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Miroslav Plohl - One of the best experts on this subject based on the ideXlab platform.
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Satellite DNA Evolution
Genome Dynamics, 2012Co-Authors: Miroslav Plohl, Nevenka Meštrović, Brankica MravinacAbstract:Satellite DNAs represent the most abundant fraction of repetitive sequences in genomes of almost all eukaryotic species. Long arrays of Satellite DNA monomers form densely packed heterochromatic genome compartments and also span over the functionally important centromere locus. Many specific features can be ascribed to the evolution of tandemly repeated genomic components. This chapter focuses on the structural and evolutionary dynamics of Satellite DNAs and the potential molecular mechanisms responsible for rapid changes of the genomic areas they constitute. Monomer sequences of a Satellite DNA evolve concertedly through a process of molecular drive in which mutations are homogenized in a genome and fixed in a population. This process results in divergence of Satellite sequences in reproductively isolated groups of organisms. However, some Satellite DNA sequences are conserved over long evolutionary periods. Since many Satellite DNAs exist in a genome, the evolution of species-specific Satellite DNA composition can be directed by copy number changes within a library of Satellite sequences common for a group of species. There are 2 important features of these Satellite DNAs: long time sequence conservation and, at the same time, proneness to rapid changes through copy number alterations. Sequence conservation may be enhanced by constraints such as those imposed on functional motifs and/or architectural features of a Satellite DNA molecule. Such features can limit the selection of sequences able to persist in a genome, and can direct the evolutionary course of Satellite DNAs spanning the functional centromeres.
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Variation in Satellite DNA profiles—causes and effects
The EMBO Journal, 2002Co-Authors: Ðurđica Ugarković, Miroslav PlohlAbstract:Heterochromatic regions of the eukaryotic genome harbour DNA sequences that are repeated many times in tandem, collectively known as Satellite DNAs. Different Satellite sequences co-exist in the genome, thus forming a set called a Satellite DNA library. Within a library, Satellite DNAs represent independent evolutionary units. Their evolution can be explained as a result of change in two parameters: copy number and nucleotide sequence, both of them ruled by the same mechanisms of concerted evolution. Individual change in either of these two parameters as well as their simultaneous evolution can lead to the genesis of species-specific Satellite profiles. In some cases, changes in Satellite DNA profiles can be correlated with chromosomal evolution and could possibly influence the evolution of species.
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variation in Satellite DNA profiles causes and effects
The EMBO Journal, 2002Co-Authors: ðurðica Ugarkovic, Miroslav PlohlAbstract:Heterochromatic regions of the eukaryotic genome harbour DNA sequences that are repeated many times in tandem, collectively known as Satellite DNAs. Different Satellite sequences co-exist in the genome, thus forming a set called a Satellite DNA library. Within a library, Satellite DNAs represent independent evolutionary units. Their evolution can be explained as a result of change in two parameters: copy number and nucleotide sequence, both of them ruled by the same mechanisms of concerted evolution. Individual change in either of these two parameters as well as their simultaneous evolution can lead to the genesis of species-specific Satellite profiles. In some cases, changes in Satellite DNA profiles can be correlated with chromosomal evolution and could possibly influence the evolution of species.
