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Nora EP, Heard E. Chromatin structure and nuclear organization dynamics during X-chromosome inactivation. Cold Spring Harb Symp Quant Biol 2011; 75:333-44. [PMID: 21447823 DOI: 10.1101/sqb.2010.75.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Early development of female mammals is accompanied by transcriptional inactivation of one of their two X chromosomes. This leads to monoallelic expression of most of the X chromosome and ensures dosage compensation with respect to males (XY). One of the most surprising aspects of this phenomenon is that the two X homologs are treated differently even though they are present within the same nucleus. In eutherian mammals, such as humans and mice, either the maternal or the paternal X is inactivated during early embryogenesis. Once set up, the silent state is epigenetically transmitted as cells divide, so that adult females are mosaics of clonal cell populations, which express either of their two X chromosomes. The past years have been marked by the discovery of several molecular events that accompany chromosome-wide silencing.
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Affiliation(s)
- E P Nora
- Institut Curie, CNRS UMR3215, INSERM U934, 75724 Paris Cedex 05, France.
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2
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Zernicka-Goetz M, Patrat C, Okamoto I, Thepot D, Peynot N, Fauque P, Daniel N, Diabangouaya P, Renard J, Duranthon V, Heard E. INVITED SESSION, SESSION 64: EPIGENETICS AND EARLY EVENTS DURING MAMMALIAN DEVELOPMENT Wednesday 6 July 2011 12:00 - 13:00. Hum Reprod 2011. [DOI: 10.1093/humrep/26.s1.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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3
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Yang S, Kohler D, Teller K, Cremer T, Le Baccon P, Heard E, Eils R, Rohr K. Nonrigid registration of 3-d multichannel microscopy images of cell nuclei. IEEE Trans Image Process 2008; 17:493-499. [PMID: 18390358 DOI: 10.1109/tip.2008.918017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We present an intensity-based nonrigid registration approach for the normalization of 3-D multichannel microscopy images of cell nuclei. A main problem with cell nuclei images is that the intensity structure of different nuclei differs very much; thus, an intensity-based registration scheme cannot be used directly. Instead, we first perform a segmentation of the images from the cell nucleus channel, smooth the resulting images by a Gaussian filter, and then apply an intensity-based registration algorithm. The obtained transformation is applied to the images from the nucleus channel as well as to the images from the other channels. To improve the convergence rate of the algorithm, we propose an adaptive step length optimization scheme and also employ a multiresolution scheme. Our approach has been successfully applied using 2-D cell-like synthetic images, 3-D phantom images as well as 3-D multichannel microscopy images representing different chromosome territories and gene regions. We also describe an extension of our approach, which is applied for the registration of 3D + t (4-D) image series of moving cell nuclei.
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Affiliation(s)
- S Yang
- Department of Bioinformatics and Functional Genomics, German Cancer Research Centre, University of Heidelberg, Heidelberg, Germany.
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4
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Augui S, Filion GJ, Huart S, Nora E, Guggiari M, Maresca M, Stewart AF, Heard E. Sensing X chromosome pairs before X inactivation via a novel X-pairing region of the Xic. Science 2007; 318:1632-6. [PMID: 18063799 DOI: 10.1126/science.1149420] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mammalian dosage compensation involves silencing of one of the two X chromosomes in females and is controlled by the X-inactivation center (Xic). The Xic, which includes Xist and its antisense transcription unit Tsix/Xite, somehow senses the number of X chromosomes and triggers Xist up-regulation from one of the two X chromosomes in females. We found that a segment of the mouse Xic lying several hundred kilobases upstream of Xist brings the two Xics together before the onset of X inactivation. This region can autonomously drive Xic trans-interactions even as an ectopic single-copy transgene. Its introduction into male embryonic stem cells is strongly selected against, consistent with a possible role in trans-activating Xist. We propose that homologous associations driven by this novel X-pairing region (Xpr) of the Xic enable a cell to sense that more than one X chromosome is present and coordinate reciprocal Xist/Tsix expression.
