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Abstract
Reverse transcriptases have shaped genomes in many ways. A remarkable example of this shaping is found on telomeres of the genus Drosophila, where retrotransposons have a vital role in chromosome structure. Drosophila lacks telomerase; instead, three telomere-specific retrotransposons maintain chromosome ends. Repeated transpositions to chromosome ends produce long head to tail arrays of these elements. In both form and function, these arrays are analogous to the arrays of repeats added by telomerase to chromosomes in other organisms. Distantly related Drosophila exhibit this variant mechanism of telomere maintenance, which was established before the separation of extant Drosophila species. Nevertheless, the telomere-specific elements still have the hallmarks that characterize non-long terminal repeat (non-LTR) retrotransposons; they have also acquired characteristics associated with their roles at telomeres. These telomeric retrotransposons have shaped the Drosophila genome, but they have also been shaped by the genome. Here, we discuss ways in which these three telomere-specific retrotransposons have been modified for their roles in Drosophila chromosomes.
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Verdaasdonk JS, Bloom K. Centromeres: unique chromatin structures that drive chromosome segregation. Nat Rev Mol Cell Biol 2011; 12:320-32. [PMID: 21508988 DOI: 10.1038/nrm3107] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fidelity during chromosome segregation is essential to prevent aneuploidy. The proteins and chromatin at the centromere form a unique site for kinetochore attachment and allow the cell to sense and correct errors during chromosome segregation. Centromeric chromatin is characterized by distinct chromatin organization, epigenetics, centromere-associated proteins and histone variants. These include the histone H3 variant centromeric protein A (CENPA), the composition and deposition of which have been widely investigated. Studies have examined the structural and biophysical properties of the centromere and have suggested that the centromere is not simply a 'landing pad' for kinetochore formation, but has an essential role in mitosis by assembling and directing the organization of the kinetochore.
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Affiliation(s)
- Jolien S Verdaasdonk
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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53
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Elde NC, Roach KC, Yao MC, Malik HS. Absence of positive selection on centromeric histones in Tetrahymena suggests unsuppressed centromere: drive in lineages lacking male meiosis. J Mol Evol 2011; 72:510-20. [PMID: 21643829 PMCID: PMC3144370 DOI: 10.1007/s00239-011-9449-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 05/19/2011] [Indexed: 12/20/2022]
Abstract
Centromere-drive is a process where centromeres compete for transmission through asymmetric "female" meiosis for inclusion into the oocyte. In symmetric "male" meiosis, all meiotic products form viable germ cells. Therefore, the primary incentive for centromere-drive, a potential transmission bias, is believed to be missing from male meiosis. In this article, we consider whether male meiosis also bears the primary cost of centromere-drive. Because different taxa carry out different combinations of meiotic programs (symmetric + asymmetric, symmetric only, asymmetric only), it is possible to consider the evolutionary consequences of centromere-drive in the context of these differing systems. Groups with both types of meiosis have large, rapidly evolving centromeric regions, and their centromeric histones (CenH3s) have been shown to evolve under positive selection, suggesting roles as suppressors of centromere-drive. In contrast, taxa with only symmetric male meiosis have shown no evidence of positive selection in their centromeric histones. In this article, we present the first evolutionary analysis of centromeric histones in ciliated protozoans, a group that only undergoes asymmetric "female" meiosis. We find no evidence of positive selection acting on CNA1, the CenH3 of Tetrahymena species. Cytological observations of a panel of Tetrahymena species are consistent with dynamic karyotype evolution in this lineage. Our findings suggest that defects in male meiosis, and not mitosis or female meiosis, are the primary selective force behind centromere-drive suppression. Our study raises the possibility that taxa like ciliates, with only female meiosis, may therefore undergo unsuppressed centromere drive.
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Affiliation(s)
- Nels C. Elde
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A2-205, Seattle, WA 98109 USA
- Present Address: Department of Human Genetics, University of Utah, Salt Lake City, UT 84112 USA
| | - Kevin C. Roach
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A2-205, Seattle, WA 98109 USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
| | - Meng-Chao Yao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A2-205, Seattle, WA 98109 USA
- HHMI, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A2-205, Seattle, WA 98109 USA
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54
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Molecular and cytological characterization of repetitive DNA sequences from the centromeric heterochromatin of Sciara coprophila. Chromosoma 2011; 120:387-97. [PMID: 21533987 DOI: 10.1007/s00412-011-0320-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 10/18/2022]
Abstract
Sciara coprophila (Diptera, Nematocera) constitutes a classic model to analyze unusual chromosome behavior such as the somatic elimination of paternal X chromosomes, the elimination of the whole paternal, plus non-disjunction of the maternal X chromosome at male meiosis. The molecular organization of the heterochromatin in S. coprophila is mostly unknown except for the ribosomal DNA located in the X chromosome pericentromeric heterochromatin. The characterization of the centromeric regions, thus, is an essential and required step for the establishment of S. coprophila as a model system to study fundamental mechanisms of chromosome segregation. To accomplish such a study, heterochromatic sections of the X chromosome centromeric region from salivary glands polytene chromosomes were microdissected and microcloned. Here, we report the identification and characterization of two tandem repeated DNA sequences from the pericentromeric region of the X chromosome, a pericentromeric RTE element and an AT-rich centromeric satellite. These sequences will be important tools for the cloning of S. coprophila centromeric heterochromatin using libraries of large genomic clones.
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55
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Cuadrado A, Jouve N. Novel simple sequence repeats (SSRs) detected by ND-FISH in heterochromatin of Drosophila melanogaster. BMC Genomics 2011; 12:205. [PMID: 21521504 PMCID: PMC3114746 DOI: 10.1186/1471-2164-12-205] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 04/26/2011] [Indexed: 12/02/2022] Open
Abstract
Background In recent years, substantial progress has been made in understanding the organization of sequences in heterochromatin regions containing single-copy genes and transposable elements. However, the sequence and organization of tandem repeat DNA sequences, which are by far the majority fraction of D. melanogaster heterochromatin, are little understood. Results This paper reports that the heterochromatin, as well as containing long tandem arrays of pentanucleotide satellites (AAGAG, AAGAC, AATAT, AATAC and AACAC), is also enriched in other simple sequence repeats (SSRs) such as A, AC, AG, AAG, ACT, GATA and GACA. Non-denaturing FISH (ND-FISH) showed these SSRs to localize to the chromocentre of polytene chromosomes, and was used to map them on mitotic chromosomes. Different distributions were detected ranging from single heterochromatic clusters to complex combinations on different chromosomes. ND-FISH performed on extended DNA fibres, along with Southern blotting, showed the complex organization of these heterochromatin sequences in long tracts, and revealed subclusters of SSRs (several kilobase in length) flanked by other DNA sequences. The chromosomal characterization of C, AAC, AGG, AAT, CCG, ACG, AGC, ATC and ACC provided further detailed information on the SSR content of D. melanogaster at the whole genome level. Conclusion These data clearly show the variation in the abundance of different SSR motifs and reveal their non-random distribution within and between chromosomes. The greater representation of certain SSRs in D. melanogaster heterochromatin suggests that its complexity may be greater than previously thought.
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Affiliation(s)
- Angeles Cuadrado
- Department of Cell Biology and Genetics, University of Alcalá de Henares, 28871 Alcalá de Henares, Madrid, Spain.
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56
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Heterochromatin is required for normal distribution of Neurospora crassa CenH3. Mol Cell Biol 2011; 31:2528-42. [PMID: 21505064 DOI: 10.1128/mcb.01285-10] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Centromeres serve as platforms for the assembly of kinetochores and are essential for nuclear division. Here we identified Neurospora crassa centromeric DNA by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) of DNA associated with tagged versions of the centromere foundation proteins CenH3 (CENP-A) and CEN-C (CENP-C) and the kinetochore protein CEN-T (CENP-T). On each chromosome we found an ∼150- to 300-kbp region of enrichment for all three proteins. These regions correspond to intervals predicted to be centromeric DNA by genetic mapping and DNA sequence analyses. By ChIP-seq we found extensive colocalization of CenH3, CEN-C, CEN-T, and histone H3K9 trimethylation (H3K9me3). In contrast, H3K4me2, which has been found at the cores of plant, fission yeast, Drosophila, and mammalian centromeres, was not enriched in Neurospora centromeric DNA. DNA methylation was most pronounced at the periphery of centromeric DNA. Mutation of dim-5, which encodes an H3K9 methyltransferase responsible for nearly all H3K9me3, resulted in altered distribution of CenH3-green fluorescent protein (GFP). Similarly, CenH3-GFP distribution was altered in the absence of HP1, the chromodomain protein that binds to H3K9me3. We conclude that eukaryotes with regional centromeres make use of different strategies for maintenance of CenH3 at centromeres, and we suggest a model in which centromere proteins nucleate at the core but require DIM-5 and HP1 for spreading.