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detection of Satellite DNA in palorus ratzeburgii analysis of curvature profiles and comparison with tenebrio molitor Satellite DNA
Biochimie, 1992Co-Authors: D Ugarkovic, Miroslav Plohl, Vlatka Lucijanicjustic, Branko BorštnikAbstract:Abstract Very abundant and homogenous Satellite DNA has been found in the flour beetle Palorus ratzeburgii, representing 40% of its genome. Sequencing of 14 randomly cloned satelite monomers revealed a conserved monomer length of 142 bp and an average A+T content of 68%. Sequence variation analysis showed that base substitutions, appearing with a frequency of 2.3%, are predominant differences among Satellite monomers. The Satellite sequence is unique without significant direct repeats and with only two potentially stable inverted repeats. After electrophoresis of Satellite monomers on native polyacrylamide gel retarded mobilities characteristic for curved DNA molecules are observed. The curvature profiles and DNA helix axis trajectory are calculated on the basis of three different algorithms. These calculations predict that P ratzeburgii Satellite DNA forms a left-handed solenoid superstructure. Comparison of described features with other Satellite DNAs reveals some striking similarities with Satellite DNA from related species Tenebrio molitor, which belongs to the same family of Tenebrionidae. Both Satellites are very abundant and homogenous with the same, highly conserved monomer length, although there is no homology at the nucleotide level. Their monomers, as well as multimers, exhibit very similar retarded electrophoretic mobilities. The calculated curvature profiles predict two bend centers in monomers of each Satellite, resulting in a model of left-handed solenoid superstructures of similar appearance.
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evidence for random distribution of sequence variants in tenebrio molitor Satellite DNA
Genetics Research, 1992Co-Authors: Miroslav Plohl, Branko Borˇstnik, Vlatka Lucijanicjustic, ðurðica UgarkovicAbstract:Tenebrio molitor Satellite DNA has been analysed in order to study sequential organization of tandemly repeated monomers, i.e. to see whether different monomer variants are distributed randomly over the whole Satellite, or clustered locally. Analysed sequence variants are products of single base substitutions in a consensus Satellite sequence, producing additional restriction sites. The ladder of Satellite multimers obtained after digestion with restriction enzymes was compared with theoretical calculations and revealed the distribution pattern of particular monomer variants within the Satellite. A defined higher order repeating structure, indicating the existence of Satellite subfamilies, could not be observed. Our results show that some sequence variants are very abundant, being present in nearly 50 % of the monomers, while others are very rare (0-1 % of monomers). However, the distribution of either very frequent, or very rare sequence variants in T. molitor Satellite DNA is always random. Monomer variants are randomly distributed in the total Satellite DNA and thus spread across all chromosomes, indicating a relatively high rate of sequence homogenization among different chromosomes. Such a distribution of monomer variants represents a transient stage in the process of sequence homogenization, indicating the high rate of spreading in comparison with the rate of sequence variant amplification.
Beth A Sullivan - One of the best experts on this subject based on the ideXlab platform.
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α Satellite DNA variation and function of the human centromere
Nucleus, 2017Co-Authors: Lori L Sullivan, Kimberline Chew, Beth A SullivanAbstract:ABSTRACTGenomic variation is a source of functional diversity that is typically studied in genic and non-coding regulatory regions. However, the extent of variation within noncoding portions of the human genome, particularly highly repetitive regions, and the functional consequences are not well understood. Satellite DNA, including α Satellite DNA found at human centromeres, comprises up to 10% of the genome, but is difficult to study because its repetitive nature hinders contiguous sequence assemblies. We recently described variation within α Satellite DNA that affects centromere function. On human chromosome 17 (HSA17), we showed that size and sequence polymorphisms within primary array D17Z1 are associated with chromosome aneuploidy and defective centromere architecture. However, HSA17 can counteract this instability by assembling the centromere at a second, “backup” array lacking variation. Here, we discuss our findings in a broader context of human centromere assembly, and highlight areas of future s...
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α Satellite DNA variation and function of the human centromere
Nucleus, 2017Co-Authors: Lori L Sullivan, Kimberline Chew, Beth A SullivanAbstract:Genomic variation is a source of functional diversity that is typically studied in genic and non-coding regulatory regions. However, the extent of variation within noncoding portions of the human genome, particularly highly repetitive regions, and the functional consequences are not well understood. Satellite DNA, including α Satellite DNA found at human centromeres, comprises up to 10% of the genome, but is difficult to study because its repetitive nature hinders contiguous sequence assemblies. We recently described variation within α Satellite DNA that affects centromere function. On human chromosome 17 (HSA17), we showed that size and sequence polymorphisms within primary array D17Z1 are associated with chromosome aneuploidy and defective centromere architecture. However, HSA17 can counteract this instability by assembling the centromere at a second, "backup" array lacking variation. Here, we discuss our findings in a broader context of human centromere assembly, and highlight areas of future study to uncover links between genomic and epigenetic features of human centromeres.
