Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin.
暂无分享,去创建一个
Miroslav Plohl | Andrea Luchetti | M. Plohl | A. Luchetti | N. Meštrović | B. Mantovani | Nevenka Mestrović | Barbara Mantovani
[1] A. Luchetti,et al. Genomic dynamics of a low-copy-number satellite DNA family in Leptestheria dahalacensis (Crustacea, Branchiopoda, Conchostraca). , 2004, Gene.
[2] O. Cuvier,et al. Displacement of D1, HP1 and topoisomerase II from satellite heterochromatin by a specific polyamide , 2006, The EMBO journal.
[3] K. Choo,et al. Centromere on the move. , 2001, Genome research.
[4] R. Martienssen,et al. Maintenance of heterochromatin by RNA interference of tandem repeats , 2003, Nature Genetics.
[5] R. Matyášek,et al. Transcription activity of rRNA genes correlates with a tendency towards intergenomic homogenization in Nicotiana allotetraploids. , 2007, The New phytologist.
[6] M. Plohl,et al. Similarity of Structural Features and Evolution of Satellite DNAs from Palorus subdepressus (Coleoptera) and Related Species , 1998, Journal of Molecular Evolution.
[7] K. Bloom. Centromere dynamics. , 2007, Current opinion in genetics & development.
[8] B. Mantovani,et al. Non-concerted evolution of the RET76 satellite DNA family in Reticulitermes taxa (Insecta, Isoptera) , 2006, Genetica.
[9] R. Martienssen,et al. RNA interference and heterochromatin in the fission yeast Schizosaccharomyces pombe. , 2005, Trends in genetics : TIG.
[10] W. Stephan,et al. Evidence of gene conversion associated with a selective sweep in Drosophila melanogaster. , 2006, Molecular biology and evolution.
[11] R Cedergren,et al. Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets. , 2000, Nucleic acids research.
[12] C. Slamovits,et al. Sequence evolution of the major satellite DNA of the genus Ctenomys (Octodontidae, Rodentia). , 2007, Gene.
[13] Jiming Jiang,et al. Transcription and evolutionary dynamics of the centromeric satellite repeat CentO in rice. , 2006, Molecular biology and evolution.
[14] Gary H Karpen,et al. Sequence analysis of a functional Drosophila centromere. , 2003, Genome research.
[15] B. Zhivotovsky,et al. Constitutive expression of the human peroxiredoxin V gene contributes to protection of the genome from oxidative DNA lesions and to suppression of transcription of noncoding DNA , 2006, The FEBS journal.
[16] S. Henikoff,et al. The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA , 2001, Science.
[17] Huntington F Willard,et al. The evolutionary dynamics of alpha-satellite. , 2005, Genome research.
[18] J. Elder,et al. Concerted Evolution of Repetitive DNA Sequences in Eukaryotes , 1995, The Quarterly Review of Biology.
[19] D. Preuss,et al. Centromere satellites from Arabidopsis populations: maintenance of conserved and variable domains. , 2003, Genome research.
[20] W. Doolittle,et al. Selfish genes, the phenotype paradigm and genome evolution , 1980, Nature.
[21] Madhu Tiwari,et al. Chromosomal localization, copy number assessment, and transcriptional status of BamHI repeat fractions in water buffalo Bubalus bubalis. , 2006, DNA and cell biology.
[22] L. Bachmann,et al. Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group. , 2000, Molecular biology and evolution.
[23] H. Willard,et al. Genomic analysis of sequence variation in tandemly repeated DNA. Evidence for localized homogeneous sequence domains within arrays of alpha-satellite DNA. , 1990, Journal of molecular biology.
[24] G. Dover. Molecular drive in multigene families: How biological novelties arise, spread and are assimilated , 1986 .
[25] P. Dollé,et al. Transcripts from opposite strands of γ satellite DNA are differentially expressed during mouse development , 1995, Mammalian Genome.
[26] G. P. Smith,et al. Evolution of repeated DNA sequences by unequal crossover. , 1976, Science.
[27] L. Bachmann,et al. The pvB370 BamHI satellite DNA family of the Drosophila virilis group and its evolutionary relation to mobile dispersed genetic pDv elements , 1995, Journal of Molecular Evolution.
