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Evolutionary origin of chromatin remodeling for dosage compensation: Lessons from epigenetic modifications of X chromosomes in germ cells of Drosophila, C.elegans and Mammals. THE NUCLEUS 2012. [DOI: 10.1007/s13237-012-0054-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Angelopoulou R, Lavranos G, Manolakou P. Regulatory RNAs and chromatin modification in dosage compensation: a continuous path from flies to humans? Reprod Biol Endocrinol 2008; 6:12. [PMID: 18355403 PMCID: PMC2324084 DOI: 10.1186/1477-7827-6-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 03/20/2008] [Indexed: 11/20/2022] Open
Abstract
Chromosomal sex determination is a widely distributed strategy in nature. In the most classic scenario, one sex is characterized by a homologue pair of sex chromosomes, while the other includes two morphologically and functionally distinct gonosomes. In mammalian diploid cells, the female is characterized by the presence of two identical X chromosomes, while the male features an XY pair, with the Y bearing the major genetic determinant of sex, i.e. the SRY gene. In other species, such as the fruitfly, sex is determined by the ratio of autosomes to X chromosomes. Regardless of the exact mechanism, however, all these animals would exhibit a sex-specific gene expression inequality, due to the different number of X chromosomes, a phenomenon inhibited by a series of genetic and epigenetic regulatory events described as "dosage compensation". Since adequate available data is currently restricted to worms, flies and mammals, while for other groups of animals, such as reptiles, fish and birds it is very limited, it is not yet clear whether this is an evolutionary conserved mechanism. However certain striking similarities have already been observed among evolutionary distant species, such as Drosophila melanogaster and Mus musculus. These mainly refer to a) the need for a counting mechanism, to determine the chromosomal content of the cell, i.e. the ratio of autosomes to gonosomes (a process well understood in flies, but still hypothesized in mammals), b) the implication of non-translated, sex-specific, regulatory RNAs (roX and Xist, respectively) as key elements in this process and the location of similar mediators in the Z chromosome of chicken c) the inclusion of a chromatin modification epigenetic final step, which ensures that gene expression remains stably regulated throughout the affected area of the gonosome. This review summarizes these points and proposes a possible role for comparative genetics, as they seem to constitute proof of maintained cell economy (by using the same basic regulatory elements in various different scenarios) throughout numerous centuries of evolutionary history.
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Affiliation(s)
- Roxani Angelopoulou
- Department of Histology-Embryology, Medical School, Athens University, Greece
| | - Giagkos Lavranos
- Department of Histology-Embryology, Medical School, Athens University, Greece
| | - Panagiota Manolakou
- Department of Histology-Embryology, Medical School, Athens University, Greece
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Abstract
The genomes of higher eukaryotes are carefully balanced systems of gene expression that compensate for the different numbers of sex chromosomes in the two sexes by adjusting gene expression levels. Different strategies for sex chromosome dosage compensation have evolved, which all involve modulating chromatin structure as a means to fine-tune transcription levels. As data accumulate, previous over-simplifications are being revised, and novel features of the compensation processes are gaining attention, many of which are of sufficient global validity to influence our view on gene expression beyond the realm of dosage compensation itself.
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Affiliation(s)
- Tobias Straub
- Adolf Butenandt Institute, Department of Molecular Biology, Ludwig Maximilians University, 80336 Munich, Germany
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McDonel P, Jans J, Peterson BK, Meyer BJ. Clustered DNA motifs mark X chromosomes for repression by a dosage compensation complex. Nature 2006; 444:614-8. [PMID: 17122774 PMCID: PMC2693371 DOI: 10.1038/nature05338] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Accepted: 10/11/2006] [Indexed: 01/11/2023]
Abstract
Gene expression in metazoans is regulated not only at the level of individual genes but also in a coordinated manner across large chromosomal domains (for example centromeres, telomeres and imprinted gene clusters) and along entire chromosomes (for example X-chromosome dosage compensation). The primary DNA sequence usually specifies the regulation of individual genes, but the nature of cis-acting information that controls genes over large regions has been elusive: higher-order DNA structure, specific histone modifications, subnuclear compartmentalization and primary DNA sequence are possibilities. One paradigm of chromosome-wide gene regulation is Caenorhabditis elegans dosage compensation in which a large dosage compensation complex (DCC) is targeted to both X chromosomes of hermaphrodites to repress transcript levels by half. This essential process equalizes X-linked gene expression between the sexes (XO males and XX hermaphrodites). Here we report the discovery and dissection of cis-acting sites that mark nematode X chromosomes as targets for gene repression by the DCC. These rex (recruitment element on X) sites are widely dispersed along X and reside in promoters, exons and intergenic regions. rex sites share at least two distinct motifs that act in combination to recruit the DCC. Mutating these motifs severely reduces or abolishes DCC binding in vivo, demonstrating the importance of primary DNA sequence in chromosome-wide regulation. Unexpectedly, the motifs are not enriched on X, but altering motif numbers within rex sites demonstrates that motif co-occurrence in unusually high densities is essential for optimal DCC recruitment. Thus, X-specific repression is established through sequences not specific to X. The distribution of common motifs provides the foundation for repression along an entire chromosome.