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human gamma Satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing
Genome Research, 2009Co-Authors: Junghyun Kim, Brankica Mravinac, Beth A Sullivan, Thomas Ebersole, Natalay Kouprina, Vladimir N Noskov, Jun Ichirou Ohzeki, Hiroshi Masumoto, Adam Pavlicek, Sinisa DovatAbstract:The role of repetitive DNA sequences in pericentromeric regions with respect to kinetochore/heterochromatin structure and function is poorly understood. Here, we use a mouse erythroleukemia cell (MEL) system for studying how repetitive DNA assumes or is assembled into different chromatin structures. We show that human gamma-Satellite DNA arrays allow a transcriptionally permissive chromatin conformation in an adjacent transgene and efficiently protect it from epigenetic silencing. These arrays contain CTCF and Ikaros binding sites. In MEL cells, this gamma-Satellite DNA activity depends on binding of Ikaros proteins involved in differentiation along the hematopoietic pathway. Given our discovery of gamma-Satellite DNA in pericentromeric regions of most human chromosomes and a dynamic chromatin state of gamma-Satellite arrays in their natural location, we suggest that gamma-Satellite DNA represents a unique region of the functional centromere with a possible role in preventing heterochromatin spreading beyond the pericentromeric region.
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characterization of neo centromeres in marker chromosomes lacking detectable alpha Satellite DNA
Human Molecular Genetics, 1997Co-Authors: Theresa W Depinet, Beth A Sullivan, Joleen L Zackowski, William C Earnshaw, Sara Kaffe, Gurbax S Sekhon, Richard Stallard, Gail H Vance, Daniel L Van Dyke, Huntington F WillardAbstract:Recent studies have implicated α-Satellite DNA as an integral part of the centromere, important for the normal segregation of human chromosomes. To explore the relationship between the normal functioning centromere and α-Satellite DNA, we have studied eight accessory marker chromosomes in which fluorescence in-situ hybridization could detect neither pancentromeric nor chromosome-specific α-Satellite DNA. These accessory marker chromosomes were present in the majority of or all cells analyzed and appeared mitotically stable, thereby indicating the presence of a functional centromere. FISH analysis with both chromosome-specific libraries and single-copy YACs, together with microSatellite DNA studies, allowed unequivocal identification of both the origin and structure of these chromosomes. All but one of the marker chromosomes were linear mirror image duplications, and they were present along with either two additional normal chromosomes or with one normal and one deleted chromosome. Indirect immunofluorescence analysis revealed that the centromere protein CENP-B was not present on these markers; however, both CENP-C and CENP-E were present at a position defining a ‘neo-centromere’. These studies provide insight into a newly defined class of marker chromosomes that lack detectable α-Satellite DNA. At least for such marker chromosomes, α-Satellite DNA at levels detectable by FISH appears unnecessary for chromosome segregation or for the association of CENP-C and CENP-E at a functional centromere.
Jiri Rubes - One of the best experts on this subject based on the ideXlab platform.
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Satellite DNA in Neotropical Deer Species.