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Affiliation(s)
- S Augui
- CNRS UMR218, Curie Institute, 26 rue d'Ulm, Paris 75005, France
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5
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Okamoto I, Heard E. The dynamics of imprinted X inactivation during preimplantation development in mice. Cytogenet Genome Res 2006; 113:318-24. [PMID: 16575196 DOI: 10.1159/000090848] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 10/07/2005] [Indexed: 11/19/2022] Open
Abstract
In the mouse, there are two forms of X chromosome inactivation (XCI), random XCI in the fetus and imprinted paternal XCI, which is limited to the extraembryonic tissues. While the mechanism of random XCI has been studied extensively using the in vitro XX ES cell differentiation system, imprinted XCI during early embryonic development has been less well characterized. Recent studies of early embryos have reported unexpected findings for the paternal X chromosome (Xp). Imprinted XCI may not be linked to meiotic silencing in the male germ line but rather to the imprinted status of the Xist gene. Furthermore, the Xp becomes inactivated in all cells of cleavage-stage embryos and then reactivated in the cells of the inner cell mass (ICM) that form the epiblast, where random XCI ensues.
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Affiliation(s)
- I Okamoto
- CNRS UMR218, Curie Institute, Paris, France.
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6
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Abstract
In female mammals, one of the two X chromosomes is converted from the active euchromatic state into inactive heterochromatin during early embryonic development. This process, known as X-chromosome inactivation, results in the transcriptional silencing of over a thousand genes and ensures dosage compensation between the sexes. Here, we discuss the possible mechanisms of action of the Xist transcript, a remarkable noncoding RNA that triggers the X-inactivation process and also seems to participate in setting up the epigenetic marks that provide the cellular memory of the inactive state. So far, no functional protein partners have been identified for Xist RNA, but different lines of evidence suggest that it may act at multiple levels, including nuclear compartmentalization, chromatin modulation, and recruitment of Polycomb group proteins.
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Affiliation(s)
- O Masui
- CNRS UMR 218, Institut Curie, Paris, France
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7
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Chaumeil J, Okamoto I, Guggiari M, Heard E. Integrated kinetics of X chromosome inactivation in differentiating embryonic stem cells. Cytogenet Genome Res 2004; 99:75-84. [PMID: 12900548 DOI: 10.1159/000071577] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2003] [Indexed: 11/19/2022] Open
Abstract
Inactivation of the X chromosome during early female development and the subsequent maintenance of this transcriptionally inert state through countless cell divisions remain a paradigm for epigenetic regulation in mammals. Nevertheless, the exact mechanisms underlying this chromosome-wide silencing process remain unclear. Using differentiating female embryonic stem (ES) cells as a model system, we recently found that histone H3 tail modifications are among the earliest known chromatin changes in the X inactivation process, appearing as soon as Xist RNA accumulates on the X chromosome, but prior to transcriptional silencing of X-linked genes (Heard et al., 2001). In this report we present an integrated analysis of the sequence of early events and chromatin modifications underlying X inactivation in differentiating female ES cells. We have extended our previous analysis concerning changes in histone tail modification states. We find that the hypomethylation of Arg-17 and that of Lys-36 on histone H3 also characterize the inactive X chromosome, and that these profiles show a similarly early onset during the initiation of X inactivation. In addition, we have investigated the kinetics of the shift in replication timing of the X chromosome undergoing inactivation. This event occurs slightly later than Xist RNA coating and the chromatin modifications. Finally, from an early stage in the X inactivation process, characteristic histone modification patterns can be found on the X chromosome at mitosis, suggesting that they represent true epigenetic marks of the inactive state.
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Affiliation(s)
- J Chaumeil
- Mammalian Developmental Epigenetics Group, CNRS UMR 218, Curie Institute, Paris, France
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8
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Affiliation(s)
- E Heard
- Mammalian Developmental Epigenetics Group, CNRS UMR218, Curie Institute, 75248 Paris Cedex 05, France.