[28] I. Alexandrov,et al. Unequal cross‐over is involved in human alpha satellite DNA rearrangements on a border of the satellite domain , 1998, FEBS letters.
[29] Evan E. Eichler,et al. An assessment of the sequence gaps: Unfinished business in a finished human genome , 2004, Nature Reviews Genetics.
[30] S. Ohno,et al. So much "junk" DNA in our genome. , 1972, Brookhaven symposia in biology.
[31] Jiming Jiang,et al. Sobo, a Recently Amplified Satellite Repeat of Potato, and Its Implications for the Origin of Tandemly Repeated Sequences , 2005, Genetics.
[32] Huntington F Willard,et al. Progressive proximal expansion of the primate X chromosome centromere. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[33] M. Plohl,et al. Sequence divergence and conservation in organizationally distinct subfamilies of Donax trunculus satellite DNA. , 2005, Gene.
[34] H. Willard,et al. Rapid creation of BAC-based human artifical chromosome vectors by transposition with synthetic alpha-satellite arrays , 2005, Nucleic acids research.
[35] C. Topp,et al. Centromeric Retroelements and Satellites Interact with Maize Kinetochore Protein CENH3 , 2002, The Plant Cell Online.
[36] W Stephan,et al. Possible role of natural selection in the formation of tandem-repetitive noncoding DNA. , 1994, Genetics.
[37] G. Drouin. Chromatin diminution in the copepod Mesocyclops edax: diminution of tandemly repeated DNA families from somatic cells. , 2006, Genome.
[38] W. Stephan. Recombination and the evolution of satellite DNA. , 1986, Genetical research.
[39] C. Desel,et al. The large-scale organization of the centromeric region in Beta species. , 2001, Genome research.
[40] E. Winzeler,et al. Genomic and Genetic Definition of a Functional Human Centromere , 2001, Science.
[41] S. Henikoff,et al. Chromatin immunoprecipitation reveals that the 180-bp satellite repeat is the key functional DNA element of Arabidopsis thaliana centromeres. , 2003, Genetics.
[42] S. Henikoff,et al. Adaptive evolution of Cid, a centromere-specific histone in Drosophila. , 2001, Genetics.
[43] P. Jeffrey,et al. Regulation of Heterochromatic Silencing and Histone H 3 Lysine-9 Methylation by RNAi , 2002 .
[44] H. Masumoto,et al. The role of CENP-B and α-satellite DNA: de novo assembly and epigenetic maintenance of human centromeres , 2004, Chromosome Research.
[45] M. P. Cummings,et al. Satellite DNA repeat sequence variation is low in three species of burying beetles in the genus Nicrophorus (Coleoptera: Silphidae). , 1997, Molecular biology and evolution.
[46] Ira M. Hall,et al. Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi , 2002, Science.
[47] H. Scherthan,et al. Characterization of ancestral chromosome fusion points in the Indian muntjac deer , 2004, Chromosoma.
[48] Contiguous arrays of satellites 1, 3, and beta form a 1.5-Mb domain on chromosome 22p. , 1997, Genomics.
[49] M. Plohl,et al. Variation in satellite DNA profiles—causes and effects , 2002, The EMBO journal.
[50] A. Shatrova,et al. Evidence for the existence of satellite DNA‐containing connection between metaphase chromosomes , 2007, Journal of cellular biochemistry.
[51] Wolfgang Stephan,et al. The evolutionary dynamics of repetitive DNA in eukaryotes , 1994, Nature.
[52] Ú. Árnason,et al. Mysticete (baleen whale) relationships based upon the sequence of the common cetacean DNA satellite. , 1992, Molecular biology and evolution.
[53] Gary H. Karpen,et al. Determining centromere identity: cyclical stories and forking paths , 2001, Nature Reviews Genetics.
[54] F. Rouleux-Bonnin,et al. Genomic organization and transcription of satellite DNA in the ant Aphaenogaster subterranea (Hymenoptera, Formicidae). , 2002, Genome.
[55] S. Henikoff,et al. Centromeric chromatin: what makes it unique? , 2005, Current opinion in genetics & development.
[56] M. Ferguson-Smith,et al. High-resolution organization of mouse centromeric and pericentromeric DNA , 2006, Cytogenetic and Genome Research.
