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1. Alpha satellite DNA biology: finding function in the recesses of the genome

Author:
McNulty, Shannon M.; Sullivan, Beth A.
Source:
Chromosome research 2018 v.26 no.3 pp. 115-138
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; epigenetics; genome; genome assembly; genomics; high-throughput nucleotide sequencing; humans; intergenic DNA; kinetochores; messenger RNA; non-coding RNA; proteins; satellite RNA; satellites; transcription (genetics); transcriptome;     Show all 16 Subjects
Abstract:
... Repetitive DNA, formerly referred to by the misnomer “junk DNA,” comprises a majority of the human genome. One class of this DNA, alpha satellite, comprises up to 10% of the genome. Alpha satellite is enriched at all human centromere regions and is competent for de novo centromere assembly. Because of the highly repetitive nature of alpha satellite, it has been difficult to achieve genome assembli ...
DOI:
10.1007/s10577-018-9582-3

2. W-enriched satellite sequence in the Indian meal moth, Plodia interpunctella (Lepidoptera, Pyralidae)

Author:
Dalíková, Martina; Zrzavá, Magda; Kubíčková, Svatava; Marec, František
Source:
Chromosome research 2017 v.25 no.3-4 pp. 241-252
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Plodia interpunctella; W chromosome; Z chromosome; adults; autosomes; butterflies; females; genome; heterochromatin; larvae; males; moths; pupae;     Show all 14 Subjects
Abstract:
... The W chromosome of most lepidopteran species represents the largest heterochromatin entity in the female genome. Although satellite DNA is a typical component of constitutive heterochromatin, there are only a few known satellite DNAs (satDNAs) located on the W chromosome in moths and butterflies. In this study, we isolated and characterized new satDNA (PiSAT1) from microdissected W chromosomes of ...
DOI:
10.1007/s10577-017-9558-8

3. Evolutionary dynamics of two satellite DNA families in rock lizards of the genus Iberolacerta (Squamata, Lacertidae): different histories but common traits

Author:
Rojo, Verónica; Martínez-Lage, Andrés; Giovannotti, Massimo; González-Tizón, Ana M.; Cerioni, Paola Nisi; Barucchi, Vincenzo Caputo; Galán, Pedro; Olmo, Ettore; Naveira, Horacio
Source:
Chromosome research 2015 v.23 no.3 pp. 441-461
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Lacertidae; chromosome aberrations; genome; karyotyping; lizards; phylogeny; satellites;     Show all 8 Subjects
Abstract:
... Satellite DNAs compose a large portion of all higher eukaryotic genomes. The turnover of these highly repetitive sequences is an important element in genome organization and evolution. However, information about the structure and dynamics of reptilian satellite DNA is still scarce. Two satellite DNA families, HindIII and TaqI, have been previously characterized in four species of the genus Iberola ...
DOI:
10.1007/s10577-015-9489-1

4. Structural and functional liaisons between transposable elements and satellite DNAs

Author:
Meštrović, Nevenka; Mravinac, Brankica; Pavlek, Martina; Vojvoda-Zeljko, Tanja; Šatović, Eva; Plohl, Miroslav
Source:
Chromosome research 2015 v.23 no.3 pp. 583-596
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; evolution; genome; sequence homology; transposons;     Show all 6 Subjects
Abstract:
... Transposable elements (TEs) and satellite DNAs (satDNAs) are typically identified as major repetitive DNA components in eukaryotic genomes. TEs are DNA segments able to move throughout a genome while satDNAs are tandemly repeated sequences organized in long arrays. Both classes of repetitive sequences are extremely diverse, and many TEs and satDNAs exist within a genome. Although they differ in st ...
DOI:
10.1007/s10577-015-9483-7

5. The molecular basis of the organization of repetitive DNA-containing constitutive heterochromatin in mammals

Author:
Nishibuchi, Gohei; Déjardin, Jérôme
Source:
Chromosome research 2017 v.25 no.1 pp. 77-87
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; databases; epigenetics; essential genes; eukaryotic cells; heterochromatin; histones; humans; intergenic DNA; methylation; molecular models; precipitin tests; telomeres; transposons; yeasts;     Show all 15 Subjects
Abstract:
... Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the ...
DOI:
10.1007/s10577-016-9547-3