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57
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Abstract
Repeated DNA in heterochromatin presents enormous difficulties for whole-genome sequencing; hence, sequence organization in a significant portion of the genomes of multicellular organisms is relatively unknown. Two sequenced BACs now allow us to compare telomeric retrotransposon arrays from Drosophila melanogaster telomeres with an array of telomeric retrotransposons that transposed into the centromeric region of the Y chromosome >13 MYA, providing a unique opportunity to compare the structural evolution of this retrotransposon in two contexts. We find that these retrotransposon arrays, both heterochromatic, are maintained quite differently, resulting in sequence organizations that apparently reflect different roles in the two chromosomal environments. The telomere array has grown only by transposition of new elements to the chromosome end; the centromeric array instead has grown by repeated amplifications of segments of the original telomere array. Many elements in the telomere have been variably 5'-truncated apparently by gradual erosion and irregular deletions of the chromosome end; however, a significant fraction (4 and possibly 5 or 6 of 15 elements examined) remain complete and capable of further retrotransposition. In contrast, each element in the centromere region has lost ≥ 40% of its sequence by internal, rather than terminal, deletions, and no element retains a significant part of the original coding region. Thus the centromeric array has been restructured to resemble the highly repetitive satellite sequences typical of centromeres in multicellular organisms, whereas, over a similar or longer time period, the telomere array has maintained its ability to provide retrotransposons competent to extend telomere ends.
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58
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Abstract
The purpose of this work is to determine the most frequent short sequences in non-coding DNA. They may play a role in maintaining the structure and function of eukaryotic chromosomes. We present a simple method for the detection and analysis of such sequences in several genomes, including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. We also study two chromosomes of man and mouse with a length similar to the whole genomes of the other species. We provide a list of the most common sequences of 9–14 bases in each genome. As expected, they are present in human Alu sequences. Our programs may also give a graph and a list of their position in the genome. Detection of clusters is also possible. In most cases, these sequences contain few alternating regions. Their intrinsic structure and their influence on nucleosome formation are not known. In particular, we have found new features of short sequences in C. elegans, which are distributed in heterogeneous clusters. They appear as punctuation marks in the chromosomes. Such clusters are not found in either A. thaliana or D. melanogaster. We discuss the possibility that they play a role in centromere function and homolog recognition in meiosis.
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Affiliation(s)
- Juan A Subirana
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Av. Diagonal 647, E-08028, Barcelona, Spain.
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59
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Singh ND, Larracuente AM, Sackton TB, Clark AG. Comparative Genomics on the Drosophila Phylogenetic Tree. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2009. [DOI: 10.1146/annurev.ecolsys.110308.120214] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the sequencing of 12 complete euchromatic Drosophila genomes, the genus Drosophila is a leading model for comparative genomics. In this review, we discuss the novel insights into evolutionary processes afforded by the newly available genomic sequences when placed in the context of the phylogeny. We focus on three levels: insights into whole-genome content, such as changes in genome size and content across the phylogeny; insights into large-scale patterns of divergence and conservation, such as selective constraints on genes and chromosome-level evolution of sex chromosomes; and insights into finer-scale processes in individual lineages and genes, such as lineage-specific evolution in response to ecological context. As the field of comparative genomics is still young, we also discuss current challenges, such as the development of more sophisticated evolutionary models to capture nonequilibrium processes and the improvement of assembly and alignment algorithms to better capture uncertainty in the data.
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Affiliation(s)
- Nadia D. Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Amanda M. Larracuente
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Timothy B. Sackton
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
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60
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Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG. Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster. Genome Biol Evol 2009; 1:449-65. [PMID: 20333214 PMCID: PMC2839279 DOI: 10.1093/gbe/evp048] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2009] [Indexed: 12/20/2022] Open
Abstract
Short-read sequencing techniques provide the opportunity to capture genome-wide sequence data in a single experiment. A current challenge is to identify questions that shallow-depth genomic data can address successfully and to develop corresponding analytical methods that are statistically sound. Here, we apply the Roche/454 platform to survey natural variation in strains of Drosophila melanogaster from an African (n = 3) and a North American (n = 6) population. Reads were aligned to the reference D. melanogaster genomic assembly, single nucleotide polymorphisms were identified, and nucleotide variation was quantified genome wide. Simulations and empirical results suggest that nucleotide diversity can be accurately estimated from sparse data with as little as 0.2x coverage per line. The unbiased genomic sampling provided by random short-read sequencing also allows insight into distributions of transposable elements and copy number polymorphisms found within populations and demonstrates that short-read sequencing methods provide an efficient means to quantify variation in genome organization and content. Continued development of methods for statistical inference of shallow-depth genome-wide sequencing data will allow such sparse, partial data sets to become the norm in the emerging field of population genomics.
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Affiliation(s)
- Timothy B Sackton
- Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA, USA.
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61
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Cheng YM, Li TS, Hsieh LJ, Hsu PC, Li YC, Lin CC. Complex genomic organization of Indian muntjac centromeric DNA. Chromosome Res 2009; 17:1051-62. [PMID: 19921447 DOI: 10.1007/s10577-009-9097-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 10/27/2009] [Accepted: 10/28/2009] [Indexed: 11/29/2022]
Abstract
A 69-kb Indian muntjac bacterial artificial chromosome (BAC) clone that screened positive for Cervid satellites I and IV was selected for complete sequence analysis and further characterization. The sequences of this BAC clone were found in the centromeres and in some interstitial sites of Indian muntjac chromosomes. Sequence analyses showed that the BAC clone contained a 14.5 kb Cervid satellite I-like DNA element and a 9 kb Cervid satellite IV-like DNA element. In addition, it contained 51 regions each organized in a complex fashion, with sequences homology to intersperse repetitive sequences such as LINEs, SINEs, LTRs, other published DNA elements, and unassigned sequences. The FISH patterns of seven non-satellite sequence elements generated from the BAC clone showed mainly specific to centromeres of the Indian muntjac representing novel centromeric DNAs of the species. Furthermore, FISH signals and Southern blot patterns of these elements suggest the existence of a not yet identified repetitive sequence with giant repeated monomers. Positive FISH signals of these elements were also detected in the centromeric regions of Formosan muntjac. This suggests that these newly identified non-Cervid satellite DNA sequences have been conserved in the centromere of the Formosan muntjac.
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Affiliation(s)
- Ya-Ming Cheng
- Department of Agronomy, National Chung Hsing University, Taichung, 402, Taiwan
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62
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Abstract
Centromeres are chromosomal elements that are both necessary and sufficient for chromosome segregation. However, the puzzlingly broad range in centromere complexity, from simple "point" centromeres to multi-megabase arrays of DNA satellites, has defied explanation. We posit that ancestral centromeres were epigenetically defined and that point centromeres, such as those of budding yeast, have derived from the partitioning elements of selfish plasmids. We further propose that the larger centromere sizes in plants and animals and the rapid evolution of their centromeric proteins is the result of an intense battle for evolutionary dominance due to the asymmetric retention of only one product of female meiosis.