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9
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Abstract
Coating of the X chromosome by Xist RNA is an essential trigger for X inactivation. However, little is known about the early chromatin remodeling events that transform this signal into transcriptional silencing. Here we report that methylation of histone H3 lysine 9 on the inactive X chromosome occurs immediately after Xist RNA coating and before transcriptional inactivation of X-linked genes. X-chromosomal H3 Lys-9 methylation occurs during the same window of time as H3 Lys-9 hypoacetylation and H3 Lys-4 hypomethylation. Histone H3 modifications thus represent the earliest known chromatin changes during X inactivation. We also identify a unique "hotspot" of H3 Lys-9 methylation 5' to Xist, and we propose that this acts as a nucleation center for Xist RNA-dependent spread of inactivation along the X chromosome via H3 Lys-9 methylation.
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Affiliation(s)
- E Heard
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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10
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Monier K, Heliot L, Rougeulle C, Heard E, Robert-Nicoud M, Vourc'h C, Bensimon A, Usson Y. Improvement of FISH mapping resolution on combed DNA molecules by iterative constrained deconvolution: a quantitative study. Cytogenet Cell Genet 2001; 92:59-62. [PMID: 11306797 DOI: 10.1159/000056869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Image restoration approaches, such as digital deconvolution, are becoming widely used for improving the quality of microscopic images. However, no quantification of the gain in resolution of fluorescence images is available. We show that, after iterative constrained deconvolution, fluorescent cosmid signals appear to be 25% smaller, and 1.2-kb fragment signals on combed molecules faithfully display the expected length.
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Affiliation(s)
- K Monier
- Laboratoire DyOGen, Unité INSERM U309, Institut Albert Bonniot, La Tronche, France.
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11
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Abstract
In many sexually dimorphic species, a mechanism is required to ensure equivalent levels of gene expression from the sex chromosomes. In mammals, such dosage compensation is achieved by X-chromosome inactivation, a process that presents a unique medley of biological puzzles: how to silence one but not the other X chromosome in the same nucleus; how to count the number of X's and keep only one active; how to choose which X chromosome is inactivated; and how to establish this silent state rapidly and efficiently during early development. The key to most of these puzzles lies in a unique locus, the X-inactivation centre and a remarkable RNA--Xist--that it encodes.
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Affiliation(s)
- P Avner
- Unité de Génétique Moléculaire Murine Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France.
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12
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Heard E, Avner P. Trans-Siberian X press report. International Symposium on X Chromosome Inactivation in Mammals, Institute of Cytology and Genetics, Novosibirsk, Russia, 6-12 September, 1999. Trends Genet 2000; 16:64-5. [PMID: 10712161 DOI: 10.1016/s0168-9525(99)01944-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France.
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13
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Abstract
X inactivation in female mammals is controlled by a key locus on the X chromosome, the X-inactivation center (Xic). The Xic controls the initiation and propagation of inactivation in cis. It also ensures that the correct number of X chromosomes undergo inactivation (counting) and determines which X chromosome becomes inactivated (choice). The Xist gene maps to the Xic region and is essential for the initiation of X inactivation in cis. Regulatory elements of X inactivation have been proposed to lie 3' to Xist. One such element, lying 15 kb downstream of Xist, is the DXPas34 locus, which was first identified as a result of its hypermethylation on the active X chromosome and the correlation of its methylation level with allelism at the X-controlling element (Xce), a locus known to affect choice. In this study, we have tested the potential function of the DXPas34 locus in Xist regulation and X-inactivation initiation by deleting it in the context of large Xist-containing yeast artificial chromosome transgenes. Deletion of DXPas34 eliminates both Xist expression and antisense transcription present in this region in undifferentiated ES cells. It also leads to nonrandom inactivation of the deleted transgene upon differentiation. DXPas34 thus appears to be a critical regulator of Xist activity and X inactivation. The expression pattern of DXPas34 during early embryonic development, which we report here, further suggests that it could be implicated in the regulation of imprinted Xist expression.
