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Mode and Tempo of Microsatellite Evolution across 300 Million Years of Insect Evolution. Genes (Basel) 2020; 11:genes11080945. [PMID: 32824315 PMCID: PMC7464534 DOI: 10.3390/genes11080945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 01/02/2023] Open
Abstract
Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. Despite their impacts on transcription, genome structure, and disease, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge, we performed comparative analyses of 304 available insect genomes. We investigated the impact of sequence assembly methods and assembly quality on the inference of microsatellite content, and we explored the influence of chromosome type and number on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet. Diploid chromosome number had no impact on the rate of microsatellite evolution or the amount of microsatellite content in genomes. We found that centromere type (holocentric or monocentric) is not associated with a difference in the amount of microsatellite content; however, in those species with monocentric chromosomes, microsatellite content tends to evolve faster than in species with holocentric chromosomes.
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Kuzu G, Kaye EG, Chery J, Siggers T, Yang L, Dobson JR, Boor S, Bliss J, Liu W, Jogl G, Rohs R, Singh ND, Bulyk ML, Tolstorukov MY, Larschan E. Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation. PLoS Genet 2016; 12:e1006120. [PMID: 27414415 PMCID: PMC4945028 DOI: 10.1371/journal.pgen.1006120] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/23/2016] [Indexed: 12/15/2022] Open
Abstract
Dosage compensation is an essential process that equalizes transcript levels of X-linked genes between sexes by forming a domain of coordinated gene expression. Throughout the evolution of Diptera, many different X-chromosomes acquired the ability to be dosage compensated. Once each newly evolved X-chromosome is targeted for dosage compensation in XY males, its active genes are upregulated two-fold to equalize gene expression with XX females. In Drosophila melanogaster, the CLAMP zinc finger protein links the dosage compensation complex to the X-chromosome. However, the mechanism for X-chromosome identification has remained unknown. Here, we combine biochemical, genomic and evolutionary approaches to reveal that expansion of GA-dinucleotide repeats likely accumulated on the X-chromosome over evolutionary time to increase the density of CLAMP binding sites, thereby driving the evolution of dosage compensation. Overall, we present new insight into how subtle changes in genomic architecture, such as expansions of a simple sequence repeat, promote the evolution of coordinated gene expression.
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Affiliation(s)
- Guray Kuzu
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Emily G. Kaye
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Jessica Chery
- Department of Cell Biology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, United States of America
| | - Trevor Siggers
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Lin Yang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Jason R. Dobson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Sonia Boor
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Jacob Bliss
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Wei Liu
- Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Gerwald Jogl
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Remo Rohs
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Nadia D. Singh
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Y. Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MYT); (EL)
| | - Erica Larschan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (MYT); (EL)
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Cuadrado Á, Jouve N. Chromosomal detection of simple sequence repeats (SSRs) using nondenaturing FISH (ND-FISH). Chromosoma 2016; 119:495-503. [PMID: 20393739 DOI: 10.1007/s00412-010-0273-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Simple Sequence Repeats (SSRs) are known to be scattered and present in high number in eukaryotic genomes. We demonstrate that dye-labeled oligodeoxyribonucleotides with repeated mono-, di-, tri, or tetranucleotide motifs (15-20 nucleotides in length) have an unexpected ability to recognize SSR target sequences in non-denatured chromosomes. The results show that all these probes are able to invade chromosomes, independent of the size of the repeat motif, their nucleotide sequence, or their ability to form alternative B-DNA structures such as triplex DNA. This novel and remarkable property of binding SSR oligonucleotides to duplex DNA targets permitted the development of a non-denaturing fluorescence in situ hybridization method that quickly and efficiently detects SSR-enriched chromosome regions in mitotic, meiotic, and polytene chromosome spreads of different model organisms. These results have implications for genome analysis and for investigating the roles of SSRs in chromosome structure and function.
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Affiliation(s)
- Ángeles Cuadrado
- Department of Cell Biology and Genetics, University of Alcalá de Henares, 28871, Alcalá de Henares, Madrid, Spain.