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Affiliation(s)
- Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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63
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Ferree PM, Barbash DA. Species-specific heterochromatin prevents mitotic chromosome segregation to cause hybrid lethality in Drosophila. PLoS Biol 2009; 7:e1000234. [PMID: 19859525 PMCID: PMC2760206 DOI: 10.1371/journal.pbio.1000234] [Citation(s) in RCA: 227] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 09/21/2009] [Indexed: 12/24/2022] Open
Abstract
Postzygotic reproductive barriers such as sterility and lethality of hybrids are important for establishing and maintaining reproductive isolation between species. Identifying the causal loci and discerning how they interfere with the development of hybrids is essential for understanding how hybrid incompatibilities (HIs) evolve, but little is known about the mechanisms of how HI genes cause hybrid dysfunctions. A previously discovered Drosophila melanogaster locus called Zhr causes lethality in F1 daughters from crosses between Drosophila simulans females and D. melanogaster males. Zhr maps to a heterochromatic region of the D. melanogaster X that contains 359-bp satellite repeats, suggesting either that Zhr is a rare protein-coding gene embedded within heterochromatin, or is a locus consisting of the noncoding repetitive DNA that forms heterochromatin. The latter possibility raises the question of how heterochromatic DNA can induce lethality in hybrids. Here we show that hybrid females die because of widespread mitotic defects induced by lagging chromatin at the time during early embryogenesis when heterochromatin is first established. The lagging chromatin is confined solely to the paternally inherited D. melanogaster X chromatids, and consists predominantly of DNA from the 359-bp satellite block. We further found that a rearranged X chromosome carrying a deletion of the entire 359-bp satellite block segregated normally, while a translocation of the 359-bp satellite block to the Y chromosome resulted in defective Y segregation in males, strongly suggesting that the 359-bp satellite block specifically and directly inhibits chromatid separation. In hybrids produced from wild-type parents, the 359-bp satellite block was highly stretched and abnormally enriched with Topoisomerase II throughout mitosis. The 359-bp satellite block is not present in D. simulans, suggesting that lethality is caused by the absence or divergence of factors in the D. simulans maternal cytoplasm that are required for heterochromatin formation of this species-specific satellite block. These findings demonstrate how divergence of noncoding repetitive sequences between species can directly cause reproductive isolation by altering chromosome segregation.
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Affiliation(s)
- Patrick M. Ferree
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Daniel A. Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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64
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Vermaak D, Bayes JJ, Malik HS. A surrogate approach to study the evolution of noncoding DNA elements that organize eukaryotic genomes. J Hered 2009; 100:624-36. [PMID: 19635763 DOI: 10.1093/jhered/esp063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Comparative genomics provides a facile way to address issues of evolutionary constraint acting on different elements of the genome. However, several important DNA elements have not reaped the benefits of this new approach. Some have proved intractable to current day sequencing technology. These include centromeric and heterochromatic DNA, which are essential for chromosome segregation as well as gene regulation, but the highly repetitive nature of the DNA sequences in these regions make them difficult to assemble into longer contigs. Other sequences, like dosage compensation X chromosomal sites, origins of DNA replication, or heterochromatic sequences that encode piwi-associated RNAs, have proved difficult to study because they do not have recognizable DNA features that allow them to be described functionally or computationally. We have employed an alternate approach to the direct study of these DNA elements. By using proteins that specifically bind these noncoding DNAs as surrogates, we can indirectly assay the evolutionary constraints acting on these important DNA elements. We review the impact that such "surrogate strategies" have had on our understanding of the evolutionary constraints shaping centromeres, origins of DNA replication, and dosage compensation X chromosomal sites. These have begun to reveal that in contrast to the view that such structural DNA elements are either highly constrained (under purifying selection) or free to drift (under neutral evolution), some of them may instead be shaped by adaptive evolution and genetic conflicts (these are not mutually exclusive). These insights also help to explain why the same elements (e.g., centromeres and replication origins), which are so complex in some eukaryotic genomes, can be simple and well defined in other where similar conflicts do not exist.
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Affiliation(s)
- Danielle Vermaak
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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65
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Mellone BG. Structural and temporal regulation of centromeric chromatin. Biochem Cell Biol 2009; 87:255-64. [PMID: 19234539 DOI: 10.1139/o08-121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Normal inheritance of genetic material requires that chromosomes segregate faithfully during mitosis and meiosis. The kinetochore is a unique structure that attaches chromosomes to the microtubule spindle, monitors proper chromosome attachment to the spindle through the mitotic checkpoint, and couples spindle and motor protein forces to move chromosomes during prometaphase and anaphase. The centromere is a specialized chromosomal site that is the structural and functional foundation for kinetochore formation, and is characterized by a unique type of chromatin that needs to be reconstituted after each replication cycle. In this review, recent progress in understanding the structural nature of this chromatin and how it is specifically maintained through cell division are discussed.
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Affiliation(s)
- Barbara G Mellone
- Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, and Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA.
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66
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Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain. Chromosome Res 2009; 17:379-96. [PMID: 19322668 DOI: 10.1007/s10577-009-9029-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Revised: 01/12/2009] [Accepted: 01/12/2009] [Indexed: 12/18/2022]
Abstract
LTR retrotransposons belong to a major group of DNA sequences that are often localized in plant centromeres. Using BAC inserts originating from the centromere of a monosomic wild beet (Beta procumbens) chromosome fragment in Beta vulgaris, two complete LTR retrotransposons were identified. Both elements, designated Beetle1 and Beetle2, possess a coding region with genes in the order characteristic for Ty3-gypsy retrotransposons. Beetle1 and Beetle2 have a chromodomain in the C-terminus of the integrase gene and are highly similar to the centromeric retrotransposons (CRs) of rice, maize, and barley. Both retroelements were localized in the centromeric region of B. procumbens chromosomes by fluorescence in-situ hybridization. They can therefore be classified as centromere-specific chromoviruses. PCR analysis using RNA as template indicated that Beetle1 and Beetle2 are transcriptionally active. On the basis of the sequence diversity between the LTR sequences, it was estimated that Beetle1 and Beetle2 transposed within the last 60,000 years and 130,000 years, respectively. The centromeric localization of Beetle1 and Beetle2 and their transcriptional activity combined with high sequence conservation within each family play an important structural role in the centromeres of B. procumbens chromosomes.
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67
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The role of repetitive DNA in structure and evolution of sex chromosomes in plants. Heredity (Edinb) 2009; 102:533-41. [PMID: 19277056 DOI: 10.1038/hdy.2009.17] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem repeats. These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (telomeres, centromeres) niches. Sex chromosomes, especially non-recombining regions of the Y chromosome, are subject to different evolutionary forces compared with autosomes. In non-recombining regions of the Y chromosome repetitive DNA sequences are accumulated, representing a dominant and early process forming the Y chromosome, probably before genes start to degenerate. Here we review the occurrence and role of repetitive DNA in Y chromosome evolution in various species with a focus on dioecious plants. We also discuss the potential link between recombination and transposition in shaping genomes.
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68
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Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species. Heredity (Edinb) 2009; 102:453-64. [PMID: 19259119 DOI: 10.1038/hdy.2009.9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Satellite DNA (satDNA) is a major component of genomes but relatively little is known about the fine-scale organization of unrelated satDNAs residing at the same chromosome location, and the sequence structure and dynamics of satDNA junctions. We studied the organization and sequence junctions of two nonhomologous satDNAs, pBuM and DBC-150, in three species from the neotropical Drosophila buzzatii cluster (repleta group). In situ hybridization to microchromosomes, interphase nuclei and extended DNA fibers showed frequent interspersion of the two satellites in D. gouveai, D. antonietae and, to a lesser extent, D. seriema. We isolated by PCR six pBuM x DBC-150 junctions: four are exclusive to D. gouveai and two are exclusive to D. antonietae. The six junction breakpoints occur at different positions within monomers, suggesting independent origin. Four junctions showed abrupt transitions between the two satellites, whereas two junctions showed a distinct 10 bp tandem duplication before the junction. Unlike pBuM, DBC-150 junction repeats are more variable than randomly cloned monomers and showed diagnostic features in common to a 3-monomer higher-order repeat seen in the sister species D. serido. The high levels of interspersion between pBuM and DBC-150 repeats suggest extensive rearrangements between the two satellites, maybe favored by specific features of the microchromosomes. Our interpretation is that the junctions evolved by multiples events of illegitimate recombination between nonhomologous satDNA repeats, with subsequent rounds of unequal crossing-over expanding the copy number of some of the junctions.
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69
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Abstract
Centromeres play a pivotal role in the life of a eukaryote cell, perform an essential and conserved function, but this has not led to a standard centromere structure. It remains currently unclear, how the centromeric function is achieved by widely differing structures. Since centromeres are often large and consist mainly of repetitive sequences they have only been analyzed in great detail in a handful of organisms. The genome of Dictyostelium discoideum, a valuable model organism, was described a few years ago but its centromere organization remained largely unclear. Using available sequence information we reconstructed the putative centromere organization in three of the six chromosomes of D. discoideum. They mainly consist of one type of transposons that is confined to centromeric regions. Centromeres are dynamic due to transposon integration, but an optimal centromere size seems to exist in D. discoideum. One centromere probably has expanded recently, whereas another underwent major rearrangements. In addition to insights into the centromere organization and dynamics of a protist eukaryote, this work also provides a starting point for the analysis of the evolution of centromere structures in social amoebas by comparative genomics.