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Affiliation(s)
- E Debrand
- Unité de Génétique Moléculaire Murine, URA CNRS 1947, Institut Pasteur, Paris 75015, France
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14
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Heard E, Mongelard F, Arnaud D, Chureau C, Vourc'h C, Avner P. Human XIST yeast artificial chromosome transgenes show partial X inactivation center function in mouse embryonic stem cells. Proc Natl Acad Sci U S A 1999; 96:6841-6. [PMID: 10359800 PMCID: PMC22003 DOI: 10.1073/pnas.96.12.6841] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Initiation of X chromosome inactivation requires the presence, in cis, of the X inactivation center (XIC). The Xist gene, which lies within the XIC region in both human and mouse and has the unique property of being expressed only from the inactive X chromosome in female somatic cells, is known to be essential for X inactivation based on targeted deletions in the mouse. Although our understanding of the developmental regulation and function of the mouse Xist gene has progressed rapidly, less is known about its human homolog. To address this and to assess the cross-species conservation of X inactivation, a 480-kb yeast artificial chromosome containing the human XIST gene was introduced into mouse embryonic stem (ES) cells. The human XIST transcript was expressed and could coat the mouse autosome from which it was transcribed, indicating that the factors required for cis association are conserved in mouse ES cells. Cis inactivation as a result of human XIST expression was found in only a proportion of differentiated cells, suggesting that the events downstream of XIST RNA coating that culminate in stable inactivation may require species-specific factors. Human XIST RNA appears to coat mouse autosomes in ES cells before in vitro differentiation, in contrast to the behavior of the mouse Xist gene in undifferentiated ES cells, where an unstable transcript and no chromosome coating are found. This may not only reflect important species differences in Xist regulation but also provides evidence that factors implicated in Xist RNA chromosome coating may already be present in undifferentiated ES cells.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, Institut Pasteur, 25 rue du Docteur Roux, F-75724 Paris Cedex 15, France.
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15
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O'Neill LP, Keohane AM, Lavender JS, McCabe V, Heard E, Avner P, Brockdorff N, Turner BM. A developmental switch in H4 acetylation upstream of Xist plays a role in X chromosome inactivation. EMBO J 1999; 18:2897-907. [PMID: 10329635 PMCID: PMC1171370 DOI: 10.1093/emboj/18.10.2897] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have investigated the role of histone acetylation in X chromosome inactivation, focusing on its possible involvement in the regulation of Xist, an essential gene expressed only from the inactive X (Xi). We have identified a region of H4 hyperacetylation extending up to 120 kb upstream from the Xist somatic promoter P1. This domain includes the promoter P0, which gives rise to the unstable Xist transcript in undifferentiated cells. The hyperacetylated domain was not seen in male cells or in female XT67E1 cells, a mutant cell line heterozygous for a partially deleted Xist allele and in which an increased number of cells fail to undergo X inactivation. The hyperacetylation upstream of Xist was lost by day 7 of differentiation, when X inactivation was essentially complete. Wild-type cells differentiated in the presence of the histone deacetylase inhibitor Trichostatin A were prevented from forming a normally inactivated X, as judged by the frequency of underacetylated X chromosomes detected by immunofluorescence microscopy. Mutant XT67E1 cells, lacking hyperacetylation upstream of Xist, were less affected. We propose that (i) hyperacetylation of chromatin upstream of Xist facilitates the promoter switch that leads to stabilization of the Xist transcript and (ii) that the subsequent deacetylation of this region is essential for the further progression of X inactivation.
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Affiliation(s)
- L P O'Neill
- Chromatin and Gene Expression Group, University of Birmingham Medical School, Birmingham B15 2TT, UK
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16
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Heard E. Rapid-fire improvement with short-cycle kaizen. Hosp Mater Manage Q 1999; 20:15-23. [PMID: 10387776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Continuous improvement is an attractive idea, but it is typically more myth than reality. SCK is no myth. It delivers dramatic improvements in traditional measures quickly. SCK accomplishes this via kaizens: rapid, repeated, time-compressed changes for the better in bite-sized chunks of the business.