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Philip P, Pettersson F, Stenberg P. Sequence signatures involved in targeting the Male-Specific Lethal complex to X-chromosomal genes in Drosophila melanogaster. BMC Genomics 2012; 13:97. [PMID: 22424303 PMCID: PMC3355045 DOI: 10.1186/1471-2164-13-97] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 03/19/2012] [Indexed: 11/18/2022] Open
Abstract
Background In Drosophila melanogaster, the dosage-compensation system that equalizes X-linked gene expression between males and females, thereby assuring that an appropriate balance is maintained between the expression of genes on the X chromosome(s) and the autosomes, is at least partially mediated by the Male-Specific Lethal (MSL) complex. This complex binds to genes with a preference for exons on the male X chromosome with a 3' bias, and it targets most expressed genes on the X chromosome. However, a number of genes are expressed but not targeted by the complex. High affinity sites seem to be responsible for initial recruitment of the complex to the X chromosome, but the targeting to and within individual genes is poorly understood. Results We have extensively examined X chromosome sequence variation within five types of gene features (promoters, 5' UTRs, coding sequences, introns, 3' UTRs) and intergenic sequences, and assessed its potential involvement in dosage compensation. Presented results show that: the X chromosome has a distinct sequence composition within its gene features; some of the detected variation correlates with genes targeted by the MSL-complex; the insulator protein BEAF-32 preferentially binds upstream of MSL-bound genes; BEAF-32 and MOF co-localizes in promoters; and that bound genes have a distinct sequence composition that shows a 3' bias within coding sequence. Conclusions Although, many strongly bound genes are close to a high affinity site neither our promoter motif nor our coding sequence signatures show any correlation to HAS. Based on the results presented here, we believe that there are sequences in the promoters and coding sequences of targeted genes that have the potential to direct the secondary spreading of the MSL-complex to nearby genes.
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Affiliation(s)
- Philge Philip
- Deptartment of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
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5
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Comparative genomic analysis of dinucleotide repeats in Tritryps. Gene 2011; 487:29-37. [PMID: 21824509 DOI: 10.1016/j.gene.2011.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 07/12/2011] [Accepted: 07/14/2011] [Indexed: 12/29/2022]
Abstract
The protozoans Trypanosoma cruzi, Trypanosoma brucei and Leishmania major (Tritryps), are evolutionarily ancient eukaryotes which cause worldwide human parasitosis. They present unique biological features. Indeed, canonical DNA/RNA cis-acting elements remain mostly elusive. Repetitive sequences, originally considered as selfish DNA, have been lately recognized as potentially important functional sequence elements in cell biology. In particular, the dinucleotide patterns have been related to genome compartmentalization, gene evolution and gene expression regulation. Thus, we perform a comparative analysis of the occurrence, length and location of dinucleotide repeats (DRs) in the Tritryp genomes and their putative associations with known biological processes. We observe that most types of DRs are more abundant than would be expected by chance. Complementary DRs usually display asymmetrical strand distribution, favoring TT and GT repeats in the coding strands. In addition, we find that GT repeats are among the longest DRs in the three genomes. We also show that specific DRs are non-uniformly distributed along the polycistronic unit, decreasing toward its boundaries. Distinctive non-uniform density patterns were also found in the intergenic regions, with predominance at the vicinity of the ORFs. These findings further support that DRs may control genome structure and gene expression.
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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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Gallach M, Arnau V, Aldecoa R, Marín I. A sequence motif enriched in regions bound by the Drosophila dosage compensation complex. BMC Genomics 2010; 11:169. [PMID: 20226017 PMCID: PMC2848247 DOI: 10.1186/1471-2164-11-169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 03/12/2010] [Indexed: 11/29/2022] Open
Abstract
Background In Drosophila melanogaster, dosage compensation is mediated by the action of the dosage compensation complex (DCC). How the DCC recognizes the fly X chromosome is still poorly understood. Characteristic sequence signatures at all DCC binding sites have not hitherto been found. Results In this study, we compare the known binding sites of the DCC with oligonucleotide profiles that measure the specificity of the sequences of the D. melanogaster X chromosome. We show that the X chromosome regions bound by the DCC are enriched for a particular type of short, repetitive sequences. Their distribution suggests that these sequences contribute to chromosome recognition, the generation of DCC binding sites and/or the local spreading of the complex. Comparative data indicate that the same sequences may be involved in dosage compensation in other Drosophila species. Conclusions These results offer an explanation for the wild-type binding of the DCC along the Drosophila X chromosome, contribute to delineate the forces leading to the establishment of dosage compensation and suggest new experimental approaches to understand the precise biochemical features of the dosage compensation system.
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Affiliation(s)
- Miguel Gallach
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
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Santos J, Serra L, Solé E, Pascual M. FISH mapping of microsatellite loci from Drosophila subobscura and its comparison to related species. Chromosome Res 2010; 18:213-26. [PMID: 20198419 DOI: 10.1007/s10577-010-9112-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 01/06/2010] [Accepted: 01/08/2010] [Indexed: 12/24/2022]
Abstract
Microsatellites are highly polymorphic markers that are distributed through all the genome being more abundant in non-coding regions. Whether they are neutral or under selection, these markers if localized can be used as co-dominant molecular markers to explore the dynamics of the evolutionary processes. Their cytological localization can allow identifying genes under selection, inferring recombination from a genomic point of view, or screening for the genomic reorganizations occurring during the evolution of a lineage, among others. In this paper, we report for the first time the localization of microsatellite loci by fluorescent in situ hybridization on Drosophila polytene chromosomes. In Drosophila subobscura, 72 dinucleotide microsatellite loci were localized by fluorescent in situ hybridization yielding unique hybridization signals. In the sex chromosome, microsatellite distribution was not uniform and its density was higher than in autosomes. We identified homologous segments to the sequence flanking the microsatellite loci by browsing the genome sequence of Drosophila pseudoobscura and Drosophila melanogaster. Their localization supports the conservation of Muller's chromosomal elements among Drosophila species and the existence of multiple intrachromosomal rearrangements within each evolutionary lineage. Finally, the lack of microsatellite repeats in the homologous D. melanogaster sequences suggests convergent evolution for high microsatellite density in the distal part of the X chromosome.