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Affiliation(s)
- Gernot Glöckner
- Leibniz Institute for Age Research-Fritz Lipmann Institute, Beutenbergstrasse 11, D-07745 Jena, Germany.
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70
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Fablet M, Lerat E, Rebollo R, Horard B, Burlet N, Martinez S, Brasset E, Gilson E, Vaury C, Vieira C. Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila. FASEB J 2009; 23:1482-9. [PMID: 19141532 DOI: 10.1096/fj.08-123513] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Combining genome sequence analysis and functional analysis, we show that some full-length copies of tirant are present in heterochromatic regions in Drosophila simulans and that when tested in vitro, these copies have a functional promoter. However, when inserted in heterochromatic regions, tirant copies are inactive in vivo, and only transcription of euchromatic copies can be detected. Thus, our data indicate that the localization of the element is a hallmark of its activity in vivo and raise the question of genomic invasions by transposable elements and the importance of their genomic integration sites.
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Affiliation(s)
- Marie Fablet
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
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71
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The centromere-drive hypothesis: a simple basis for centromere complexity. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 48:33-52. [PMID: 19521811 DOI: 10.1007/978-3-642-00182-6_2] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Centromeres are far more complex and evolutionarily labile than expected based on their conserved, essential function. The rapid evolution of both centromeric DNA and proteins strongly argue that centromeres are locked in an evolutionary conflict to increase their odds of transmission during asymmetric (female) meiosis. Evolutionary success for "cheating" centromeres can result in highly deleterious consequences for the species, either in terms of skewed sex ratios or male sterility. Centromeric proteins evolve rapidly to suppress the deleterious effects of "centromere-drive." This chapter summarizes the mounting evidence in favor of the centromere-drive model, and its implications for centromere evolution in taxa with variations in meiosis.
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72
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Panchenko T, Black BE. The epigenetic basis for centromere identity. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 48:1-32. [PMID: 19521810 DOI: 10.1007/978-3-642-00182-6_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The centromere serves as the control locus for chromosome segregation at mitosis and meiosis. In most eukaryotes, including mammals, the location of the centromere is epigenetically defined. The contribution of both genetic and epigenetic determinants to centromere function is the subject of current investigation in diverse eukaryotes. Here we highlight key findings from several organisms that have shaped the current view of centromeres, with special attention to experiments that have elucidated the epigenetic nature of their specification. Recent insights into the histone H3 variant, CENP-A, which assembles into centromeric nucleosomes that serve as the epigenetic mark to perpetuate centromere identity, have added important mechanistic understanding of how centromere identity is initially established and subsequently maintained in every cell cycle.
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Affiliation(s)
- Tanya Panchenko
- Department of Biochemistry, University of Pennsylvania, Philadelphia, PA 19104-6059, USA
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73
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Nagaki K, Walling J, Hirsch C, Jiang J, Murata M. Structure and evolution of plant centromeres. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 48:153-79. [PMID: 19521815 DOI: 10.1007/978-3-642-00182-6_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Investigations of centromeric DNA and proteins and centromere structures in plants have lagged behind those conducted with yeasts and animals; however, many attractive results have been obtained from plants during this decade. In particular, intensive investigations have been conducted in Arabidopsis and Gramineae species. We will review our understanding of centromeric components, centromere structures, and the evolution of these attributes of centromeres among plants using data mainly from Arabidopsis and Gramineae species.
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Affiliation(s)
- Kiyotaka Nagaki
- Research Institute for Bioresources, Okayama University, Kurashiki 710-0046, Japan
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74
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Ugarković DI. Centromere-competent DNA: structure and evolution. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2009; 48:53-76. [PMID: 19521812 DOI: 10.1007/978-3-642-00182-6_3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although extant data favour centromere being an epigenetic structure, it is also clear that centromere formation is based on DNA, in particular, tandemly repeated satellite DNA and its transcripts. Presence of conserved structural motifs within satellite DNAs such as periodically distributed AT tracts, protein binding sites, or promoter elements indicate that despite sequence flexibility, there are structural determinants that are prerequisite for centromere function. In addition, existence of functional centromeric DNA transcripts indicates possible importance of structural elements at the level of RNA secondary or tertiary structure. Rapid centromere evolution is explained by homologous recombination followed by extrachromosomal rolling circle replication. This could lead to amplification of different satellite sequences within a genome. However, only those satellites that have inherent centromere-competence in the form of structural requirements necessary for centromere function are after amplification fixed in a population as a new centromere.
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Affiliation(s)
- Durd Ica Ugarković
- Department of Molecular Biology, Rud er Bosković Institute, Bijenicka 54, HR-10002, Zagreb, Croatia.
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75
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Birchler JA, Gao Z, Han F. A tale of two centromeres--diversity of structure but conservation of function in plants and animals. Funct Integr Genomics 2008; 9:7-13. [PMID: 19083033 DOI: 10.1007/s10142-008-0104-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 11/24/2008] [Accepted: 11/25/2008] [Indexed: 02/04/2023]
Abstract
The structural and functional aspects of two specific centromeres, one drawn from the animal kingdom (Drosophila) and the other from the plant kingdom (maize), are compared. Both cases illustrate an epigenetic component to centromere specification. The observations of neocentromeres in Drosophila and inactive centromeres in maize constitute one line of evidence for this hypothesis. Another common feature is the divisibility of centromere function with reduced stability as the size decreases. The systems differ in that Drosophila has no common sequence repeat at all centromeres, whereas maize has a 150-bp unit present in tandem arrays together with a centromere-specific transposon, centromere retrotransposon maize, present at all primary constrictions. Aspects of centromere structure known only from one or the other system might be common to both, namely, the presence of centromere RNAs in the kinetochore as found in maize and the organization of the centromeric histone 3 in tetrameric nucleosomes.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA.
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76
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Artificial chromosome formation in maize (Zea mays L.). Chromosoma 2008; 118:157-77. [DOI: 10.1007/s00412-008-0191-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 10/22/2008] [Accepted: 10/23/2008] [Indexed: 12/11/2022]
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77
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Functional analysis of the Arabidopsis centromere by T-DNA insertion-induced centromere breakage. Proc Natl Acad Sci U S A 2008; 105:7511-6. [PMID: 18495926 DOI: 10.1073/pnas.0802828105] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two minichromosomes (alpha and delta) in addition to two other aberrant chromosomes (beta and gamma) were found in a transgenic Arabidopsis plant produced by an in planta vacuum infiltration technique. The minichromosomes were successfully separated by successive crossing and selfing and added to wild-type Columbia (Col-0) as a supernumerary chromosome. FISH indicated that both of the two minichromosomes originated from the short arm of chromosome 2. The mini alpha chromosome contained the whole short-arm 2S and a truncated centromere (180-bp repeat cluster), whereas mini delta lacked the terminal region including telomere repeats. Pachytene FISH clearly revealed that mini delta comprised a ring chromosome carrying two copies of the region from the 180-bp repeat cluster to BAC-F3C11. Both of the 180-bp clusters (each approximately 500 kb in length) were thought to possess normal centromere functions because the centromere-specific histone H3 variant (HTR12) was detected on both clusters. Notwithstanding this dicentric and ring form, mini delta was stably transmitted to the next generations, perhaps because of its compact size (<4 Mb). Chromosome beta also comprised a dicentric-like structure, with one of the two 180-bp repeat sites derived from chromosome 1 and the other from chromosome 2. However, the latter was quite small and failed to bind HTR12. The data obtained in this study indicated that 500 kb of the 180-bp array of the chromosome 2 centromere, from the edge of the 180-bp array on the short-arm side, is sufficient to form a functional domain.
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78
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Abstract
The study of insect satellite DNAs (satDNAs) indicates the evolutionary conservation of certain features despite their sequence heterogeneity. Such features can include total length, monomer length, motifs, particular regions and/or secondary and tertiary structures. satDNAs may act as protein-binding sites, structural domains or sites for epigenetic modifications. The selective constraints in the evolution of satDNAs may be due to the satDNA sequence interaction with specific proteins important in heterochromatin formation and possible a role in controlling gene expression. The transcription of satDNA has been described in vertebrates, invertebrates and plants. In insects, differential satDNA expression has been observed in different cells, developmental stages, sex and caste of the individuals. These transcription differences may suggest their involvement in gene-regulation processes. In addition, the satDNA or its transcripts appear to be involved in heterochromatin formation and in chromatin-elimination processes. The importance of transposable elements to insect satDNA is shown by their presence as a constituent of satDNA in several species of insects (including possible active elements). In addition, they may be involved in the formation of centromeres and telomeres and in the homogenization and expansion of satDNA.
