während alle Rob(14; 20) Chromosomen ein starkes Hybridisierungssignal aufwiesen. Die Mikrosatelliten in der Kopplungsgruppe, welche durch die Fusion entstanden ist, zeigten eine charakteristische Allelkombination für das Rob(1; 29) Chromsom und konnten Untersuchungen an den Metaphasen von 220 Töchtern eines heterozygoten Trägers bestätigen. Die Ergebnisse weisen darauf hin, dass Rob(1; 29) Chromosomen einen Teil beider Zentromere verloren haben und dass die 1.715 Satelliten DNA für ein funktionierendes Chromosom nicht notwendig ist. Die Rob(1; 29) Chromosomen scheinen eine identische Abstammung aufzuweisen und werden nach den Mendel'schen Regeln vererbt. [source]

Satellite DNA and chromosomes in Neotropical fishes: methods, applications and perspectives

Comparison by restriction fragment differential display RT‐PCR of gene expression pattern in bovine oocytes matured in the presence or absence of fetal calf serum

MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 1 2001
S. Jacek Rzucidlo
Abstract A novel restriction fragment differential display (RFDD) RT‐PCR has been used to compare patterns of mRNA expression in bovine oocytes matured in vitro in the presence (10%) or absence of fetal calf serum (FCS). Total RNA extracted from matured and denuded oocytes was processed using display Profile kit (Display System Biotech). RFDD RT‐PCR products were separated on 6% polyacrylamide gel and analyzed using a Storm 860 scanner. Selected bands representing potentially differentially expressed fragments were excised from the gel and re‐amplified. Re‐amplified fragments with size matched to the original fragment were cloned into the TA vector and sequenced. Initially, 10 and 15 differentially expressed fragments were isolated from oocytes matured in the presence and absence of FCS, respectively. Eight out of 10 and 10 out of 15 fragments were re‐amplified successfully as evidenced bysize similarity to the original fragments. Finally, the size of six inserts sequenced from each group matched the size of corresponding original as well as re‐amplified fragments. Sequence comparison search revealed similarity of some isolated fragments to 18s ribosomal RNA, bovine apolipoprotein A‐I, bovine mitochondrion DNA, human CGI‐79 mRNA, human Ab1‐interactor protein, and bovine satellite DNA. The other sequenced fragments may represent novel genes. We showed that RFDD RT‐PCR can be effectively applied to contrast gene expression pattern in bovine oocytes and that presence or absence of FCS during maturation interval affects gene expression pattern in matured bovine oocytes. Mol. Reprod. Dev. 59:90–96, 2001. © 2001 Wiley‐Liss, Inc. [source]

Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice

THE PLANT JOURNAL, Issue 3 2010
Huihuang Yan
Summary We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The chromosomal distribution pattern of methylated DNA is similar to the heterochromatin distribution pattern on rice chromosomes. The DNA methylation patterns of rice genes are similar to those in Arabidopsis thaliana, including distinct methylation patterns asssociated with gene bodies and promoters. The DNA sequences in the core domains of rice Cen4, Cen5 and Cen8 showed elevated methylation levels compared with sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains, compared with the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared with the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin. [source]