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Affiliation(s)
- Josiane Santos
- Departament de Genètica, Universitat de Barcelona, Spain
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Riddle NC, Shaffer CD, Elgin SCR. A lot about a little dot - lessons learned from Drosophila melanogaster chromosome 4. Biochem Cell Biol 2009; 87:229-41. [PMID: 19234537 DOI: 10.1139/o08-119] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The fourth chromosome of Drosophila melanogaster has a number of unique properties that make it a convenient model for the study of chromatin structure. Only 4.2 Mb overall, the 1.2 Mb distal arm of chromosome 4 seen in polytene chromosomes combines characteristics of heterochromatin and euchromatin. This domain has a repeat density of ~35%, comparable to some pericentric chromosome regions, while maintaining a gene density similar to that of the other euchromatic chromosome arms. Studies of position-effect variegation have revealed that heterochromatic and euchromatic domains are interspersed on chromosome 4, and both cytological and biochemical studies have demonstrated that chromosome 4 is associated with heterochromatic marks, such as heterochromatin protein 1 and histone 3 lysine 9 methylation. Chromosome 4 is also marked by POF (painting-of-fourth), a chromosome 4-specific chromosomal protein, and utilizes a dedicated histone methyltransferase, EGG. Studies of chromosome 4 have helped to shape our understanding of heterochromatin domains and their establishment and maintenance. In this review, we provide a synthesis of the work to date and an outlook to the future.
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Affiliation(s)
- Nicole C Riddle
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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10
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Bouilly K, Chaves R, Leitão A, Benabdelmouna A, Guedes-Pinto H. Chromosomal organization of simple sequence repeats in the Pacific oyster (Crassostrea gigas): (GGAT)(4), (GT)(7) and (TA)(10) chromosome patterns. J Genet 2008; 87:119-25. [PMID: 18776639 DOI: 10.1007/s12041-008-0018-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Chromosome identification is essential in oyster genomic research. Fluorescence in situ hybridization (FISH) offers new opportunities for the identification of oyster chromosomes. It has been used to locate satellite DNAs, telomeres or ribosomal DNA sequences. However, regarding chromosome identification, no study has been conducted with simple sequence repeats (SSRs). FISH was used to probe the physical organization of three particular SSRs, (GGAT)(4), (GT)(7) and (TA)(10) onto metaphase chromosomes of the Pacific oyster, Crassostrea gigas. Hybridization signals were observed in all the SSR probes, but the distribution and intensity of signals varied according to the oligonucleotide repeat. The intercalary, centromeric and telomeric bands were observed along the chromosomes, and for each particular repeat every chromosome pair presented a similar pattern, allowing karyotypic analysis with all the SSRs tested. Our study is the first in mollusks to show the application of SSR in situ hybridization for chromosome identification and karyotyping. This technique can be a useful tool for oyster comparative studies and to understand genome organization in different oyster taxa.
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Affiliation(s)
- K Bouilly
- Institute for Biotechnology and Bioengineering, Centre of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, (IBB/CGB-UTAD), 5001-801 Vila Real, Portugal.
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11
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Gallach M, Arnau V, Marín I. Global patterns of sequence evolution in Drosophila. BMC Genomics 2007; 8:408. [PMID: 17996078 PMCID: PMC2180185 DOI: 10.1186/1471-2164-8-408] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 11/09/2007] [Indexed: 01/30/2023] Open
Abstract
Background Sequencing of the genomes of several Drosophila allows for the first precise analyses of how global sequence patterns change among multiple, closely related animal species. A basic question is whether there are characteristic features that differentiate chromosomes within a species or between different species. Results We explored the euchromatin of the chromosomes of seven Drosophila species to establish their global patterns of DNA sequence diversity. Between species, differences in the types and amounts of simple sequence repeats were found. Within each species, the autosomes have almost identical oligonucleotide profiles. However, X chromosomes and autosomes have, in all species, a qualitatively different composition. The X chromosomes are less complex than the autosomes, containing both a higher amount of simple DNA sequences and, in several cases, chromosome-specific repetitive sequences. Moreover, we show that the right arm of the X chromosome of Drosophila pseudoobscura, which evolved from an autosome 10 – 18 millions of years ago, has a composition which is identical to that of the original, left arm of the X chromosome. Conclusion The consistent differences among species, differences among X chromosomes and autosomes and the convergent evolution of X and neo-X chromosomes demonstrate that strong forces are acting on drosophilid genomes to generate peculiar chromosomal landscapes. We discuss the relationships of the patterns observed with differential recombination and mutation rates and with the process of dosage compensation.