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Affiliation(s)
- T Palomeque
- Departamento de Biología Experimental, Area de Genética, Universidad de Jaén, Jaén, Spain.
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79
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Dalal Y, Wang H, Lindsay S, Henikoff S. Tetrameric structure of centromeric nucleosomes in interphase Drosophila cells. PLoS Biol 2008; 5:e218. [PMID: 17676993 PMCID: PMC1933458 DOI: 10.1371/journal.pbio.0050218] [Citation(s) in RCA: 197] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 06/12/2007] [Indexed: 01/24/2023] Open
Abstract
Centromeres, the specialized chromatin structures that are responsible for equal segregation of chromosomes at mitosis, are epigenetically maintained by a centromere-specific histone H3 variant (CenH3). However, the mechanistic basis for centromere maintenance is unknown. We investigated biochemical properties of CenH3 nucleosomes from Drosophila melanogaster cells. Cross-linking of CenH3 nucleosomes identifies heterotypic tetramers containing one copy of CenH3, H2A, H2B, and H4 each. Interphase CenH3 particles display a stable association of approximately 120 DNA base pairs. Purified centromeric nucleosomal arrays have typical “beads-on-a-string” appearance by electron microscopy but appear to resist condensation under physiological conditions. Atomic force microscopy reveals that native CenH3-containing nucleosomes are only half as high as canonical octameric nucleosomes are, confirming that the tetrameric structure detected by cross-linking comprises the entire interphase nucleosome particle. This demonstration of stable half-nucleosomes in vivo provides a possible basis for the instability of centromeric nucleosomes that are deposited in euchromatic regions, which might help maintain centromere identity. The octameric structure of eukaryotic nucleosomes is universally accepted as the basic unit of chromatin. This is certainly the case for the vast bulk of nucleosomes; however, there have been no reports of the in vivo structure of nucleosomes associated with centromeres. Though centromeres make up only a minute fraction of the genomic landscape, their role in segregating chromosomes during mitosis is essential for maintaining genomic integrity. We report the characterization of centromeric chromatin from Drosophila cells, using detailed biochemical, electron microscopic, and atomic force microscopic analyses. Surprisingly, we found that, in striking contrast to bulk chromatin, centromeric nucleosomes are stable heterotypic tetramers in vivo, with one copy of CenH3 (the centromere-specific H3 variant), H2A, H2B, and H4 each, wrapping one full turn of DNA at interphase (the cell growth phase of the cell cycle). This results in nucleosome particles that are only half as high as bulk nucleosomes. These unexpected findings can help account for the dynamic behavior of CenH3-containing nucleosomes, whereby they are deposited promiscuously but are turned over in noncentromeric regions. Our demonstration of the existence of stable half-nucleosomes at centromeres suggests a novel mechanism for maintaining centromere identity. The centromeric nucleosomes of Drosophila are histone tetramers rather than the canonical octomer of the rest of chromatin. This unprecedented arrangement of stable half-nucleosomes might help maintain centromere identity.
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Affiliation(s)
- Yamini Dalal
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Hongda Wang
- Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Steven Henikoff
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail:
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80
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Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 2008; 177:1277-90. [PMID: 18039867 DOI: 10.1534/genetics.107.075069] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The size of eukaryotic genomes can vary by several orders of magnitude, yet genome size does not correlate with the number of genes nor with the size or complexity of the organism. Although "whole"-genome sequences, such as those now available for 12 Drosophila species, provide information about euchromatic DNA content, they cannot give an accurate estimate of genome sizes that include heterochromatin or repetitive DNA content. Moreover, genome sequences typically represent only one strain or isolate of a single species that does not reflect intraspecies variation. To more accurately estimate whole-genome DNA content and compare these estimates to newly assembled genomes, we used flow cytometry to measure the 2C genome values, relative to Drosophila melanogaster. We estimated genome sizes for the 12 sequenced Drosophila species as well as 91 different strains of 38 species of Drosophilidae. Significant differences in intra- and interspecific 2C genome values exist within the Drosophilidae. Furthermore, by measuring polyploid 16C ovarian follicle cell underreplication we estimated the amount of satellite DNA in each of these species. We found a strong correlation between genome size and amount of satellite underreplication. Addition and loss of heterochromatin satellite repeat elements appear to have made major contributions to the large differences in genome size observed in the Drosophilidae.
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81
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Plohl M, Luchetti A, Mestrović N, Mantovani B. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 2007; 409:72-82. [PMID: 18182173 DOI: 10.1016/j.gene.2007.11.013] [Citation(s) in RCA: 230] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 11/08/2007] [Accepted: 11/20/2007] [Indexed: 12/21/2022]
Abstract
Satellite DNAs (tandemly repeated, non-coding DNA sequences) stretch over almost all native centromeres and surrounding pericentromeric heterochromatin. Once considered as inert by-products of genome dynamics in heterochromatic regions, recent studies showed that satellite DNA evolution is interplay of stochastic events and selective pressure. This points to a functional significance of satellite sequences, which in (peri)centromeres may play some fundamental functional roles. First, specific interactions with DNA-binding proteins are proposed to complement sequence-independent epigenetic processes. The second role is achieved through RNAi mechanism, in which transcripts of satellite sequences initialize heterochromatin formation. In addition, satellite DNAs in (peri)centromeric regions affect chromosomal dynamics and genome plasticity. Paradoxically, while centromeric function is conserved through eukaryotes, the profile of satellite DNAs in this region is almost always species-specific. We argue that tandem repeats may be advantageous forms of DNA sequences in (peri)centromeres due to concerted evolution, which maintains high intra-array and intrapopulation sequence homogeneity of satellite arrays, while allowing rapid changes in nucleotide sequence and/or composition of satellite repeats. This feature may be crucial for long-term stability of DNA-protein interactions in centromeric regions.
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Affiliation(s)
- Miroslav Plohl
- Department of Molecular Genetics, Ruder Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia.
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82
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Deryusheva S, Krasikova A, Kulikova T, Gaginskaya E. Tandem 41-bp repeats in chicken and Japanese quail genomes: FISH mapping and transcription analysis on lampbrush chromosomes. Chromosoma 2007; 116:519-30. [PMID: 17619894 DOI: 10.1007/s00412-007-0117-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 06/09/2007] [Accepted: 06/10/2007] [Indexed: 10/23/2022]
Abstract
The chromosomal distribution of 41-bp repeats, known as CNM and PO41 repeats in the chicken genome and BglII repeats in the Japanese quail, was analyzed precisely using giant lampbrush chromosomes (LBC) from chicken, Japanese quail, and turkey growing oocytes. The PO41 repeat is conserved in all galliform species, whereas the other repeats are species specific. In chicken and quail, the centromere and subtelomere regions share homologous satellite sequences. RNA polymerase II transcribes the 41-bp repeats in both centromere and subtelomere regions. Ongoing transcription of these repeats was demonstrated by incorporation of BrUTP injected into oocytes at the lampbrush stage. RNA complementary to both strands of CNM and PO41 repeats is present on chicken LBC loops, whereas strand-specific G-rich transcripts are characteristic of BglII repeats in the Japanese quail. The RNA from 41-bp repeats does not undergo cotranscriptional U snRNP-dependent splicing. At the same time, the ribonucleoprotein matrix of transcription units with C-rich RNA of CNM and PO41 repeats was enriched with hnRNP protein K. Potential promoters for satellite transcription are discussed.