[57] M. Garrido-Ramos,et al. Evolution of centromeric satellite DNA and its use in phylogenetic studies of the Sparidae family (Pisces, Perciformes). , 1999, Molecular phylogenetics and evolution.
[58] S. Jackson,et al. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. , 2005, Genome research.
[59] M. Plohl,et al. Conserved patterns in the evolution of Tribolium satellite DNAs. , 2004, Gene.
[60] F. Crick,et al. Selfish DNA: the ultimate parasite , 1980, Nature.
[61] A. Tinaut,et al. Evolutionary dynamics of satellite DNA in species of the Genus Formica (Hymenoptera, Formicidae). , 2004, Gene.
[62] F. Müller,et al. Chromatin diminution leads to rapid evolutionary changes in the organization of the germ line genomes of the parasitic nematodes A. suum and P. univalens. , 2004, Molecular and biochemical parasitology.
[63] H. Masumoto,et al. Distribution of CENP-B boxes reflected in CREST centromere antigenic sites on long-range alpha-satellite DNA arrays of human chromosome 21. , 1994, Human molecular genetics.
[64] M. Plohl,et al. Sequence of PRAT Satellite DNA ``Frozen'' in Some Coleopteran Species , 2002, Journal of Molecular Evolution.
[65] M. Rocchi,et al. Molecular structure and evolution of DNA sequences located at the alpha satellite boundary of chromosome 20. , 2000, Gene.
[66] T. Cavalier-smith,et al. Selfish DNA and the origin of introns , 1985, Nature.
[67] A. Ludwig,et al. Evolution of ancient satellite DNAs in sturgeon genomes. , 2004, Gene.
[68] E. Bastos,et al. Amplification of the major satellite DNA family (FA-SAT) in a cat fibrosarcoma might be related to chromosomal instability. , 2006, The Journal of heredity.
[69] K. Choo,et al. Mouse telocentric sequences reveal a high rate of homogenization and possible role in Robertsonian translocation. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[70] D. Schindelhauer,et al. Evidence for a fast, intrachromosomal conversion mechanism from mapping of nucleotide variants within a homogeneous alpha-satellite DNA array. , 2002, Genome research.
[71] M. Oshimura,et al. Dicer is essential for formation of the heterochromatin structure in vertebrate cells , 2004, Nature Cell Biology.
[72] R. Flavell,et al. Molecular coevolution: DNA divergence and the maintenance of function , 1984, Cell.
[73] K. Keith,et al. The rapidly evolving field of plant centromeres. , 2004, Current opinion in plant biology.
[74] P. Dimitri,et al. Cis-effects of heterochromatin on heterochromatic and euchromatic gene activity in Drosophila melanogaster. , 1995, Genetics.
[75] M. V. Vol’kenshtein. [Molecular drive]. , 1990, Molekuliarnaia biologiia.
[76] S. Grewal,et al. Transcription and RNA interference in the formation of heterochromatin , 2007, Nature.
[77] M. Baron,et al. Concerted Evolution Within the Drosophila dumpy Gene , 2007, Genetics.
[78] J. Jurka,et al. L1 repeat is a basic unit of heterochromatin satellites in cetaceans. , 1998, Molecular biology and evolution.
[79] H. Willard,et al. Pulsed-field gel analysis of alpha-satellite DNA at the human X chromosome centromere: high-frequency polymorphisms and array size estimate. , 1990, Genomics.
[80] Evolution of low-copy number and major satellite DNA sequences coexisting in two Pimelia species-groups (Coleoptera). , 2003, Gene.
[81] J. S. Heslop-Harrison,et al. Molecular diversification of tandemly organized DNA sequences and heterochromatic chromosome regions in some triticeae species , 1996, Chromosome Research.
[82] Mari Nakamura,et al. Composition and Structure of the Centromeric Region of Rice Chromosome 8 , 2004, The Plant Cell Online.
[83] A. Fisher,et al. Epigenetic aspects of differentiation , 2004, Journal of Cell Science.
[84] E. Eichler,et al. Chromosome evolution in eukaryotes: a multi-kingdom perspective. , 2005, Trends in genetics : TIG.
[85] G. Karpen,et al. Position-effect variegation and the new biology of heterochromatin. , 1994, Current opinion in genetics & development.
[86] C. Coutelle,et al. Contiguous Arrays of Satellites 1, 3, and β Form a 1.5-Mb Domain on Chromosome 22p , 1997 .