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Affiliation(s)
- Miguel Gallach
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain.
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12
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Cuadrado A, Jouve N. The nonrandom distribution of long clusters of all possible classes of trinucleotide repeats in barley chromosomes. Chromosome Res 2007; 15:711-20. [PMID: 17874212 DOI: 10.1007/s10577-007-1156-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 04/26/2007] [Accepted: 04/26/2007] [Indexed: 10/22/2022]
Abstract
This paper is the first to report the long-range organization of all possible classes of trinucleotide motifs in a higher plant genome. Fluorescent in situ hybridization (FISH), employing the synthetic oligonucleotides (AAC)5, (AAG)5, (AAT)5, (AGG)5, (CAC)5, (CAT)5, (CAG)5, (ACT)5, (ACG)5 and (GCC)5, was used to characterize the nonrandom and motif-dependent distribution of tandem arrays of trinucleotide repeats in the metaphase chromosomes and interphase nuclei of barley (Hordeum vulgare L.). This provided detailed information on the sequence content of barley chromatin and allowed the saturation of the physical map of all barley chromosomes. The following conclusions were also drawn: (1) Except for (AAT)5 and (GCC)5, the studied repetitive motifs have a characteristic pattern of distribution in terms of their in situ FISH signals. Some permit the accurate identification of individual chromosomes. (2) (CAG)5, (CAT)5 and (ACT)5 are not found in all barley chromosomes. (3) With the exception of (ACT)5, the remaining trinucleotide repeats occur predominantly in the heterochromatin and are largely absent from the euchromatic regions. Moreover, (CAC)5, (ACG)5 and (CAG)5 are exclusively concentrated in the centromeres. The employment of simple synthetic probes for the identification of chromosomes and genomic characterization, and their importance in studies on genome organization, function and evolution, are discussed.
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Affiliation(s)
- Angeles Cuadrado
- Department of Cell Biology and Genetics, University of Alcalá, 28871 Alcalá de Henares, Madrid, Spain.
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13
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Gilfillan GD, Straub T, de Wit E, Greil F, Lamm R, van Steensel B, Becker PB. Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex. Genes Dev 2006; 20:858-70. [PMID: 16547172 PMCID: PMC1475731 DOI: 10.1101/gad.1399406] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The dosage compensation complex (DCC) of Drosophila melanogaster is capable of distinguishing the single male X from the other chromosomes in the nucleus. It selectively interacts in a discontinuous pattern with much of the X chromosome. How the DCC identifies and binds the X, including binding to the many genes that require dosage compensation, is currently unknown. To identify bound genes and attempt to isolate the targeting cues, we visualized male-specific lethal 1 (MSL1) protein binding along the X chromosome by combining chromatin immunoprecipitation with high-resolution microarrays. More than 700 binding regions for the DCC were observed, encompassing more than half the genes found on the X chromosome. In addition, several rare autosomal binding sites were identified. Essential genes are preferred targets, and genes binding high levels of DCC appear to experience the most compensation (i.e., greatest increase in expression). DCC binding clearly favors genes over intergenic regions, and binds most strongly to the 3' end of transcription units. Within the targeted genes, the DCC exhibits a strong preference for exons and coding sequences. Our results demonstrate gene-specific binding of the DCC, and identify several sequence elements that may partly direct its targeting.
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Affiliation(s)
- Gregor D Gilfillan
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, 80336 München, Germany
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14
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McNeil JA, Smith KP, Hall LL, Lawrence JB. Word frequency analysis reveals enrichment of dinucleotide repeats on the human X chromosome and [GATA]n in the X escape region. Genome Res 2006; 16:477-84. [PMID: 16533911 PMCID: PMC1457025 DOI: 10.1101/gr.4627606] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Most of the human genome encodes neither protein nor known functional RNA, yet available approaches to seek meaningful information in the "noncoding" sequence are limited. The unique biology of the X chromosome, one of which is silenced in mammalian females, can yield clues into sequence motifs involved in chromosome packaging and function. Although autosomal chromatin has some capacity for inactivation, evidence indicates that sequences enriched on the X chromosome render it fully competent for silencing, except in specific regions that escape inactivation. Here we have used a linguistic approach by analyzing the frequency and distribution of nine base-pair genomic "words" throughout the human genome. Results identify previously unknown sequence differences on the human X chromosome. Notably, the dinucleotide repeats [AT]n, [AC]n, and [AG]n are significantly enriched across the X chromosome compared with autosomes. Moreover, a striking enrichment (>10-fold) of [GATA]n is revealed throughout the 10-Mb segment at Xp22 that escapes inactivation, and is confirmed by fluorescence in situ hybridization. A similar enrichment is found in other eutherian genomes. Our findings clearly demonstrate sequence differences relevant to the novel biology and evolution of the X chromosome. Furthermore, they implicate simple sequence repeats, linked to gene regulation and unusual DNA structures, in the regulation and formation of facultative heterochromatin. Results suggest a new paradigm whereby a regional escape from X inactivation is due to the presence of elements that prevent heterochromatinization, rather than the lack of other elements that promote it.