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Affiliation(s)
- E Heard
- Ed Heard and Associates, Brentwood, TN, USA
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18
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Heard E, Mongelard F, Arnaud D, Avner P. Xist yeast artificial chromosome transgenes function as X-inactivation centers only in multicopy arrays and not as single copies. Mol Cell Biol 1999; 19:3156-66. [PMID: 10082582 PMCID: PMC84109 DOI: 10.1128/mcb.19.4.3156] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
X-chromosome inactivation in female mammals is controlled by the X-inactivation center (Xic). This locus is required for inactivation in cis and is thought to be involved in the counting process which ensures that only a single X chromosome remains active per diploid cell. The Xist gene maps to the Xic region and has been shown to be essential for inactivation in cis. Transgenesis represents a stringent test for defining the minimal region that can carry out the functions attributed to the Xic. Although YAC and cosmid Xist-containing transgenes have previously been reported to be capable of cis inactivation and counting, the transgenes were all present as multicopy arrays and it was unclear to what extent individual copies are functional. Using two different yeast artificial chromosomes (YACs), we have found that single-copy transgenes, unlike multicopy arrays, can induce neither inactivation in cis nor counting. These results demonstrate that despite their large size and the presence of Xist, the YACs that we have tested lack sequences critical for autonomous function with respect to X inactivation.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, CNRS URA 1968, Institut Pasteur, F-75724 Paris Cedex 15, France.
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19
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Abstract
The murine Xce locus, first identified by Bruce Cattanach, influences the primary choice of the X chromosome to be inactivated. Methylation of a GC-rich region (DXPas34) that includes multiple 34 bp repeats and lies some 15 kb 3' to Xist has been shown to vary with Xce haplotype. The degree of methylation on the active X chromosome at this locus represents one of the few molecular correlates of Xce action currently available. Data relating to the specificity and other characteristics of this association are presented.
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Affiliation(s)
- P Avner
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France.
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20
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Debrand E, Heard E, Avner P. Cloning and localization of the murine Xpct gene: evidence for complex rearrangements during the evolution of the region around the Xist gene. Genomics 1998; 48:296-303. [PMID: 9545634 DOI: 10.1006/geno.1997.5173] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The overall organization of the X-inactivation center (XIC/Xic) candidate region seems poorly conserved between human and mouse. The orientation of a region containing the X-inactive-specific transcript (Xist/ XIST) gene and three genes located 3' of Xist/XIST has been shown to be inverted between the two species, although the actual extent of this rearrangement is unknown. We have cloned and mapped the mouse homolog of the human XPCT (X-linked PEST-containing transporter) gene, which encodes a putative transmembrane transporter. Human XPCT is located about 200 kb outside of the XIC candidate region and 600 kb 5' of or telomeric to the XIST gene. The mouse Xpct gene, which lies approximately 300 kb 5' of and centromeric to Xist, displays 85% identity at the nucleotide level with the human gene, and the overall protein structure is conserved. The transcriptional orientation of mouse Xpct with respect to Xist is the opposite of that in human. Consequently, the evolution of the region between human and mouse appears to be highly complex, with structural rearrangements involving a region of up to 600 kb or more around the Xist gene.
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Affiliation(s)
- E Debrand
- Unité de Génétique Moléculaire Murine, CNRS URA 1968, Institut Pasteur, Paris, France.
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21
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Abstract
The inactive X chromosome differs from the active X in a number of ways; some of these, such as allocyclic replication and altered histone acetylation, are associated with all types of epigenetic silencing, whereas others, such as DNA methylation, are of more restricted use. These features are acquired progressively by the inactive X after onset of initiation. Initiation of X-inactivation is controlled by the X-inactivation center (Xic) and influenced by the X chromosome controlling element (Xce), which causes primary nonrandom X-inactivation. Other examples of nonrandom X-inactivation are also presented in this review. The definition of a major role for Xist, a noncoding RNA, in X-inactivation has enabled investigation of the mechanism leading to establishment of the heterochromatinized X-chromosome and also of the interactions between X-inactivation and imprinting as well as between X-inactivation and developmental processes in the early embryo.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, URA CNRS 1968, Institut Pasteur, Paris, France.