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Affiliation(s)
- Svetlana Deryusheva
- Biological Research Institute, Saint-Petersburg State University, Oranienbaumskoie sch. 2, Stary Peterhof, Saint-Petersburg 198504, Russia
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83
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Mishra PK, Baum M, Carbon J. Centromere size and position in Candida albicans are evolutionarily conserved independent of DNA sequence heterogeneity. Mol Genet Genomics 2007; 278:455-65. [PMID: 17588175 DOI: 10.1007/s00438-007-0263-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 05/30/2007] [Indexed: 01/22/2023]
Abstract
The centromere regions (CEN) of all eight chromosomes in Candida albicans have been characterized in terms of nucleotide sequence and size. The boundaries of each of the eight CEN DNA regions were mapped by chromatin immunoprecipitation-PCR using polyclonal rabbit antibodies generated against C. albicans centromere-specific protein CaCse4p (CENP-A homolog). A single 3-4.5 kb unique DNA sequence on each chromosome was found to be bound to CaCse4p. Sequence analysis revealed that the eight CEN regions in C. albicans lack any conserved DNA sequence motifs common to the group; all are quite different in overall DNA sequence. In contrast to centromeres in many organisms, the C. albicans centromeres are generally free of repeated DNA elements and transposons. However, a few small inverted repeats and long terminal repeats do occur in the centromeric and pericentric regions on a few chromosomes. We also characterized the CEN DNAs in four groups of phylogenetically divergent C. albicans strains, estimated to be separated from each other by 1-3 million years. The same eight different and unique 3-4.5 kb DNA sequences are utilized as centromeres in all of these strains. The chromosomal locations and the sizes of CEN DNAs have remained conserved, in agreement with the idea that CEN function in C. albicans is templated by heritable epigenetic mechanisms.
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Affiliation(s)
- Prashant K Mishra
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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84
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Villasante A, Abad JP, Méndez-Lago M. Centromeres were derived from telomeres during the evolution of the eukaryotic chromosome. Proc Natl Acad Sci U S A 2007; 104:10542-7. [PMID: 17557836 PMCID: PMC1965549 DOI: 10.1073/pnas.0703808104] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Indexed: 12/24/2022] Open
Abstract
The centromere is the DNA region of the eukaryotic chromosome that determines kinetochore formation and sister chromatid cohesion. Centromeres interact with spindle microtubules to ensure the segregation of chromatids during mitosis and of homologous chromosomes in meiosis. The origin of centromeres, therefore, is inseparable from the evolution of cytoskeletal components that distribute chromosomes to offspring cells. Although the origin of the nucleus has been debated, no explanation for the evolutionary appearance of centromeres is available. We propose an evolutionary scenario: The centromeres originated from telomeres. The breakage of the ancestral circular genophore activated the transposition of retroelements at DNA ends that allowed the formation of telomeres by a recombination-dependent replication mechanism. Afterward, the modification of the tubulin-based cytoskeleton that allowed specific subtelomeric repeats to be recognized as new cargo gave rise to the first centromere. This switch from actin-based genophore partition to a tubulin-based mechanism generated a transition period during which both types of cytoskeleton contributed to fidelity of chromosome segregation. During the transition, pseudodicentric chromosomes increased the tendency toward chromosomal breakage and instability. This instability generated multiple telocentric chromosomes that eventually evolved into metacentric or holocentric chromosomes.
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Affiliation(s)
- Alfredo Villasante
- Centro de Biología Molecular Severo Ochoa, Universidad Autonóma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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85
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Ahmed FE. Colorectal cancer epigenetics: the role of environmental factors and the search for molecular biomarkers. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2007; 25:101-54. [PMID: 17558783 DOI: 10.1080/10590500701399184] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This review presents an evenhanded evaluation of the role of epigenetics in the development of colorectal cancer, and investigates the extent of environmental influences on modulating this disease. Advances in our understanding of chromatin structure, histone modification, transcriptional activity and DNA methylation have lead to an integrated approach to the role of epigenetics in carcinogenesis. Epigenetic mechanisms appear to permit response of individuals to environment through change in gene expression and are involved in inactivating one of the two X chromosomes in women. Epigenetic changes play an important role in development and can also arise stochastically as individuals age. Because epigenetic alterations are potentially reversible, thereby allowing malignant cells to revert to the normal state, there is potential to develop effective strategies to prevent or even reverse this curable cancer. Moreover, because the methylation status of a specific sequence or the pattern of methylation across the genome can now be measured accurately, molecular biomarkers of screening, diagnosis, prognosis, prediction of treatment and those related to risk assessment can be developed using sophisticated molecular genetic technologies. Although in many cases a high sensitivity and specificity of the detection assays has been achieved, there still remains ample room for improvement in areas of sample preparation, assay design and marker selection.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine, East Carolina University, Greenville, North Carolina 27858, USA.
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86
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Abstract
Noncoding RNA has long been proposed to control gene expression via sequence-specific interactions with regulatory regions. Here, we review the role of noncoding RNA in heterochromatic silencing and in the silencing of transposable elements (TEs), unpaired DNA in meiosis, and developmentally excised DNA. The role of cotranscriptional processing by RNA interference and by other mechanisms is discussed, as well as parallels with RNA silencing in imprinting, paramutation, polycomb silencing, and X inactivation. Interactions with regulatory sequences may well occur, but at the RNA rather than at the DNA level.
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Affiliation(s)
- Mikel Zaratiegui
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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87
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Bergman CM, Quesneville H, Anxolabéhère D, Ashburner M. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome. Genome Biol 2007; 7:R112. [PMID: 17134480 PMCID: PMC1794594 DOI: 10.1186/gb-2006-7-11-r112] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 11/13/2006] [Accepted: 11/29/2006] [Indexed: 11/10/2022] Open
Abstract
An analysis of high-resolution transposable element annotations in Drosophila melanogaster suggests the existence of a global surveillance system against the majority of transposable elements families in the fly. Background The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the contribution of TEs to genomes sequences. Results Using a high-resolution annotation of TEs in Release 4 genome sequence, we revise estimates of TE abundance in Drosophila melanogaster. We show that TEs are non-randomly distributed within regions of high and low TE abundance, and that pericentromeric regions with high TE abundance are mosaics of distinct regions of extreme and normal TE density. Comparative analysis revealed that this punctate pattern evolves jointly by transposition and duplication, but not by inversion of TE-rich regions from unsequenced heterochromatin. Analysis of genome-wide patterns of TE nesting revealed a 'nesting network' that includes virtually all of the known TE families in the genome. Numerous directed cycles exist among TE families in the nesting network, implying concurrent or overlapping periods of transpositional activity. Conclusion Rapid restructuring of the genomic landscape by transposition and duplication has recently added hundreds of kilobases of TE sequence to pericentromeric regions in D. melanogaster. These events create ragged transitions between unique and repetitive sequences in the zone between euchromatic and beta-heterochromatic regions. Complex relationships of TE nesting in beta-heterochromatic regions raise the possibility of a co-suppression network that may act as a global surveillance system against the majority of TE families in D. melanogaster.
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Affiliation(s)
- Casey M Bergman
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Hadi Quesneville
- Laboratoire de Bioinformatique et Génomique, Institut Jacques Monod, place Jussieu, 75251 Paris cedex 05, France
| | - Dominique Anxolabéhère
- Laboratoire Dynamique du Génome et Évolution, Institut Jacques Monod, place Jussieu, 75251 Paris cedex 05, France
| | - Michael Ashburner
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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88
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Mravinac B, Plohl M. Satellite DNA junctions identify the potential origin of new repetitive elements in the beetle Tribolium madens. Gene 2007; 394:45-52. [PMID: 17379457 DOI: 10.1016/j.gene.2007.01.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 01/24/2007] [Accepted: 01/26/2007] [Indexed: 11/25/2022]
Abstract
Two related satellite DNA families (satellite I and satellite II) with complex higher-order repeat (HOR) monomers represent major DNA components equilocated in the pericentromeric heterochromatin of all Tribolium madens chromosomes. Fragments obtained upon genomic DNA restriction revealed two subfamilies of satellite II monomers, and also identified regions of transition between satellite I and satellite II sequences. The two subfamilies differ not only in diagnostic nucleotides, but also in flipped orientation of constituent subunits. Hybrid genomic fragments comprise directly linked satellite I and satellite II monomers that cannot be distinguished from randomly cloned monomers of corresponding families. An exception is the most proximal satellite I monomer in the hybrid fragment named TMADhinf, which shows sequence divergence typical for repeats evolving at array ends, in zones of low homogenization efficiency. This pattern points to the extensive rearrangement processes generating abrupt transitions between satellite arrays combined with array maintenance by unequal crossover. Switching points between adjacent satellites as well as the edges of flipped subunits are localized within a short sequence segment, indicating a preferential site of recombination within satellite subunits. Multiple copies of TMADhinf junction fragment support the hypothesis that sites of evolutionary origin of novel satellite repeat (sub)families can be localized at array ends, in regions of enhanced sequence divergence.