Genes, 2021Co-Authors: Miluse Vozdova, Svatava Kubickova, Halina Cernohorska, Natalia Martinkova, David Javier Galindo, Agda Maria Bernegossi, Dita Kadlčíková, Petra Musilova, José Maurício Barbanti Duarte, Jiri RubesAbstract:The taxonomy and phylogenetics of Neotropical deer have been mostly based on morphological criteria and needs a critical revision on the basis of new molecular and cytogenetic markers. In this study, we used the variation in the sequence, copy number, and chromosome localization of Satellite I-IV DNA to evaluate evolutionary relationships among eight Neotropical deer species. Using FISH with satI-IV probes derived from Mazama gouazoubira, we proved the presence of Satellite DNA blocks in peri/centromeric regions of all analyzed deer. Satellite DNA was also detected in the interstitial chromosome regions of species of the genus Mazama with highly reduced chromosome numbers. In contrast to Blastocerus dichotomus, Ozotoceros bezoarticus, and Odocoileus virginianus, Mazama species showed high abundance of satIV DNA by FISH. The phylogenetic analysis of the Satellite DNA showed close relationships between O. bezoarticus and B. dichotomus. Furthermore, the Neotropical and Nearctic populations of O. virginianus formed a single clade. However, the Satellite DNA phylogeny did not allow resolving the relationships within the genus Mazama. The high abundance of the Satellite DNA in centromeres probably contributes to the formation of chromosomal rearrangements, thus leading to a fast and ongoing speciation in this genus, which has not yet been reflected in the Satellite DNA sequence diversification.
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Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae.
Genes, 2020Co-Authors: Miluse Vozdova, Svatava Kubickova, Halina Cernohorska, Natalia Martinkova, Jan Fröhlich, Jiri RubesAbstract:Centromeric and pericentromeric chromosome regions are occupied by Satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced Satellite DNA I-IV in 11 species of Cervidae. The obtained Satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important Satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of Satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the Satellite I-IV DNA relationships generally support the present cervid taxonomy.
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Tribe-specific Satellite DNA in non-domestic Bovidae
Chromosome Research, 2014Co-Authors: Olga Kopecna, Svatava Kubickova, Halina Cernohorska, Katerina Cabelova, Jiri Vahala, Natalia Martinkova, Jiri RubesAbstract:Satellite sequences present in the centromeric and pericentric regions of chromosomes represent useful source of information. Changes in Satellite DNA composition may coincide with the speciation and serve as valuable markers of phylogenetic relationships. Here, we examined Satellite DNA clones isolated by laser microdissection of centromeric regions of 38 bovid species and categorized them into three types. Sat I sequences from members of Bovini/Tragelaphini/Boselaphini are similar to the well-documented 1.715 sat I DNA family. Sat I DNA from Caprini/Alcelaphini/Hippotragini/Reduncini/Aepycerotini/Cephalophini/Antilopini/Neotragini/Oreotragini form the second group homologous to the common 1.714 sat I DNA. The analysis of sat II DNAs isolated in our study confirmed conservativeness of these sequences within Bovidae. Newly described centromeric clones from Madoqua kirkii and Strepsiceros strepsiceros were similar in length and repetitive tandem arrangement but showed no similarity to any other Satellite DNA in the GenBank database. Phylogenetic analysis of sat I sequences isolated in our study from 38 bovid species enabled the description of relationships at the subfamily and tribal levels. The maximum likelihood and Bayesian inference analyses showed a basal position of sequences from Oreotragini in the subfamily Antilopinae. According to the Bayesian inference analysis based on the indels in a partitioned mixed model, Antilopinae Satellite DNA split into two groups with those from Neotragini as a basal tribe, followed by a stepwise, successive branching of Cephalophini, Aepycerotini and Antilopini sequences. In the second group, Reduncini sequences were basal followed by Caprini, Alcelaphini and Hippotragini.
ðurðica Ugarkovic - One of the best experts on this subject based on the ideXlab platform.
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variation in Satellite DNA profiles causes and effects
The EMBO Journal, 2002Co-Authors: ðurðica Ugarkovic, Miroslav PlohlAbstract:Heterochromatic regions of the eukaryotic genome harbour DNA sequences that are repeated many times in tandem, collectively known as Satellite DNAs. Different Satellite sequences co-exist in the genome, thus forming a set called a Satellite DNA library. Within a library, Satellite DNAs represent independent evolutionary units. Their evolution can be explained as a result of change in two parameters: copy number and nucleotide sequence, both of them ruled by the same mechanisms of concerted evolution. Individual change in either of these two parameters as well as their simultaneous evolution can lead to the genesis of species-specific Satellite profiles. In some cases, changes in Satellite DNA profiles can be correlated with chromosomal evolution and could possibly influence the evolution of species.