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Affiliation(s)
- John A. McNeil
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Kelly P. Smith
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Lisa L. Hall
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Jeanne B. Lawrence
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Corresponding author.E-mail ; fax (508) 856-5178
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Slawson EE, Shaffer CD, Malone CD, Leung W, Kellmann E, Shevchek RB, Craig CA, Bloom SM, Bogenpohl J, Dee J, Morimoto ETA, Myoung J, Nett AS, Ozsolak F, Tittiger ME, Zeug A, Pardue ML, Buhler J, Mardis ER, Elgin SCR. Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biol 2006; 7:R15. [PMID: 16507169 PMCID: PMC1431729 DOI: 10.1186/gb-2006-7-2-r15] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2005] [Revised: 09/15/2005] [Accepted: 01/25/2006] [Indexed: 11/10/2022] Open
Abstract
Sequencing and analysis of fosmid hybridization to the dot chromosomes of Drosophila virilis and D. melanogaster suggest that repetitive elements and density are important in determining higher-order chromatin packaging. Background Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago. Results Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4 %). Conclusion Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.
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Affiliation(s)
| | | | - Colin D Malone
- Biology Department, Washington University, St Louis, MO 63130, USA
| | - Wilson Leung
- Biology Department, Washington University, St Louis, MO 63130, USA
| | - Elmer Kellmann
- Biology Department, Washington University, St Louis, MO 63130, USA
| | | | - Carolyn A Craig
- Biology Department, Washington University, St Louis, MO 63130, USA
| | - Seth M Bloom
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - James Bogenpohl
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - James Dee
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Emiko TA Morimoto
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Jenny Myoung
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Andrew S Nett
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Fatih Ozsolak
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Mindy E Tittiger
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Andrea Zeug
- Member, Bio 4342 class, Washington University, St Louis, MO 63130, USA
| | - Mary-Lou Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jeremy Buhler
- Computer Science and Engineering, Washington University, St Louis, MO 63130, USA
| | - Elaine R Mardis
- Genome Sequencing Center and Department of Genetics, Washington University, St Louis, MO 63108, USA
| | - Sarah CR Elgin
- Biology Department, Washington University, St Louis, MO 63130, USA
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16
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Dahlsveen IK, Gilfillan GD, Shelest VI, Lamm R, Becker PB. Targeting determinants of dosage compensation in Drosophila. PLoS Genet 2006; 2:e5. [PMID: 16462942 PMCID: PMC1359073 DOI: 10.1371/journal.pgen.0020005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 12/05/2005] [Indexed: 11/19/2022] Open
Abstract
The dosage compensation complex (DCC) in Drosophila melanogaster is responsible for up-regulating transcription from the single male X chromosome to equal the transcription from the two X chromosomes in females. Visualization of the DCC, a large ribonucleoprotein complex, on male larval polytene chromosomes reveals that the complex binds selectively to many interbands on the X chromosome. The targeting of the DCC is thought to be in part determined by DNA sequences that are enriched on the X. So far, lack of knowledge about DCC binding sites has prevented the identification of sequence determinants. Only three binding sites have been identified to date, but analysis of their DNA sequence did not allow the prediction of further binding sites. We have used chromatin immunoprecipitation to identify a number of new DCC binding fragments and characterized them in vivo by visualizing DCC binding to autosomal insertions of these fragments, and we have demonstrated that they possess a wide range of potential to recruit the DCC. By varying the in vivo concentration of the DCC, we provide evidence that this range of recruitment potential is due to differences in affinity of the complex to these sites. We were also able to establish that DCC binding to ectopic high-affinity sites can allow nearby low-affinity sites to recruit the complex. Using the sequences of the newly identified and previously characterized binding fragments, we have uncovered a number of short sequence motifs, which in combination may contribute to DCC recruitment. Our findings suggest that the DCC is recruited to the X via a number of binding sites of decreasing affinities, and that the presence of high- and moderate-affinity sites on the X may ensure that lower-affinity sites are occupied in a context-dependent manner. Our bioinformatics analysis suggests that DCC binding sites may be composed of variable combinations of degenerate motifs.