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22
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Simmler MC, Heard E, Rougeulle C, Cruaud C, Weissenbach J, Avner P. Localization and expression analysis of a novel conserved brain expressed transcript, Brx/BRX, lying within the Xic/XIC candidate region. Mamm Genome 1997; 8:760-6. [PMID: 9321471 DOI: 10.1007/s003359900561] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The X inactivation center candidate region (Xic/XIC in mouse and human) is poorly characterized for the presence of transcription units. Only two conserved genes have been isolated to date, Xist/XIST and Cdx4/CDX4. The other known gene lying within this region, Tsx, has been identified so far only in rodents by analyzing the complete genomic sequence of a 94-kb region distal to Xist. Here, we report the characterization of an additional gene lying within this 94-kb sequenced region. Brx, for Brain X-linked gene, is a rare transcript preferentially expressed in the brain. It is normally X-inactivated in the mouse. Localisation of BRX, its human homolog has shown the gene to be located within the orthologous but inverted human CDX4-XIST segment. These results suggest that the gene order of the region encompassing the Cdx4-Xist interval in the mouse is similar in human. Comparison of the Xist-Brx and Brx-Cdx4 regions in mouse and human indicates that these intervals are three times longer in human than in mouse. BRX is a new potential candidate for one of the X-linked mental retardation syndromes mapped within the pericentromeric region of the human X Chromosome (Chr).
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Affiliation(s)
- M C Simmler
- CNRS UA 1968, Génétique Moléculaire Murine, Institut Pasteur, Paris, France
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23
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Heard E, Kress C, Mongelard F, Courtier B, Rougeulle C, Ashworth A, Vourc'h C, Babinet C, Avner P. Transgenic mice carrying an Xist-containing YAC. Hum Mol Genet 1996; 5:441-50. [PMID: 8845836 DOI: 10.1093/hmg/5.4.441] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The initiation of X-chromosome inactivation in female mammals is controlled by a key locus, the X-inactivation centre (Xic). The Xist gene, which maps to the candidate region for Xic and is expressed exclusively from the inactive X chromosome, is thought to be an essential component of the Xic. To test whether sequences spanning several hundred kilobases and including Xist from the Xic region are capable of initiating inactivation, we have created a series of transgenic mice using a 460 kb yeast artificial chromosome (YAC). Analysis in these mice of the expression of Xist, of a LacZ reporter gene and of two genes in the region that are normally silent on the inactive X chromosome, suggests that essential sequences for Xist expression and X-inactivation may be absent in these transgenic animals.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France
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24
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Fairhead C, Heard E, Arnaud D, Avner P, Dujon B. Insertion of unique sites into YAC arms for rapid physical analysis following YAC transfer into mammalian cells. Nucleic Acids Res 1995; 23:4011-2. [PMID: 7479056 PMCID: PMC307330 DOI: 10.1093/nar/23.19.4011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- C Fairhead
- Unité de Génétique Moléculaire des Levures, CNRS URA 1149, Paris, France
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25
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Abstract
During early mammalian embryogenesis, one of the two X chromosomes in somatic cells of the female becomes inactivated through a process that is thought to depend on a unique initiator region, the X-chromosome inactivation center (Xic). The recently characterized Xist sequence (X-inactive-specific transcript) is thought to be a possible candidate for Xic. In mice a further genetic element, the X chromosome-controlling element (Xce), is also known to influence the choice of which of the two X chromosomes is inactivated. We report that a region of the mouse X chromosome lying 15 kb distal to Xist contains several sites that show hypermethylation specifically associated with the active X chromosome. Analysis of this region in various Xce strains has revealed a correlation between the strength of the Xce allele carried and the methylation status of this region. We propose that such a region could be involved in the initial stages of the inactivation process and in particular in the choice of which of the two X chromosomes present in a female cell will be inactivated.
