The Experts below are selected from a list of 2019 Experts worldwide ranked by ideXlab platform
Huntington F Willard - One of the best experts on this subject based on the ideXlab platform.
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chromatin of the Barr Body histone and non histone proteins associated with or excluded from the inactive x chromosome
Human Molecular Genetics, 2003Co-Authors: Brian P Chadwick, Huntington F WillardAbstract:The Barr Body has long been recognized as the cytological manifestation of the inactive X chromosome (Xi) in interphase nuclei. Despite being known for over 50 years, relatively few components of the Barr Body have been identified. In this study, we have screened over 30 histone variants, modified histones and non-histone proteins for their association with or exclusion from the Barr Body. We demonstrate that, similar to the histone variant macroH2A, heterochromatin protein-1 (HP1), histone H1 and the high mobility group protein HMG-I/Y are elevated at the territory of the Xi in interphase in human cell lines, but only when the Xi chromatin is heteropycnotic, implicating each as a component of the Barr Body. Surprisingly, however, virtually all other candidate proteins involved in establishing heterochromatin and gene silencing are notably absent from the Barr Body despite being localized generally elsewhere throughout the nucleus, indicating that the Barr Body represents a discrete subnuclear compartment that is not freely accessible to most chromatin proteins. A similar dichotomous pattern of association or exclusion describes the spatial relationship of a number of specific histone methylation patterns in relation to the Barr Body. Notably, though, several methylated forms of histone H3 that are deficient in Xi chromatin generally are present at a region near the macrosatellite repeat DXZ4, as are the chromatin proteins CTCF and SAP30, indicating a distinctive chromatin state in this region of the Xi. Taken together, our data imply that the Xi adopts a distinct chromatin configuration in interphase nuclei and are consistent with a mechanism by which HP1, through histone H3 lysine-9 methylation, recognizes and assists in maintaining heterochromatin and gene silencing at the human Xi.
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chromatin of the Barr Body histone and non histone proteins associated with or excluded from the inactive x chromosome
Human Molecular Genetics, 2003Co-Authors: Brian P Chadwick, Huntington F WillardAbstract:The Barr Body has long been recognized as the cytological manifestation of the inactive X chromosome (Xi)in interphase nuclei. Despite being known for over 50 years, relatively few components of the Barr Body havebeen identified. In this study, we have screened over 30 histone variants, modified histones and non-histoneproteins for their association with or exclusion from the Barr Body. We demonstrate that, similar to thehistone variant macroH2A, heterochromatin protein-1 (HP1), histone H1 and the high mobility group proteinHMG-I/Y are elevated at the territory of the Xi in interphase in human cell lines, but only when the Xi chromatinis heteropycnotic, implicating each as a component of the Barr Body. Surprisingly, however, virtually all othercandidate proteins involved in establishing heterochromatin and gene silencing are notably absent from theBarr Body despite being localized generally elsewhere throughout the nucleus, indicating that the Barr Bodyrepresents a discrete subnuclear compartment that is not freely accessible to most chromatin proteins. Asimilar dichotomous pattern of association or exclusion describes the spatial relationship of a number ofspecific histone methylation patterns in relation to the Barr Body. Notably, though, several methylated formsof histone H3 that are deficient in Xi chromatin generally are present at a region near the macrosatellite repeatDXZ4, as are the chromatin proteins CTCF and SAP30, indicating a distinctive chromatin state in this regionof the Xi. Taken together, our data imply that the Xi adopts a distinct chromatin configuration in interphasenuclei and are consistent with a mechanism by which HP1, through histone H3 lysine-9 methylation,recognizes and assists in maintaining heterochromatin and gene silencing at the human Xi.INTRODUCTIONEarly in mammalian development, X-inactivation transcrip-tionally silences all but one X chromosome per cell in order toequalize the levels of X-linked gene expression between thesexes (1). The Barr Body has long been recognized as thecytological manifestation of the inactive X chromosome (Xi)in interphase nuclei (2). However, what accounts for theformation of a Barr Body is uncertain, as one is visible in only asubset of female cells (3) and as it is not a feature of the Xi inmouse cultured cells (4). Since its discovery over 50 yearsago (2), the constituents of the Barr Body remain largelyunknown.A critical component of the X-inactivation process is a largenon-coding but functional RNA, the Xi-specific transcript(XIST), that is expressed from and associates in cis with the Xias part of the Barr Body (5,6). Other features of the Xi and