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evidence for random distribution of sequence variants in tenebrio molitor Satellite DNA
Genetics Research, 1992Co-Authors: Miroslav Plohl, Branko Borˇstnik, Vlatka Lucijanicjustic, ðurðica UgarkovicAbstract:Tenebrio molitor Satellite DNA has been analysed in order to study sequential organization of tandemly repeated monomers, i.e. to see whether different monomer variants are distributed randomly over the whole Satellite, or clustered locally. Analysed sequence variants are products of single base substitutions in a consensus Satellite sequence, producing additional restriction sites. The ladder of Satellite multimers obtained after digestion with restriction enzymes was compared with theoretical calculations and revealed the distribution pattern of particular monomer variants within the Satellite. A defined higher order repeating structure, indicating the existence of Satellite subfamilies, could not be observed. Our results show that some sequence variants are very abundant, being present in nearly 50 % of the monomers, while others are very rare (0-1 % of monomers). However, the distribution of either very frequent, or very rare sequence variants in T. molitor Satellite DNA is always random. Monomer variants are randomly distributed in the total Satellite DNA and thus spread across all chromosomes, indicating a relatively high rate of sequence homogenization among different chromosomes. Such a distribution of monomer variants represents a transient stage in the process of sequence homogenization, indicating the high rate of spreading in comparison with the rate of sequence variant amplification.
đurđica Ugarkovic - One of the best experts on this subject based on the ideXlab platform.
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Satellite DNA modulates gene expression in the beetle tribolium castaneum after heat stress
PLOS Genetics, 2015Co-Authors: Isidoro Feliciello, Ivana Akrap, đurđica UgarkovicAbstract:Non-coding repetitive DNAs have been proposed to perform a gene regulatory role, however for tandemly repeated Satellite DNA no such role was defined until now. Here we provide the first evidence for a role of Satellite DNA in the modulation of gene expression under specific environmental conditions. The major Satellite DNA TCAST1 in the beetle Tribolium castaneum is preferentially located within pericentromeric heterochromatin but is also dispersed as single repeats or short arrays in the vicinity of protein-coding genes within euchromatin. Our results show enhanced suppression of activity of TCAST1-associated genes and slower recovery of their activity after long-term heat stress relative to the same genes without associated TCAST1 Satellite DNA elements. The level of gene suppression is not influenced by the distance of TCAST1 elements from the associated genes up to 40 kb from the genes’ transcription start sites, but it does depend on the copy number of TCAST1 repeats within an element, being stronger for the higher number of copies. The enhanced gene suppression correlates with the enrichment of the repressive histone marks H3K9me2/3 at dispersed TCAST1 elements and their flanking regions as well as with increased expression of TCAST1 Satellite DNA. The results reveal transient, RNAi based heterochromatin formation at dispersed TCAST1 repeats and their proximal regions as a mechanism responsible for enhanced silencing of TCAST1-associated genes. Differences in the pattern of distribution of TCAST1 elements contribute to gene expression diversity among T. castaneum strains after long-term heat stress and might have an impact on adaptation to different environmental conditions.
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Satellite DNA as a driver of population divergence in the red flour beetle tribolium castaneum
Genome Biology and Evolution, 2015Co-Authors: Isidoro Feliciello, Ivana Akrap, Josip Brajkovic, Ivo Zlatar, đurđica UgarkovicAbstract:Tandemly repeated Satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, Satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of Satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected. Here, we characterize minor TCAST2 Satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 Satellite DNA which differ in monomer size, genome organization, and subfamily specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin whereas Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 Satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific Satellite DNA profiles. Partial organization of TCAST2 Satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level.