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Affiliation(s)
- Ina K Dahlsveen
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
| | - Gregor D Gilfillan
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
| | | | - Rosemarie Lamm
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
| | - Peter B Becker
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-Universität München, München, Germany
- * To whom correspondence should be addressed. E-mail:
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17
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Bull LN, Pabón-Peña CR, Freimer NB. Compound microsatellite repeats: practical and theoretical features. Genome Res 1999; 9:830-8. [PMID: 10508841 PMCID: PMC310808 DOI: 10.1101/gr.9.9.830] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Most linkage and population genetic studies that use microsatellites assume that the polymorphism observed at these loci is due simply to variation in the number of units of a single repeat. Variation is far more complex, however, for the numerous microsatellites that contain interruptions within the repeat or contain more than one type of repeat. We observed that for D18S58, a compound microsatellite containing (CG)(m), as well as (CA)(n) repeats, the apparent length of certain alleles varied between genotyping experiments. Similar results were obtained with other (CG)(m)-(CA)(n) repeats. Sequencing demonstrated that the D18S58 alleles demonstrating variable mobility contained longer (CG)(m) stretches than those alleles whose length did not appear to vary between experiments. These results suggest that (CG)(m) repeats, which are frequently present in compound human microsatellites, are prone to form an unusually stable secondary structure. We discuss the relative frequency of different classes of compound microsatellites identified through database searches, as well as their patterns of sequence and variation. Further characterization of such variation is important for elucidating the origin, mutational processes, and structure of these widely used, but incompletely understood, sequences.
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Affiliation(s)
- L N Bull
- Neurogenetics Laboratory, Department of Psychiatry, University of California, San Francisco, California 94143 USA
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18
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Bailey AD, Pavelitz T, Weiner AM. The microsatellite sequence (CT)n x (GA)n promotes stable chromosomal integration of large tandem arrays of functional human U2 small nuclear RNA genes. Mol Cell Biol 1998; 18:2262-71. [PMID: 9528797 PMCID: PMC121475 DOI: 10.1128/mcb.18.4.2262] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/1997] [Accepted: 01/20/1998] [Indexed: 02/07/2023] Open
Abstract
The multigene family encoding human U2 small nuclear RNA (snRNA) is organized as a single large tandem array containing 5 to 25 copies of a 6.1-kb repeat unit (the RNU2 locus). Remarkably, each of the repeat units within an individual U2 tandem array appears to be identical except for an irregular dinucleotide tract, known as the CT microsatellite, which exhibits minor length and sequence polymorphism. Using a somatic cell genetic assay, we previously noticed that the CT microsatellite appeared to stabilize artificial tandem arrays of U2 snRNA genes. We now demonstrate that the CT microsatellite is required to establish large tandem arrays of transcriptionally active U2 genes, increasing both the average and maximum size of the resulting arrays. In contrast, the CT microsatellite has no effect on the average or maximal size of artificial arrays containing transcriptionally inactive U2 genes that lack key promoter elements. Our data reinforce the connection between recombination and transcription. Active U2 transcription interferes with establishment or maintenance of the U2 tandem array, and the CT microsatellite opposes these effects, perhaps by binding GAGA or GAGA-related factors which alter local chromatin structure. We speculate that the mechanisms responsible for maintenance of tandem arrays containing active promoters may differ from those that maintain tandem arrays of transcriptionally inactive sequences.
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Affiliation(s)
- A D Bailey
- Department of Molecular Biophysics, Yale University, New Haven, Connecticut 06520-8114, USA
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19
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Schmidt T, Heslop-Harrison JS. The physical and genomic organization of microsatellites in sugar beet. Proc Natl Acad Sci U S A 1996; 93:8761-5. [PMID: 8710945 PMCID: PMC38747 DOI: 10.1073/pnas.93.16.8761] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Microsatellites, tandem arrays of short (2-5 bp) nucleotide motifs, are present in high numbers in most eukaryotic genomes. We have characterized the physical distribution of microsatellites on chromosomes of sugar beet (Beta vulgaris L.). Each microsatellite sequence shows a characteristic genomic distribution and motif-dependent dispersion, with site-specific amplification on one to seven pairs of centromeres or intercalary chromosomal regions and weaker, dispersed hybridization along chromosomes. Exclusion of some microsatellites from 18S-5.8S-25S rRNA gene sites, centromeres, and intercalary sites was observed. In-gel and in situ hybridization patterns are correlated, with highly repeated restriction fragments indicating major centromeric sites of microsatellite arrays. The results have implications for genome evolution and the suitability of particular microsatellite markers for genetic mapping and genome analysis.