6. Human centromere repositioning within euchromatin after partial chromosome deletion

Author:
Sullivan, Lori L.; Maloney, Kristin A.; Towers, Aaron J.; Gregory, Simon G.; Sullivan, Beth A.
Source:
Chromosome research 2016 v.24 no.4 pp. 451-466
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; Homo sapiens; centromeres; chromosome elimination; gene expression; genes; heterochromatin; histones; humans; hybrids; mutants; nucleosomes; viability;     Show all 14 Subjects
Abstract:
... Centromeres are defined by a specialized chromatin organization that includes nucleosomes that contain the centromeric histone variant centromere protein A (CENP-A) instead of canonical histone H3. Studies in various organisms have shown that centromeric chromatin (i.e., CENP-A chromatin or centrochromatin) exhibits plasticity, in that it can assemble on different types of DNA sequences. However, ...
DOI:
10.1007/s10577-016-9536-6
PubMed:
27581771
PubMed Central:
PMC5366066

7. Completing the human genome: the progress and challenge of satellite DNA assembly

Author:
Miga, Karen H.
Source:
Chromosome research 2015 v.23 no.3 pp. 421-426
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA assembly; chromosomes; evolution; genome; genomics; humans; models; tandem repeat sequences;     Show all 9 Subjects
Abstract:
... Genomic studies rely on accurate chromosome assemblies to explore sequence-based models of cell biology, evolution and biomedical disease. However, even the extensively studied human genome has not yet reached a complete, ‘telomere-to-telomere’, chromosome assembly. The largest assembly gaps remain in centromeric regions and acrocentric short arms, sites known to contain megabase-sized arrays of t ...
DOI:
10.1007/s10577-015-9488-2

8. Satellite non-coding RNAs: the emerging players in cells, cellular pathways and cancer

Author:
Ferreira, Daniela; Meles, Susana; Escudeiro, Ana; Mendes-da-Silva, Ana; Adega, Filomena; Chaves, Raquel
Source:
Chromosome research 2015 v.23 no.3 pp. 479-493
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; biomarkers; gene overexpression; genome; heterochromatin; neoplasms; non-coding RNA; prognosis; satellites; transcription (genetics);     Show all 11 Subjects
Abstract:
... For several decades, transcriptional inactivity was considered as one of the particular features of constitutive heterochromatin and, therefore, of its major component, satellite DNA sequences. However, more recently, succeeding evidences have demonstrated that these sequences can indeed be transcribed, yielding satellite non-coding RNAs with important roles in the organization and regulation of g ...
DOI:
10.1007/s10577-015-9482-8

9. Transcription of tandemly repetitive DNA: functional roles

Author:
Biscotti, Maria Assunta; Canapa, Adriana; Forconi, Mariko; Olmo, Ettore; Barucca, Marco
Source:
Chromosome research 2015 v.23 no.3 pp. 463-477
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; centromeres; chromosome pairing; genome; heterochromatin; non-coding RNA; satellites; telomeres; transcription (genetics);     Show all 10 Subjects
Abstract:
... A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptiona ...
DOI:
10.1007/s10577-015-9494-4

10. LINE-related component of mouse heterochromatin and complex chromocenters’ composition

Author:
Kuznetsova, Inna S.; Ostromyshenskii, Dmitrii I.; Komissarov, Alexei S.; Prusov, Andrei N.; Waisertreiger, Irina S.; Gorbunova, Anna V.; Trifonov, Vladimir A.; Ferguson-Smith, Malcolm A.; Podgornaya, Olga I.
Source:
Chromosome research 2016 v.24 no.3 pp. 309-323
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; chromocenters; clones; databases; fluorescence in situ hybridization; genome; heterochromatin; humans; interphase; metaphase; mice; molecular cloning; open reading frames; protein content; satellites; sequence analysis; sex chromosomes;     Show all 18 Subjects
Abstract:
... Chromocenters are interphase nuclear landmark structures of constitutive heterochromatin. The tandem repeat (TR)-enriched parts of different chromosomes cluster together in chromocenters. There has been progress in recent years in determining the protein content of chromocenters, although it is not clear which DNA sequences underly constitutive heterochromatin apart from the TRs. The aim of the cu ...
DOI:
10.1007/s10577-016-9525-9