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Affiliation(s)
- Patrick McDonel
- Howard Hughes Medical Institute, University of California-Berkeley, 16 Barker Hall, Berkeley, California 94720-3204, USA
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Abstract
Over the past 100 years Drosophila has been developed into an outstanding model system for the study of evolutionary processes. A fascinating aspect of evolution is the differentiation of sex chromosomes. Organisms with highly differentiated sex chromosomes, such as the mammalian X and Y, must compensate for the imbalance in gene dosage that this creates. The need to adjust the expression of sex-linked genes is a potent force driving the rise of regulatory mechanisms that act on an entire chromosome. This review will contrast the process of dosage compensation in Drosophila with the divergent strategies adopted by other model organisms. While the machinery of sex chromosome compensation is different in each instance, all share the ability to direct chromatin modifications to an entire chromosome. This review will also explore the idea that chromosome-targeting systems are sometimes adapted for other purposes. This appears the likely source of a chromosome-wide targeting system displayed by the Drosophila fourth chromosome.
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Affiliation(s)
- Jan Larsson
- Umeå Center for Molecular Pathogenesis, Umeå University, SE-901 87, Umeå, Sweden.
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Deng X, Meller VH. Non-coding RNA in fly dosage compensation. Trends Biochem Sci 2006; 31:526-32. [PMID: 16890440 DOI: 10.1016/j.tibs.2006.07.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 06/15/2006] [Accepted: 07/20/2006] [Indexed: 01/27/2023]
Abstract
Dosage compensation modulates global expression of an X chromosome and is necessary to restore the balance between X-chromosome and autosome expression in both sexes. A central question in the field is how this regulation is directed. Large non-coding RNAs, such as Xist in mammals and roX in flies, have pivotal roles in targeting chromosome-wide modification for dosage compensation. Several recent studies in Drosophila provide new insight into the principles of X-chromosome recognition and the function of non-coding RNA in this process.
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Affiliation(s)
- Xinxian Deng
- Department of Biological Science, Wayne State University, Detroit, MI 48201, USA
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Hüttenhofer A, Schattner P. The principles of guiding by RNA: chimeric RNA-protein enzymes. Nat Rev Genet 2006; 7:475-82. [PMID: 16622413 DOI: 10.1038/nrg1855] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The non-protein-coding transcriptional output of the cell is far greater than previously thought. Although the functions, if any, of the vast majority of these RNA transcripts remain elusive, out of those for which functions have already been established, most act as RNA guides for protein enzymes. Common features of these RNAs provide clues about the evolutionary constraints that led to the development of RNA-guided proteins and the specific biological environments in which target specificity and diversity are most crucial to the cell.
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Affiliation(s)
- Alexander Hüttenhofer
- Innsbruck Biocenter, Medical University Innsbruck, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria.
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Kalantry S, Magnuson T. The Polycomb group protein EED is dispensable for the initiation of random X-chromosome inactivation. PLoS Genet 2006; 2:e66. [PMID: 16680199 PMCID: PMC1456320 DOI: 10.1371/journal.pgen.0020066] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Accepted: 03/17/2006] [Indexed: 12/01/2022] Open
Abstract
The Polycomb group (PcG) proteins are thought to silence gene expression by modifying chromatin. The Polycomb repressive complex 2 (PRC2) plays an essential role in mammalian X-chromosome inactivation (XCI), a model system to investigate heritable gene silencing. In the mouse, two different forms of XCI occur. In the preimplantation embryo, all cells undergo imprinted inactivation of the paternal X-chromosome (Xp). During the peri-implantation period, cells destined to give rise to the embryo proper erase the imprint and randomly inactivate either the maternal X-chromosome or the Xp; extraembryonic cells, on the other hand, maintain imprinted XCI of the Xp. PRC2 proteins are enriched on the inactive-X during early stages of both imprinted and random XCI. It is therefore thought that PRC2 contributes to the initiation of XCI. Mouse embryos lacking the essential PRC2 component EED harbor defects in the maintenance of imprinted XCI in differentiating trophoblast cells. Assessment of PRC2 requirement in the initiation of XCI, however, has been hindered by the presence of maternally derived proteins in the early embryo. Here we show that Eed-/- embryos initiate and maintain random XCI despite lacking any functional EED protein prior to the initiation of random XCI. Thus, despite being enriched on the inactive X-chromosome, PcGs appear to be dispensable for the initiation and maintenance of random XCI. These results highlight the lineage- and differentiation state-specific requirements for PcGs in XCI and argue against PcG function in the formation of the facultative heterochromatin of the inactive X-chromosome.