[87] H. Willard,et al. Patterns of intra- and interarray sequence variation in alpha satellite from the human X chromosome: evidence for short-range homogenization of tandemly repeated DNA sequences. , 1989, Genomics.
[88] M. Maden. Biolistics: The retinoic acid supergun affair , 1994, Current Biology.
[89] G. Karpen,et al. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin , 2004, Nature Structural &Molecular Biology.
[90] M. Plohl,et al. Evolution of satellite DNAs from the genus Palorus--experimental evidence for the "library" hypothesis. , 1998, Molecular biology and evolution.
[91] S. Henikoff,et al. Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[92] S. Henikoff,et al. Adaptive evolution of centromere proteins in plants and animals , 2004, Journal of biology.
[93] D. Franjević,et al. Long Inversely Oriented Subunits Form a Complex Monomer of Triboliumbrevicornis Satellite DNA , 2004, Journal of Molecular Evolution.
[94] P. Castagnone-Sereno,et al. High conservation of the differentially amplified MPA2 satellite DNA family in parthenogenetic root-knot nematodes. , 2006, Gene.
[95] W. Jin,et al. Chromatin immunoprecipitation cloning reveals rapid evolutionary patterns of centromeric DNA in Oryza species. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[96] H. Kotani,et al. The size and sequence organization of the centromeric region of arabidopsis thaliana chromosome 5. , 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.
[97] J. S. Heslop-Harrison,et al. Genomes, genes and junk: the large-scale organization of plant chromosomes , 1998 .
[98] H. Bünemann,et al. Molecular Aspects of Intron Evolution in Dynein Encoding Mega-Genes on The Heterochromatic Y Chromosome of Drosophila sp. , 2004, Genetica.
[99] P. Castagnone-Sereno,et al. Interplay of selective pressure and stochastic events directs evolution of the MEL172 satellite DNA library in root-knot nematodes. , 2006, Molecular biology and evolution.
[100] E. Frise,et al. Sequence Finishing and Mapping of Drosophila melanogaster Heterochromatin , 2007, Science.
[101] H. Kasinsky,et al. Meiotic chromatin diminution in a vertebrate, the holocephalan fish Hydrolagus collie (Chondrichthyes, Holocephali). , 1984, Tissue & cell.
[102] S Henikoff,et al. Something from nothing: the evolution and utility of satellite repeats. , 1998, Trends in genetics : TIG.
[103] W. Szybalski. [124] Use of cesium sulfate for equilibrium density gradient centrifugation☆ , 1968 .
[104] G. Roizes. Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning , 2006, Nucleic acids research.
[105] T. Ohta,et al. The cohesive population genetics of molecular drive. , 1984, Genetics.
[106] T. Ryan Gregory,et al. Eukaryotic genome size databases , 2006, Nucleic Acids Res..
[107] W. Modi,et al. Concerted Evolution and Higher-Order Repeat Structure of the 1.709 (Satellite IV) Family in Bovids , 2004, Journal of Molecular Evolution.
[108] G. Dover. DNA turnover and the molecular clock , 2005, Journal of Molecular Evolution.
[109] Sonja Durajlija Zinic,et al. A Novel Interspersed Type of Organization of Satellite DNAs in Tribolium Madens Heterochromatin , 2004, Chromosome Research.
[110] W. Stephan. Tandem-repetitive noncoding DNA: forms and forces. , 1989, Molecular biology and evolution.
[111] P. Abad,et al. Conserved and variable domains in satellite DNAs of mitotic parthenogenetic root-knot nematode species. , 2005, Gene.
[112] Molecular drive. , 2002, Science.
[113] T. Strachan,et al. Transition stages of molecular drive in multiple‐copy DNA families in Drosophila , 1985, The EMBO journal.
[114] J N Anderson,et al. Conserved patterns of bending in satellite and nucleosome positioning DNA. , 1994, The Journal of biological chemistry.
[115] J. Werren,et al. Evolution of Tandemly Repeated Sequences: What Happens at the End of an Array? , 1999, Journal of Molecular Evolution.
[116] M. Cardone,et al. Evolution of beta satellite DNA sequences: evidence for duplication-mediated repeat amplification and spreading. , 2004, Molecular biology and evolution.