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Affiliation(s)
- T Schmidt
- Department of Cell Biology, John Innes Centre, Norwich, United Kingdom
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20
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Losada A, Villasante A. Autosomal location of a new subtype of 1.688 satellite DNA of Drosophila melanogaster. Chromosome Res 1996; 4:372-83. [PMID: 8871826 DOI: 10.1007/bf02257273] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
During the screening of a Drosophila melanogaster YAC library with DNA from the minichromosome Dp(1;f)1187 we isolated a clone, yw20D5, which contains a new subtype of 1.688 satellite DNA. Although the sequences of several monomers subcloned from the YAC show a considerable variation in length, the derived consensus sequence is 356-bp long. This new subtype and the one constituted by the 353-bp repeats are both located on the left arm heterochromatin of chromosome 3, arranged in separate arrays. Despite their autosomal location, phylogenetic relationships among 1.688 satellite sequences suggest that they may have originated from the 359-bp repeats of the X chromosome heterochromatin. We have used the new 356-bp repeats to investigate whether sequences related to the 1.688 satellite are dispersed along the euchromatic arms of the autosomes in a similar way to that in which they are found along the X chromosome euchromatin.
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Affiliation(s)
- A Losada
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM)
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21
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Marín I, Fontdevila A. Characterization of Gandalf, a new inverted-repeat transposable element of Drosophila koepferae. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:423-33. [PMID: 7565606 DOI: 10.1007/bf02191642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The cloning and characterization of Gandalf, a new DNA-transposing mobile element obtained from the Drosophila koepferae (repleta group) genome is described. A fragment of Gandalf was found in a middle repetitive clone that shows variable chromosomal localization. Restriction, Southern blot, PCR and sequencing analyses have shown that most Gandalf copies are about 1 kb long, are flanked by 12 bp inverted terminal repeats and contain subterminal repetitive regions on both sides of the element. As with other elements of the DNA-transposing type (known as the 'Ac family'), the Gandalf element generates 8 bp direct duplications at the insertion point. Coding region analysis has shown that the longer open reading frame found in Gandalf copies could encode part of a protein. However, whether or not the 1 kb copies of the element are actually the active transposons remains to be elucidated. Gandalf shows a very low copy number in D. buzzatii, a sibling species of D. koepferae. An attempt to induce interspecific hybrid dysgenesis in hybrids of these two species has been unsuccessful.
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Affiliation(s)
- I Marín
- Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Spain
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22
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Simmler MC, Cattanach BM, Rasberry C, Rougeulle C, Avner P. Mapping the murine Xce locus with (CA)n repeats. Mamm Genome 1993; 4:523-30. [PMID: 8118102 DOI: 10.1007/bf00364788] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The X Chromosome (Chr) controlling element locus (Xce) in the mouse has been shown to influence the X inactivation process. Xce maps to the central region of the X Chr, which also contains the Xist sequence, itself possibly implicated in the X inactivation process. Three microsatellite markers spanning the Xist locus have been isolated from an Xist containing YAC. All three microsatellite markers showed complete linkage with Xce in recombinants for the central span of the mouse X Chr between Ta and Moblo and strong linkage disequilibrium with Xce in all but one of the inbred mouse strains tested. In the standard Xceb typing strain JU/Ct, the two microsatellites most closely flanking Xist fail to carry the allelic forms expected if Xist and Xce are synonymous. Alternative explanations for this finding are presented in the context of our search for understanding the relation between Xist and Xce.
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Affiliation(s)
- M C Simmler
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France
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23
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Abstract
All eukaryotic genomes thus far examined contain simple sequence repeats. A particularly common simple sequence in many organisms (including humans) consists of tracts of alternating GT residues on one strand. Allelic poly(GT) tracts are often of different lengths in different individuals, indicating that they are likely to be unstable. We examined the instability of poly(GT) and poly(G) tracts in the yeast Saccharomyces cerevisiae. We found that these tracts were dramatically unstable, altering length at a minimal rate of 10(-4) events per division. Most of the changes involved one or two repeat unit additions or deletions, although one alteration involved an interaction with the yeast telomeres.
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24
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Abstract
All eukaryotic genomes thus far examined contain simple sequence repeats. A particularly common simple sequence in many organisms (including humans) consists of tracts of alternating GT residues on one strand. Allelic poly(GT) tracts are often of different lengths in different individuals, indicating that they are likely to be unstable. We examined the instability of poly(GT) and poly(G) tracts in the yeast Saccharomyces cerevisiae. We found that these tracts were dramatically unstable, altering length at a minimal rate of 10(-4) events per division. Most of the changes involved one or two repeat unit additions or deletions, although one alteration involved an interaction with the yeast telomeres.