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Affiliation(s)
- Sundeep Kalantry
- Department of Genetics and the Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Terry Magnuson
- Department of Genetics and the Carolina Center for the Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Duncan K, Grskovic M, Strein C, Beckmann K, Niggeweg R, Abaza I, Gebauer F, Wilm M, Hentze MW. Sex-lethal imparts a sex-specific function to UNR by recruiting it to the msl-2 mRNA 3' UTR: translational repression for dosage compensation. Genes Dev 2006; 20:368-79. [PMID: 16452508 PMCID: PMC1361707 DOI: 10.1101/gad.371406] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MSL-2 (male-specific lethal 2) is the limiting component of the Drosophila dosage compensation complex (DCC) that specifically increases transcription from the male X chromosome. Ectopic expression of MSL-2 protein in females causes DCC assembly on both X chromosomes and lethality. Inhibition of MSL-2 synthesis requires the female-specific protein sex-lethal (SXL), which binds to the msl-2 mRNA 5' and 3' untranslated regions (UTRs) and blocks translation through distinct UTR-specific mechanisms. Here, we purify translationally silenced msl-2 mRNPs and identify UNR (upstream of N-ras) as a protein recruited to the 3' UTR by SXL. We demonstrate that SXL requires UNR as a corepressor for 3'-UTR-mediated regulation, imparting a female-specific function to the ubiquitously expressed UNR protein. Our results reveal a novel functional role for UNR as a translational repressor and indicate that UNR is a key component of a "fail-safe" dosage compensation regulatory system that prevents toxic MSL-2 synthesis in female cells.
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Affiliation(s)
- Kent Duncan
- Gene Expression Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Huang Y, Myers MP, Xu RM. Crystal Structure of the HP1-EMSY Complex Reveals an Unusual Mode of HP1 Binding. Structure 2006; 14:703-12. [PMID: 16615912 DOI: 10.1016/j.str.2006.01.007] [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] [Received: 10/19/2005] [Revised: 12/09/2005] [Accepted: 01/07/2006] [Indexed: 11/27/2022]
Abstract
Heterochromatin protein-1 (HP1) plays an essential role in both the assembly of higher-order chromatin structure and epigenetic inheritance. The C-terminal chromo shadow domain (CSD) of HP1 is responsible for homodimerization and interaction with a number of chromatin-associated nonhistone proteins, including EMSY, which is a BRCA2-interacting protein that has been implicated in the development of breast and ovarian cancer. We have determined the crystal structure of the HP1beta CSD in complex with the N-terminal domain of EMSY at 1.8 A resolution. Surprisingly, the structure reveals that EMSY is bound by two HP1 CSD homodimers, and the binding sequences differ from the consensus HP1 binding motif PXVXL. This structural information expands our understanding of HP1 binding specificity and provides insights into interactions between HP1 homodimers that are likely to be important for heterochromatin formation.
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Affiliation(s)
- Ying Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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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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12
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Hamada FN, Park PJ, Gordadze PR, Kuroda MI. Global regulation of X chromosomal genes by the MSL complex in Drosophila melanogaster. Genes Dev 2005; 19:2289-94. [PMID: 16204180 PMCID: PMC1240037 DOI: 10.1101/gad.1343705] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A long-standing model postulates that X-chromosome dosage compensation in Drosophila occurs by twofold up-regulation of the single male X, but previous data cannot exclude an alternative model, in which male autosomes are down-regulated to balance gene expression. To distinguish between the two models, we used RNA interference to deplete Male-Specific Lethal (MSL) complexes from male-like tissue culture cells. We found that expression of many genes from the X chromosome decreased, while expression from the autosomes was largely unchanged. We conclude that the primary role of the MSL complex is to up-regulate the male X chromosome.
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Affiliation(s)
- Fumika N Hamada
- Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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