[117] L. Bachmann,et al. Gradual evolution of a specific satellite DNA family in Drosophila ambigua, D. tristis, and D. obscura. , 1993, Molecular biology and evolution.
[118] Y. Bigot,et al. Heterochromatin condensation and evolution of unique satellite-DNA families in two parasitic wasp species: Diadromus pulchellus and Eupelmus vuilleti (Hymenoptera). , 1990, Molecular biology and evolution.
[119] C. Mungall,et al. The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin , 2007, Science.
[120] S. Henikoff,et al. Centromeres put epigenetics in the driver's seat. , 2006, Trends in biochemical sciences.
[121] G. Dover,et al. Molecular drive: a cohesive mode of species evolution , 1982, Nature.
[122] Jiming Jiang,et al. Rice as a model for centromere and heterochromatin research , 2007, Chromosome Research.
[123] B. Mantovani. Satellite sequence turnover in parthenogenetic systems: the apomictic triploid hybrid Bacillus lynceorum (Insecta, Phasmatodea). , 1998, Molecular biology and evolution.
[124] T. Kakutani,et al. Ecotype-specific and chromosome-specific expansion of variant centromeric satellites in Arabidopsis thaliana , 2006, Molecular Genetics and Genomics.
[125] F. Azorín,et al. Satellite DNAs contain sequences that induced curvature. , 1990, Biochemistry.
[126] H. Willard,et al. Physical and genetic mapping of the human X chromosome centromere: repression of recombination. , 1998, Genome research.
[127] B John,et al. Functional aspects of satellite DNA and heterochromatin. , 1979, International review of cytology.
[128] F. Blattner,et al. Functional Rice Centromeres Are Marked by a Satellite Repeat and a Centromere-Specific Retrotransposon Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.003079. , 2002, The Plant Cell Online.
[129] D. M. Skinner,et al. Cytoplasmic localization of transcripts of a complex G+C-rich crab satellite DNA , 1994, Chromosoma.
[130] C. Topp,et al. Centromere-encoded RNAs are integral components of the maize kinetochore. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[131] T. Schwarzacher,et al. Tandemly repeated DNA sequences and centromeric chromosomal regions of Arabidopsis species , 2004, Chromosome Research.
[132] W. Salser,et al. Nucleotide sequences of HS-α satellite DNA from kangaroo rat dipodomys ordii and characterization of similar sequences in other rodents , 1977, Cell.
[133] H. Kotani,et al. The size and sequence organization of the centromeric region of Arabidopsis thaliana chromosome 4. , 2001, DNA research : an international journal for rapid publication of reports on genes and genomes.
[134] A. Luchetti,et al. Polymerase chain reaction amplification of the Bag320 satellite family reveals the ancestral library and past gene conversion events in Bacillus rossius (Insecta Phasmatodea). , 2003, Gene.
[135] A. Luchetti,et al. Unisexuality and Molecular Drive: Bag320 Sequence Diversity in Bacillus Taxa (Insecta Phasmatodea) , 2003, Journal of Molecular Evolution.
[136] M. Barucca,et al. A satellite DNA containing CENP-B box-like motifs is present in the antarctic scallop Adamussium colbecki. , 2000, Gene.
[137] H. Kotani,et al. Physical map-based sizes of the centromeric regions of Arabidopsis thaliana chromosomes 1, 2, and 3. , 2002, DNA research : an international journal for rapid publication of reports on genes and genomes.
[138] S. Henikoff,et al. Sequencing of a rice centromere uncovers active genes , 2004, Nature Genetics.
[139] C. Slamovits,et al. Recurrent amplifications and deletions of satellite DNA accompanied chromosomal diversification in South American tuco-tucos (genus Ctenomys, Rodentia: Octodontidae): a phylogenetic approach. , 2001, Molecular biology and evolution.
[140] Francesca Antonacci,et al. Evolutionary Formation of New Centromeres in Macaque , 2007, Science.
[141] H. Willard,et al. Analysis of the centromeric regions of the human genome assembly. , 2004, Trends in genetics : TIG.
[142] Huntington F. Willard,et al. Chromosome-specific subsets of human alpha satellite DNA: Analysis of sequence divergence within and between chromosomal subsets and evidence for an ancestral pentameric repeat , 2005, Journal of Molecular Evolution.