11. Repetitive DNA in eukaryotic genomes

Author:
Biscotti, Maria Assunta; Olmo, Ettore; Heslop-Harrison, J. S. (Pat)
Source:
Chromosome research 2015 v.23 no.3 pp. 415-420
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; RNA; bioinformatics; centromeres; evolution; gene expression regulation; genes; genetic markers; high-throughput nucleotide sequencing; nuclear genome; transposons;     Show all 12 Subjects
Abstract:
... Repetitive DNA—sequence motifs repeated hundreds or thousands of times in the genome—makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals ...
DOI:
10.1007/s10577-015-9499-z

12. Tribe-specific satellite DNA in non-domestic Bovidae

Author:
Kopecna, Olga; Kubickova, Svatava; Cernohorska, Halina; Cabelova, Katerina; Vahala, Jiri; Martinkova, Natalia; Rubes, Jiri
Source:
Chromosome research 2014 v.22 no.3 pp. 277-291
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Bovidae; DNA; chromosomes; clones; databases; gene banks; molecular cloning; phylogeny; statistical models;     Show all 10 Subjects
Abstract:
... 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 t ...
DOI:
10.1007/s10577-014-9401-4
PubMed:
24452783

13. Human centromere genomics: now it's personal

Author:
Hayden, Karen E.
Source:
Chromosome research 2012 v.20 no.5 pp. 621-633
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; centromeres; data collection; evolution; genomics; humans; microtubules; models;     Show all 8 Subjects
Abstract:
... Advances in human genomics have accelerated studies in evolution, disease, and cellular regulation. However, centromere sequences, defining the chromosomal interface with spindle microtubules, remain largely absent from ongoing genomic studies and disconnected from functional, genome-wide analyses. This disparity results from the challenge of predicting the linear order of multi-megabase-sized reg ...
DOI:
10.1007/s10577-012-9295-y
PubMed:
22801774

14. Helitrons shaping the genomic architecture of Drosophila: enrichment of DINE-TR1 in α- and β-heterochromatin, satellite DNA emergence, and piRNA expression

Author:
Dias, Guilherme B.; Heringer, Pedro; Svartman, Marta; Kuhn, Gustavo C. S.
Source:
Chromosome research 2015 v.23 no.3 pp. 597-613
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Bactrocera tryoni; Drosophila americana; Drosophila virilis; Y chromosome; animal ovaries; genome; heterochromatin; messenger RNA; phylogeny; satellites; sequence analysis; tandem repeat sequences; telomeres; testes;     Show all 15 Subjects
Abstract:
... Drosophila INterspersed Elements (DINEs) constitute an abundant but poorly understood group of Helitrons present in several Drosophila species. The general structure of DINEs includes two conserved blocks that may or not contain a region with tandem repeats in between. These central tandem repeats (CTRs) are similar within species but highly divergent between species. It has been assumed that CTRs ...
DOI:
10.1007/s10577-015-9480-x

15. De novo formed satellite DNA-based mammalian artificial chromosomes and their possible applications

Author:
Katona, Robert L.
Source:
Chromosome research 2015 v.23 no.1 pp. 143-157
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; adults; chromosomes; embryonic stem cells; gene expression; gene therapy; genes; genetic vectors; germ cells; mammals; milk; transgenic animals;     Show all 13 Subjects
Abstract:
... Mammalian artificial chromosomes (MACs) are non-integrating, autonomously replicating natural chromosome-based vectors that may carry a vast amount of genetic material, which in turn enable potentially prolonged, safe, and regulated therapeutic transgene expression and render MACs as attractive genetic vectors for “gene replacement” or for controlling differentiation pathways in target cells. Sate ...
DOI:
10.1007/s10577-014-9458-0

16. Developing de novo human artificial chromosomes in embryonic stem cells using HSV-1 amplicon technology

Author:
Moralli, Daniela; Monaco, Zoia L.
Source:
Chromosome research 2015 v.23 no.1 pp. 105-110
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; DNA; cell membranes; centromeres; chromatin; embryonic stem cells; gene expression; harvesting; humans; metaphase; mice; models; neoplasm cells; neurons; regulator genes;     Show all 15 Subjects
Abstract:
... De novo artificial chromosomes expressing genes have been generated in human embryonic stem cells (hESc) and are maintained following differentiation into other cell types. Human artificial chromosomes (HAC) are small, functional, extrachromosomal elements, which behave as normal chromosomes in human cells. De novo HAC are generated following delivery of alpha satellite DNA into target cells. HAC ...
DOI:
10.1007/s10577-014-9456-2
PubMed:
25657030
PubMed Central:
PMC4365269

17. Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica

Author:
Heitkam, Tony; Petrasch, Stefan; Zakrzewski, Falk; Kögler, Anja; Wenke, Torsten; Wanke, Stefan; Schmidt, Thomas
Source:
Chromosome research 2015 v.23 no.4 pp. 791-806
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Camellia japonica; Camellia sinensis; Southern blotting; bioinformatics; centromeres; evolution; fluorescence; genome; genomic libraries; high-throughput nucleotide sequencing; ribosomal DNA; satellites; tandem repeat sequences; tea; Germany; Northern European region;     Show all 17 Subjects
Abstract:
... Northern Europe’s oldest and largest Camellia japonica growing at the Pillnitz Castle (Germany) for over 200 years is of botanical and cultural importance and is a reference for C. japonica molecular scale analysis. In order to provide a fundament for genome analysis of the genus Camellia, we characterize the C. japonica tandem repeat fraction, constituting 12.5 % of the Pillnitz camellia’s genome ...
DOI:
10.1007/s10577-015-9500-x

18. Functional centromeres in Astragalus sinicus include a compact centromere-specific histone H3 and a 20-bp tandem repeat

Author:
Tek, Ahmet L.; Kashihara, Kazunari; Murata, Minoru; Nagaki, Kiyotaka
Source:
Chromosome research 2011 v.19 no.8 pp. 969-978
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Astragalus sinicus; DNA; centromeres; chromosome segregation; eukaryotic cells; histones; legumes; nucleotides;     Show all 9 Subjects
Abstract:
... The centromere plays an essential role for proper chromosome segregation during cell division and usually harbors long arrays of tandem repeated satellite DNA sequences. Although this function is conserved among eukaryotes, the sequences of centromeric DNA repeats are variable. Most of our understanding of functional centromeres, which are defined by localization of a centromere-specific histone H ...
DOI:
10.1007/s10577-011-9247-y
PubMed:
22065151

19. Rapid, independent, and extensive amplification of telomeric repeats in pericentromeric regions in karyotypes of arvicoline rodents

Author:
Rovatsos, M. Th.; Marchal, J. A.; Romero-Fernández, I.; Fernández, F. J.; Giagia-Athanosopoulou, E. B.; Sánchez, Antonio
Source:
Chromosome research 2011 v.19 no.7 pp. 869-882
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Arvicola; Chionomys; Microtus; chromosome morphology; evolution; fluorescence in situ hybridization; rodents; telomeres;     Show all 9 Subjects
Abstract:
... The distribution of telomeric repeats was analyzed by fluorescence in situ hybridization in 15 species of arvicoline rodents, included in three different genera: Chionomys, Arvicola, and Microtus. The results demonstrated that in most or the analyzed species, telomeric sequences are present, in addition to normal telomeres localization, as large blocks in pericentromeric regions. The number, local ...
DOI:
10.1007/s10577-011-9242-3
PubMed:
21979796

20. Robertsonian fusions, pericentromeric repeat organization and evolution: a case study within a highly polymorphic rodent species, Gerbillus nigeriae

Author:
Gauthier, Philippe; Hima, Karmadine; Dobigny, Gauthier
Source:
Chromosome research 2010 v.18 no.4 pp. 473-486
ISSN:
0967-3849
Subject:
satellite DNA,   etc   ; Gerbillus; Mus musculus; acrocentric chromosomes; case studies; diploidy; evolution; genome; gerbils; humans; models; races;     Show all 12 Subjects
Abstract:
... Pericentromeric repeats have been claimed to mediate centric fusions through heterologous recombination of arrays of tandemly repeated and highly homogenized motifs. However, mammalian case studies are essentially restricted to pathologic fusions in human, or to the house mouse Roberstonian (Rb) races. We here provide an example in a wild gerbil rodent, Gerbillus nigeriae, which displays an extens ...
DOI:
10.1007/s10577-010-9128-9
PubMed:
20361248