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Affiliation(s)
- Brankica Mravinac
- Department of Molecular Biology, Ruder Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia
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89
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Paris C, Geinguenaud F, Gouyette C, Liquier J, Lacoste J. Mechanism of copper mediated triple helix formation at neutral pH in Drosophila satellite repeats. Biophys J 2007; 92:2498-506. [PMID: 17208971 PMCID: PMC1864847 DOI: 10.1529/biophysj.106.099788] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The highly repeated Drosophila melanogaster AAGAGAG satellite sequence is present at each chromosome centromere of the fly. We demonstrate here how, under nearly physiological pH conditions, these sequences can form a pyrimidine triple helix containing T.A-T and CCu.G-C base triplets, stabilized by Cu2+ metal ions in amounts mirroring in vivo concentrations. Ultraviolet experiments were used to monitor the triple helix formation at pH 7.2 in presence of Cu2+ ions. Triplex melting is observed at 23 degrees C. Furthermore, a characteristic signature of triple helix formation was obtained by Fourier transform infrared spectroscopy. The stabilization of the C.G-C base triplets at pH 7.2 is shown to occur via interactions of Cu2+ ions on the third strand cytosine N3 atom and on the guanine N7 atom of the polypurine target strand forming CCu.G-C triplets. Under the same neutral pH conditions in absence of Cu2+ ions, the triple helix fails to form. Possible biological implications are discussed.
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Affiliation(s)
- C Paris
- Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire (BioMoCeTi), Unité Mixte de Recherche, Centre National de la Recherche Scientifique 7033, Université Paris 13, 93017 Bobigny cedex, France
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90
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Sharakhova MV, Hammond MP, Lobo NF, Krzywinski J, Unger MF, Hillenmeyer ME, Bruggner RV, Birney E, Collins FH. Update of the Anopheles gambiae PEST genome assembly. Genome Biol 2007; 8:R5. [PMID: 17210077 PMCID: PMC1839121 DOI: 10.1186/gb-2007-8-1-r5] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 10/24/2006] [Accepted: 01/08/2007] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The genome of Anopheles gambiae, the major vector of malaria, was sequenced and assembled in 2002. This initial genome assembly and analysis made available to the scientific community was complicated by the presence of assembly issues, such as scaffolds with no chromosomal location, no sequence data for the Y chromosome, haplotype polymorphisms resulting in two different genome assemblies in limited regions and contaminating bacterial DNA. RESULTS Polytene chromosome in situ hybridization with cDNA clones was used to place 15 unmapped scaffolds (sizes totaling 5.34 Mbp) in the pericentromeric regions of the chromosomes and oriented a further 9 scaffolds. Additional analysis by in situ hybridization of bacterial artificial chromosome (BAC) clones placed 1.32 Mbp (5 scaffolds) in the physical gaps between scaffolds on euchromatic parts of the chromosomes. The Y chromosome sequence information (0.18 Mbp) remains highly incomplete and fragmented among 55 short scaffolds. Analysis of BAC end sequences showed that 22 inter-scaffold gaps were spanned by BAC clones. Unmapped scaffolds were also aligned to the chromosome assemblies in silico, identifying regions totaling 8.18 Mbp (144 scaffolds) that are probably represented in the genome project by two alternative assemblies. An additional 3.53 Mbp of alternative assembly was identified within mapped scaffolds. Scaffolds comprising 1.97 Mbp (679 small scaffolds) were identified as probably derived from contaminating bacterial DNA. In total, about 33% of previously unmapped sequences were placed on the chromosomes. CONCLUSION This study has used new approaches to improve the physical map and assembly of the A. gambiae genome.
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Affiliation(s)
- Maria V Sharakhova
- Center for Global Health and Infectious Diseases, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN 46556-0369, USA.
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91
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Demakova OV, Pokholkova GV, Kolesnikova TD, Demakov SA, Andreyeva EN, Belyaeva ES, Zhimulev IF. The SU(VAR)3-9/HP1 complex differentially regulates the compaction state and degree of underreplication of X chromosome pericentric heterochromatin in Drosophila melanogaster. Genetics 2006; 175:609-20. [PMID: 17151257 PMCID: PMC1800617 DOI: 10.1534/genetics.106.062133] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In polytene chromosomes of Drosophila melanogaster, regions of pericentric heterochromatin coalesce to form a compact chromocenter and are highly underreplicated. Focusing on study of X chromosome heterochromatin, we demonstrate that loss of either SU(VAR)3-9 histone methyltransferase activity or HP1 protein differentially affects the compaction of different pericentric regions. Using a set of inversions breaking X chromosome heterochromatin in the background of the Su(var)3-9 mutations, we show that distal heterochromatin (blocks h26-h29) is the only one within the chromocenter to form a big "puff"-like structure. The "puffed" heterochromatin has not only unique morphology but also very special protein composition as well: (i) it does not bind proteins specific for active chromatin and should therefore be referred to as a pseudopuff and (ii) it strongly associates with heterochromatin-specific proteins SU(VAR)3-7 and SUUR, despite the fact that HP1 and HP2 are depleted particularly from this polytene structure. The pseudopuff completes replication earlier than when it is compacted as heterochromatin, and underreplication of some DNA sequences within the pseudopuff is strongly suppressed. So, we show that pericentric heterochromatin is heterogeneous in its requirement for SU(VAR)3-9 with respect to the establishment of the condensed state, time of replication, and DNA polytenization.
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Affiliation(s)
- Olga V Demakova
- Laboratory of Molecular Cytogenetics, Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
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92
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Malik HS, Bayes JJ. Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochem Soc Trans 2006; 34:569-73. [PMID: 16856863 DOI: 10.1042/bst0340569] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Centromeric DNA evolves rapidly, ranging in size and complexity over several orders of magnitude. Traditional attempts at studying centromeres have left unexplained the causes underlying this complexity and rapid evolution. Instead of directly studying centromeric DNA sequence, our approach has been to study the proteins that epigenetically determine centromere identity. We have discovered that centromeric histones (CenH3s) have evolved under positive selection in multiple lineages, suggesting an involvement in recurrent genetic conflict. Our hypothesis is that 'centromere-drive' is the source of this conflict. Under this model, centromeres compete via microtubule attachments for preferential transmission in female meioses occurring in animals and plants. Since only one of four meiotic products will become the egg, this competition confers a selfish advantage to chromosomes that can make more microtubule attachments, resulting in runaway expansions of centromeric satellites. While beneficial to the 'driving' chromosome, these expansions can have deleterious effects on the fitness of an organism and of the species. CenH3s as well as other heterochromatin proteins have evolved under positive selection to suppress the deleterious consequences of 'centromere-drive' by restoring meiotic parity.
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Affiliation(s)
- H S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, A1-162, Seattle, WA 98109, USA.
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93
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Yan H, Ito H, Nobuta K, Ouyang S, Jin W, Tian S, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC, Jiang J. Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. THE PLANT CELL 2006; 18:2123-33. [PMID: 16877494 PMCID: PMC1560911 DOI: 10.1105/tpc.106.043794] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most multicellular eukaryotes, centromeres are composed of long tracts of satellite repeats that are recalcitrant to sequencing and fine-scale genetic mapping. Here, we report the genomic and genetic characterization of the complete centromere of rice (Oryza sativa) chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains approximately 441 kb of the centromeric satellite repeat CentO. Cen3 includes an approximately 1,881-kb domain associated with the centromeric histone CENH3. This CENH3-associated chromatin domain is embedded within a 3,113-kb region that lacks genetic recombination. Extensive transcription was detected within the CENH3 binding domain based on comprehensive annotation of protein-coding genes coupled with empirical measurements of mRNA levels using RT-PCR and massively parallel signature sequencing. Genes <10 kb from the CentO satellite array were expressed in several rice tissues and displayed histone modification patterns consistent with euchromatin, suggesting that rice centromeric chromatin accommodates normal gene expression. These results support the hypothesis that centromeres can evolve from gene-containing genomic regions.
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Affiliation(s)
- Huihuang Yan
- Department of Horticulture, University of Wisconsin, Madison, 53706, USA
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94
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95
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Carroll CW, Straight AF. Centromere formation: from epigenetics to self-assembly. Trends Cell Biol 2006; 16:70-8. [PMID: 16412639 DOI: 10.1016/j.tcb.2005.12.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Revised: 12/05/2005] [Accepted: 12/21/2005] [Indexed: 12/31/2022]
Abstract
This review is part of the Chromosome segregation and Aneuploidy series that focuses on the importance of chromosome segregation mechanisms in maintaining genome stability. Centromeres are specialized chromosomal domains that serve as the foundation for the mitotic kinetochore, the interaction site between the chromosome and the mitotic spindle. The chromatin of centromeres is distinguished from other chromosomal loci by the unique incorporation of the centromeric histone H3 variant, centromere protein A. Here, we review the genetic and epigenetic factors that control the formation and maintenance of centromeric chromatin and propose a chromatin self-assembly model for organizing the higher-order structure of the centromere.