ofthe Barr Body include enrichment for the H2A variantmacroH2A (7–9) and several general characteristics ofconstitutive heterochromatin such as DNA methylation(10,11) and replication in late S-phase (12,13).Notably, chromatin of the Xi is marked by a distinctiveconfiguration of histone modifications. Certain amino acidresidues within the tail regions of core histones have thepotential of acquiring a range of covalent modifications,including acetylation, methylation and phosphorylation (14).A specific combination of modifications confers a particularproperty to the local chromatin, referred to as the ‘histonecode’ (15). Histone tails of the Xi are hypoacetylated (16–19),and histone H3 is both hypomethylated at lysine-4 (20) andhypermethylated at lysine residues 9 (20,21) and 27 (22,23).How the histone code at the Xi determines or influences
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histone h2a variants and the inactive x chromosome identification of a second macroh2a variant
Human Molecular Genetics, 2001Co-Authors: Brian P Chadwick, Huntington F WillardAbstract:MacroH2A1 is an unusual variant of the core histone H2A which is enriched in chromatin on the inactive X chromosome of female mammals. The N-terminal third of the protein shares 65% amino acid identity with core histone H2A, while the remaining two-thirds of the protein are novel, with a small stretch of basic amino acids and a putative leucine zipper motif. We have now cloned a second macroH2A gene, encoding macroH2A2 which shares 80% amino acid identity with macroH2A1. Despite mapping to different chromosomes, the genomic organization of the macroH2A2 and macroH2A1 genes are nearly identical. The leucine zipper motif of macroH2A1 is not conserved in macroH2A2. Like macroH2A1, macroH2A2 forms a Macro Chromatin Body in the nuclei of female cells which is coincident with an X chromosome and co-localizes with macroH2A1. To address the distribution of other histone H2A variants in relation to macroH2A and the inactive X chromosome, we constructed a series of epitope-tagged versions of other histone H2A variants. Like the recently described H2A-Bbd (Barr Body-deficient) variant, the histone variant H2A.Z was found to be deficient in chromatin on the inactive X chromosome in a significant proportion of female nuclei. This study provides further information about the nucleosomal composition of chromatin on the inactive X chromosome and indicates that a number of H2A variants are non-randomly distributed on the active and inactive X chromosomes.
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xist rna paints the inactive x chromosome at interphase evidence for a novel rna involved in nuclear chromosome structure
Journal of Cell Biology, 1996Co-Authors: Christine Moulton Clemson, Huntington F Willard, John Mcneil, Jeanne B LawrenceAbstract:The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr Body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.
Jeanne B Lawrence - One of the best experts on this subject based on the ideXlab platform.
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heterochromatin instability in cancer from the Barr Body to satellites and the nuclear periphery
Seminars in Cancer Biology, 2013Co-Authors: Dawn M Carone, Jeanne B LawrenceAbstract:In recent years it has been recognized that the development of cancer involves a series of not only genetic but epigenetic changes across the genome. At the same time, connections between epigenetic regulation, chromatin packaging, and overall nuclear architecture are increasingly appreciated. The cell-type specific organization of heterochromatin, established upon cell differentiation, is responsible for maintaining much of the genome in a repressed state, within a highly compartmentalized nucleus. This review focuses on recent evidence that in cancer the normal packaging and higher organization of heterochromatin is often compromised. Gross changes in nuclear morphology have long been a criterion for pathologic diagnosis of many cancers, but the specific nuclear components impacted, the mechanisms involved, and the implications for cancer progression have barely begun to emerge. We discuss recent findings regarding distinct heterochromatin types, including the inactive X chromosome, constitutive heterochromatin of peri/centric satellites, and the peripheral heterochromatic compartment (PHC). A theme developed here is that the higher-order organization of satellites and the peripheral heterochromatic compartment may be tightly linked, and that compromise of this organization may promote broad epigenomic imbalance in cancer. Recent studies into the potential role(s) of the breast cancer tumor suppressor, BRCA1, in maintaining heterochromatin will be highlighted. Many questions remain about this new area of cancer epigenetics, which is likely more important in cancer development and progression than widely appreciated. We propose that broad, stochastic compromise in heterochromatin maintenance would create a diversity of expression profiles, and thus a rich opportunity for one or more cells to emerge with a selective growth advantage and potential for neoplasia.