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Affiliation(s)
- B Courtier
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France
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26
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Abstract
Initiation of X-inactivation is known to depend on the presence of a unique region or locus known as the X-inactivation center, or Xic, defined by the study of chromosomal rearrangements. Its mode of action is currently unknown but is the scene of much research effort. This review explores the recent literature concerning the definition of Xic and its relationship both to Xist and to another genetic entity thought to play a role in the initiation of X-inactivation, the X-controlling element, or Xce.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France
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27
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Abstract
Two mouse YACs, PA-2 and PA-3, contain the Xist gene and are 460 kb and 3.3 Mb long respectively. While PA-2 is non-chimeric, PA-3 contains a substantial proportion of non-contiguous DNA. As a prerequisite to functional studies of the role of this region in X inactivation, we have created a deletion series of YACs that are spaced at approximately 50 kb intervals and were able to eliminate the unwanted chimeric sequences in YAC PA-3. For this purpose, we have constructed mouse B1 fragmentation vectors based on those described for human Alu fragmentation. Having created this series of YAC deletion derivatives, we were able to eliminate efficiently the 10-15% aberrant YACs that arise during the course of a fragmentation experiment by assessing their marker content. The overlap and the opposite orientation of the two YAC inserts permitted the creation of deletions on both sides of the 500 kb region around Xist. The use of this series of YACs in a biological assay will help us define the extent of the sequences necessary to bring about X chromosome inactivation.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, CNRS URA 1445, Institut Pasteur, Paris, France
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Heard E, Simmler MC, Larin Z, Rougeulle C, Courtier B, Lehrach H, Avner P. Physical mapping and YAC contig analysis of the region surrounding Xist on the mouse X chromosome. Genomics 1993; 15:559-69. [PMID: 8468050 DOI: 10.1006/geno.1993.1108] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The Xist sequence has been proposed as a potential candidate for the X-inactivation center based both on its localization within the candidate region for the X-inactivation center in man and mouse and on its unique pattern of expression from the inactive X chromosome. We have cloned 550 kb of DNA surrounding the mouse Xist sequence in contiguously overlapping YAC clones and have developed a long-range restriction map that spans almost 1 Mb of this region and includes this YAC contig. The detailed restriction map we have established provides a framework for the identification of expressed sequences other than Xist that may equally exhibit unusual expression characteristics associated with X inactivation. The presence of possible structural or methylation differences within this region between the active and inactive X chromosomes has been investigated through comparative analysis of male and female genomic DNA, and we report here the identification of certain CpG-containing restriction sites around Xist that have an interesting differential methylation status on the inactive and active X chromosomes.
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Affiliation(s)
- E Heard
- Unité de Génétique Moléculaire Murine, Institut Pasteur, Paris, France
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29
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Abstract
In the polyoma virus (Py) transformed 3B rat cell line the Py oncogene and adjacent cellular DNA are amplified in arrays of very large inverted duplications. A region of the 3B amplified DNA was cloned as a 550 kb insert in a Yeast Artificial Chromosome (YAC) vector, designated y3B01. Analysis of the y3B01 cloned insert revealed it contained a large inverted duplicated DNA region which was approximately 400 kb in size (two palindromic arms of about 200 kb). At least 420 kb of the 550 kb YAC insert has been identified as being derived from the 3B amplified DNA and the amplicon in 3B cells is at least 220 kb in size. No DNA instability of the y3B01 YAC clone was detected. The y3B01 DNA replicated as efficiently as yeast chromosomes and was structurally stable in yeast cells during more than 30 cell divisions. Comparison of the restriction endonuclease maps of the inverted duplicated region of the y3B01 DNA insert and the amplified 3B genomic DNA did not reveal any gross differences suggesting that no rearrangements had occurred during or after the cloning into the YAC vector. These results suggest that large inverted duplications, which can show instability in prokaryotic cloning systems, can be stably cloned and maintained in YAC vectors in yeast.