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Affiliation(s)
- Christopher W Carroll
- Department of Biochemistry, Stanford University, Beckman Building, Rm. 409, 279 Campus Drive, Stanford, CA 94305-5307, USA
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96
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Boeva V, Regnier M, Papatsenko D, Makeev V. Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression. Bioinformatics 2006; 22:676-84. [PMID: 16403795 DOI: 10.1093/bioinformatics/btk032] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
MOTIVATION Genomic sequences are highly redundant and contain many types of repetitive DNA. Fuzzy tandem repeats (FTRs) are of particular interest. They are found in regulatory regions of eukaryotic genes and are reported to interact with transcription factors. However, accurate assessment of FTR occurrences in different genome segments requires specific algorithm for efficient FTR identification and classification. RESULTS We have obtained formulas for P-values of FTR occurrence and developed an FTR identification algorithm implemented in TandemSWAN software. Using TandemSWAN we compared the structure and the occurrence of FTRs with short period length (up to 24 bp) in coding and non-coding regions including UTRs, heterochromatic, intergenic and enhancer sequences of Drosophila melanogaster and Drosophila pseudoobscura. Tandems with period three and its multiples were found in coding segments, whereas FTRs with periods multiple of six are overrepresented in all non-coding segment. Periods equal to 5-7 and 11-14 were characteristic of the enhancer regions and other non-coding regions close to genes. AVAILABILITY TandemSWAN web page, stand-alone version and documentation can be found at http://bioinform.genetika.ru/projects/swan/www/ SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Valentina Boeva
- Department of Bioengineering and Bioinformatics, Moscow State University Moscow, Russia.
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97
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Ma J, Bennetzen JL. Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice. Proc Natl Acad Sci U S A 2006; 103:383-8. [PMID: 16381819 PMCID: PMC1326179 DOI: 10.1073/pnas.0509810102] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Centromeres have many unusual biological properties, including kinetochore attachment and severe repression of local meiotic recombination. These properties are partly an outcome, partly a cause, of unusual DNA structure in the centromeric region. Although several plant and animal genomes have been sequenced, most centromere sequences have not been completed or analyzed in depth. To shed light on the unique organization, variability, and evolution of centromeric DNA, detailed analysis of a 1.97-Mb sequence that includes centromere 8 (CEN8) of japonica rice was undertaken. Thirty-three long-terminal repeat (LTR)-retrotransposon families (including 11 previously unknown) were identified in the CEN8 region, totaling 245 elements and fragments that account for 67% of the region. The ratio of solo LTRs to intact elements in the CEN8 region is approximately 0.9:1, compared with approximately 2.2:1 in noncentromeric regions of rice. However, the ratio of solo LTRs to intact elements in the core of the CEN8 region ( approximately 2.5:1) is higher than in any other region investigated in rice, suggesting a hotspot for unequal recombination. Comparison of the CEN8 region of japonica and its orthologous segments from indica rice indicated that approximately 15% of the intact retrotransposons and solo LTRs were inserted into CEN8 after the divergence of japonica and indica from a common ancestor, compared with approximately 50% for previously studied euchromatic regions. Frequent DNA rearrangements were observed in the CEN8 region, including a 212-kb subregion that was found to be composed of three rearranged tandem repeats. Phylogenetic analysis also revealed recent segmental duplication and extensive rearrangement and reshuffling of the CentO satellite repeats.
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Affiliation(s)
- Jianxin Ma
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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98
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Ma J, Jackson SA. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res 2005; 16:251-9. [PMID: 16354755 PMCID: PMC1361721 DOI: 10.1101/gr.4583106] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The abundance of repetitive DNA varies greatly across centromeres within an individual or between different organisms. To shed light on the molecular mechanisms of centromere repeat proliferation, we performed structural analysis of LTR-retrotransposons, mostly centromere retrotransposons of rice (CRRs), and phylogenetic analysis of CentO satellite repeats harbored in the core region of the rice chromosome 4 centromere (CEN4). The data obtained demonstrate that the CRRs in the centromeric region we investigated have been enriched more significantly by recent rounds of segmental duplication than by original integration of active elements, suggesting that segmental duplication is an important process for CRR accumulation in the centromeric region. Our results also indicate that segmental duplication of large arrays of satellite repeats is primarily responsible for the amplification of satellite repeats, contributing to rapid reshuffling of CentO satellites. Intercentromere satellite homogenization was revealed by genome-wide comparison of CentO satellite monomers. However, a 10-bp duplication present in nearly half of the CEN4 monomers was found to be completely absent in rice centromere 8 (CEN8), suggesting that CEN4 and CEN8 may represent two different stages in the evolution of rice centromeres. These observations, obtained from the only complex eukaryotic centromeres to have been completely sequenced thus far, depict the evolutionary dynamics of rice centromeres with respect to the nature, timing, and process of centromeric repeat amplification.
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Affiliation(s)
- Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
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99
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Mestrović N, Randig O, Abad P, Plohl M, Castagnone-Sereno P. Conserved and variable domains in satellite DNAs of mitotic parthenogenetic root-knot nematode species. Gene 2005; 362:44-50. [PMID: 16229973 DOI: 10.1016/j.gene.2005.07.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Revised: 06/28/2005] [Accepted: 07/19/2005] [Indexed: 10/25/2022]
Abstract
Two satellite DNAs have been characterized in the mitotic parthenogenetic root-knot nematodes Meloidogyne javanica and M. paranaensis, agriculturally important phytoparasitic species. The satellite repeat variants cloned from M. javanica could not be resolved from those described earlier in M. arenaria [Castagnone-Sereno, P., Leroy, F., Abad, P., 2000. Cloning and characterization of an extremely conserved satellite DNA family from the root-knot nematode Meloidogyne arenaria. Genome 43, 346-353] and are therefore classified as a single satellite named MARJA. However, this satellite shows 34.3% sequence divergence in comparison with the MPA1 satellite characterized in M. paranaensis, and monomer variants of both satellites are clearly distinguished by homogenized nucleotide substitutions. Nucleotide variability analysis revealed in one segment of the satellite monomer domains of high and low variability, conserved both within and between monomer variants of the two satellites. Intersatellite conservation of these domains indicates evolution of satellite sequence under different constraints, probably due to some functional interactions. In addition, high intrasatellite homogeneity, presence of ancestral mutations in groups of MARJA monomers in both M. javanica and M. arenaria and highly homogenized divergent positions in comparison with the MPA1 indicate similar sequence dynamics in mitotic parthenogenetic taxa to that observed in amphimictic species.
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100
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Cervantes MD, Xi X, Vermaak D, Yao MC, Malik HS. The CNA1 histone of the ciliate Tetrahymena thermophila is essential for chromosome segregation in the germline micronucleus. Mol Biol Cell 2005; 17:485-97. [PMID: 16251352 PMCID: PMC1345684 DOI: 10.1091/mbc.e05-07-0698] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Ciliated protozoans present several features of chromosome segregation that are unique among eukaryotes, including their maintenance of two nuclei: a germline micronucleus, which undergoes conventional mitosis and meiosis, and a somatic macronucleus that divides by an amitotic process. To study ciliate chromosome segregation, we have identified the centromeric histone gene in the Tetrahymena thermophila genome (CNA1). CNA1p specifically localizes to peripheral centromeres in the micronucleus but is absent in the macronucleus during vegetative growth. During meiotic prophase of the micronucleus, when chromosomes are stretched to twice the length of the cell, CNA1p is found localized in punctate spots throughout the length of the chromosomes. As conjugation proceeds, CNA1p appears initially diffuse, but quickly reverts to discrete dots in those nuclei destined to become micronuclei, whereas it remains diffuse and is gradually lost in developing macronuclei. In progeny of germline CNA1 knockouts, we see no defects in macronuclear division or viability of the progeny cells immediately following the knockout. However, within a few divisions, progeny show abnormal mitotic segregation of their micronucleus, with most cells eventually losing their micronucleus entirely. This study reveals a strong dependence of the germline micronucleus on centromeric histones for proper chromosome segregation.
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Affiliation(s)
- Marcella D Cervantes
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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