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Affiliation(s)
- S T Henderson
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637
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25
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Abstract
The distribution of functions within genomes of higher organisms relative to processes that lead to the spread of mutations in populations is examined in its general outlines. A number of points are enumerated that collectively put in question the concept of junk DNA: the plausible compatibility of DNA function with rapid substitution rates; the likelihood of superimposed functions along much of eukaryotic DNA; the potential for a merely conditional functionality in sequence repeats; the apparent adoption of macromolecular waste as a strategy for maintaining a function without selective grooming of individual sequence repeats that carry out the function; the likely requirement that any DNA sequence must be "polite" vis-'a-vis (compatible with) functional sequences in its genomic environment; the existence in germ-cell lineages of selective constraints that are not apparent in populations of individuals; and the fact that DNA techtonics - the appearance and disappearance of genomic DNA - are not incompatible with function. It is pointed out that the inverse correlation between functional constraints and rates of substitution cannot be claimed to be pillar of the neutral theory, because it is also predicted from a selectionist viewpoint. The dispensability of functional structures is brought into relation with the concept of reproductive sufficiency the survivability of genotypes in the absence of fitter alleles.
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Affiliation(s)
- E Zuckerkandl
- Linus Pauling Institute of Science and Medicine, Palo Alto, CA 94306
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26
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Sass H, Meselson M. Dosage compensation of the Drosophila pseudoobscura Hsp82 gene and the Drosophila melanogaster Adh gene at ectopic sites in D. melanogaster. Proc Natl Acad Sci U S A 1991; 88:6795-9. [PMID: 1907376 PMCID: PMC52175 DOI: 10.1073/pnas.88.15.6795] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Measurements were made of the amounts of larval RNA transcribed from the autosomal Adh gene of Drosophila melanogaster and the X chromosomal Hsp82 gene of Drosophila pseudoobscura carried on the same P-element transposon inserted at various sites in the D. melanogaster genome. Both genes were fully compensated at sites in euchromatic regions of the X chromosome but neither was compensated at a site in the centric beta-heterochromatin of the X chromosome. No compensation of the D. pseudoobscura Hsp82 gene was found at any of 10 autosomal insertion sites tested. The compensation behavior of the transposed genes was, therefore, not determined by closely linked sequences but instead was determined in each case by their new chromosomal environment.
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Affiliation(s)
- H Sass
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138
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27
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Abstract
The mouse X-linked Pgk-1 gene encodes phosphoglycerate kinase. When transfected into human cells, the Pgk-1b allele causes the appearance of mouse PGK-1b enzyme activity. We describe here cloning of mouse Pgk-1a, an allele of Pgk-1 which encodes an enzyme, PGK-1a, with distinct electrophoretic mobility. We constructed recombinants between the DNA encoding Pgk-1b and Pgk-1a and transfected these constructs into human cells to assess the electrophoretic characteristics of each recombinant. In this way the charge variation between the two proteins was localized to exons 4 or 5. Sequencing of these exons revealed a single base-pair difference between the two alleles at codon 155, which predicts the amino acids lysine and threonine in PGK-1b and PGK-1a, respectively. A number of other DNA sequence polymorphisms exist between Pgk-1b and Pgk-1a including part of an L1 repeated element unique to Pgk-1a.
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28
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Vogt P. Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code". Hum Genet 1990; 84:301-36. [PMID: 2407640 DOI: 10.1007/bf00196228] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This review is based on a thorough description of the structure and sequence organization of tandemly organized repetitive DNA sequence families in the human genome; it is aimed at revealing the locus-specific sequence organization of tandemly repetitive sequence structures as a highly conserved DNA sequence code. These repetitive so-called "super-structures" or "higher-order" structures are able to attract specific nuclear proteins. I shall define this code therefore as a "chromatin folding code". Since locus-specific superstructures of tandemly repetitive sequence units are present not only in the chromosome centromere or telomere region but also on the arms of the chromosomes, I assume that their chromatin folding code may contribute to, or even organize, the folding pathway of the chromatin chain in the nucleus. The "chromatin folding code" is based on its specific "chromatin code", which describes the sequence dependence of the helical pathway of the DNA primary sequence (i.e., secondary structure) entrapping the histone octamers in preferential positions. There is no periodicity in the distribution of the nucleosomes along the DNA chain. The folding pathway of the nucleosomal chromatin chain is however still flexible and determined by e.g., the length of the DNA chain between the nucleosomes. The fixation and stabilization of the chromatin chain in the space of the nucleus (i.e., its "functional state") may be mediated by additionally unique DNA protein interactions that are dictated by the "chromatin folding code". The unique DNA-protein interactions around the centromeres of human chromosomes are revealed for example by their "C-banding". I wish to stress that it is not my aim to relate each block of repetitive DNA sequences to a specific "chromatin folding code", but I shall demonstrate that there is an inherent potential for tandem repeated sequence units to develop a locus-specific repetitive higher order structure; this potential may create a specific chromatin folding code whenever a selection force exists at the position of this repetitive DNA structure in the genome.
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Affiliation(s)
- P Vogt
- Institut für Humangenetik und Anthropologie der Universität, Heidelberg, Federal Republic of Germany
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