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Affiliation(s)
- Y Hayashi
- Eukaryotic Gene Organization, Imperial Cancer Research Fund, London, UK
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30
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Affiliation(s)
- M Fried
- Eukaryotic Gene Organization and Expression Laboratory, Imperial Cancer Research Fund, London, U.K
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31
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Heard E, Williams SV, Sheer D, Fried M. Gene amplification accompanied by the loss of a chromosome containing the native allele and the appearance of the amplified DNA at a new chromosomal location. Proc Natl Acad Sci U S A 1991; 88:8242-6. [PMID: 1654562 PMCID: PMC52483 DOI: 10.1073/pnas.88.18.8242] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The organization of amplified DNA in mammalian cells in the form of inverted repeats rather than tandem repeats was first observed and studied in the 3B rat cell line. The structure and chromosomal location of the amplified inverted duplications in this cell line have been further analyzed by cloning, long-range mapping, and fluorescence in situ hybridization. The amplification unit is at least 450 kilobases in size and all of the amplicons are located in a single chromosomal location of approximately 10 or 11 megabases. No heterogeneity in either size or molecular structure is detected between the 3B amplicons, indicating that the 20- to 40-fold amplification occurred in a single event and not through a series of events, which would result in heterogeneity among the amplicons. Thus the amplification in 3B cells may reflect more closely the situation seen in tumors containing amplified oncogenes/protooncogenes than the amplifications present in cell lines after multiple selections with cytotoxic drugs. The progenitor Rat-2 cell line contains three alleles of the region of DNA that is amplified in 3B cells; two are located on the two normal homologues of rat chromosome 2 and the third is at the equivalent position on a marker chromosome, der(3)t(2;3). 3B cells contain only one of the two normal homologues of chromosome 2 in addition to chromosome der(3)t(2;3). All of the amplified DNA is located on a new marker chromosome, M2, whose amplified DNA region does not resemble chromosome 2. These results are consistent with the amplification model proposed by Passananti et al. [Passananti, C., Davies, B., Ford, M. & Fried, M. (1987) EMBO J. 6, 1697-1703], in which the excision from a chromosome of the DNA to be amplified results in the loss of rearrangement of that chromosome. In this model the excised DNA can be amplified extrachromosomally during a single S phase before becoming stabilized by integration into a chromosome, probably at a different location to that of its unamplified allele.
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Affiliation(s)
- E Heard
- Eukaryotic Gene Organization and Expression Laboratory, Imperial Cancer Research Fund, London, United Kingdom
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32
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Heard E, Fried M. The use of 5-azacytidine to increase cleavage of methylation sensitive rare cutting restriction enzymes sites in amplified DNA. Nucleic Acids Res 1990; 18:6147-8. [PMID: 1700369 PMCID: PMC332436 DOI: 10.1093/nar/18.20.6147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- E Heard
- Department of Eukaryotic Gene Organization and Expression, Imperial Cancer Research Fund, London, UK
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33
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Davies B, Feo S, Heard E, Fried M. A strategy to detect and isolate an intron-containing gene in the presence of multiple processed pseudogenes. Proc Natl Acad Sci U S A 1989; 86:6691-5. [PMID: 2771953 PMCID: PMC297911 DOI: 10.1073/pnas.86.17.6691] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We have devised a strategy that utilizes the polymerase chain reaction (PCR) for the detection and isolation of intron-containing genes in the presence of an abundance of processed pseudogenes. The method depends on the genomic DNA sequence between the PCR primers spanning at least one intron in the gene of interest, resulting in the generation of a larger intron-containing PCR product in addition to the smaller PCR product amplified from the intronless pseudogenes. A unique intron probe isolated from the larger PCR product is used for the detection of intron-containing clones from recombinant DNA libraries that also contain pseudogene clones. This method has been used successfully for the selective isolation of an intron-containing rat L19 ribosomal protein gene in the presence of multiple pseudogenes. Analysis of a number of mammalian ribosomal protein multigene families by PCR indicates that they all contain only a single gene with introns.
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Affiliation(s)
- B Davies
- Department of Eukaryotic Genome Organization and Expression, Imperial Cancer Research Fund, London, United Kingdom
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34
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Affiliation(s)
- E Heard
- Eukaryotic Gene Organisation and Expression Laboratory, Imperial Cancer Research Fund, London, UK
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35
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Abstract
Hemodialysis and related methods of treatment are keeping renal patients alive and able to carry on many of their daily activities. These patients, however, are limited in the scope within which they can function. Dietary requirements, fluid intake, and most medications must be rigidly controlled. Many commonly used drugs can damage the kidneys and must be avoided. Dentists who treat patients with renal insufficiency must avoid prescribing or administering nephrotoxic drugs or agents that become dangerous with loss of kidney function.
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