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the disappearing Barr Body in breast and ovarian cancers
Nature Reviews Cancer, 2007Co-Authors: Gayle Jeannette Pageau, Lisa L Hall, Shridar Ganesan, David M Livingston, Jeanne B LawrenceAbstract:Interest has recently reawakened in whether loss of the heterochromatic X chromosome (Barr Body) is prevalent in certain breast and ovarian cancers, and new insights into the mechanisms involved have emerged. Mitotic segregation errors commonly explain the loss of the inactive X chromosome (Xi), but compromise of Xi heterochromatin in some cancers may signal broader deficits of nuclear heterochromatin. The debated link between BRCA1 and Xi might reflect a general relationship between BRCA1 and heterochromatin, which could connect BRCA1 to both epigenetic and genetic instability. We suggest that heterochromatic instability is a common but largely unexplored mechanism, leading to widespread genomic misregulation and the evolution of some cancers.
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xist rna paints the inactive x chromosome at interphase evidence for a novel rna involved in nuclear chromosome structure
Journal of Cell Biology, 1996Co-Authors: Christine Moulton Clemson, Huntington F Willard, John Mcneil, Jeanne B LawrenceAbstract:The XIST gene is implicated in X chromosome inactivation, yet the RNA contains no apparent open reading frame. An accumulation of XIST RNA is observed near its site of transcription, the inactive X chromosome (Xi). A series of molecular cytogenetic studies comparing properties of XIST RNA to other protein coding RNAs, support a critical distinction for XIST RNA; XIST does not concentrate at Xi simply because it is transcribed and processed there. Most notably, morphometric and 3-D analysis reveals that XIST RNA and Xi are coincident in 2- and 3-D space; hence, the XIST RNA essentially paints Xi. Several results indicate that the XIST RNA accumulation has two components, a minor one associated with transcription and processing, and a spliced major component, which stably associates with Xi. Upon transcriptional inhibition the major spliced component remains in the nucleus and often encircles the extra-prominent heterochromatic Barr Body. The continually transcribed XIST gene and its polyadenylated RNA consistently localize to a nuclear region devoid of splicing factor/poly A RNA rich domains. XIST RNA remains with the nuclear matrix fraction after removal of chromosomal DNA. XIST RNA is released from its association with Xi during mitosis, but shows a unique highly particulate distribution. Collective results indicate that XIST RNA may be an architectural element of the interphase chromosome territory, possibly a component of nonchromatin nuclear structure that specifically associates with Xi. XIST RNA is a novel nuclear RNA which potentially provides a specific precedent for RNA involvement in nuclear structure and cis-limited gene regulation via higher-order chromatin packaging.
Brian P Chadwick - One of the best experts on this subject based on the ideXlab platform.
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chromatin of the Barr Body histone and non histone proteins associated with or excluded from the inactive x chromosome
Human Molecular Genetics, 2003Co-Authors: Brian P Chadwick, Huntington F WillardAbstract:The Barr Body has long been recognized as the cytological manifestation of the inactive X chromosome (Xi) in interphase nuclei. Despite being known for over 50 years, relatively few components of the Barr Body have been identified. In this study, we have screened over 30 histone variants, modified histones and non-histone proteins for their association with or exclusion from the Barr Body. We demonstrate that, similar to the histone variant macroH2A, heterochromatin protein-1 (HP1), histone H1 and the high mobility group protein HMG-I/Y are elevated at the territory of the Xi in interphase in human cell lines, but only when the Xi chromatin is heteropycnotic, implicating each as a component of the Barr Body. Surprisingly, however, virtually all other candidate proteins involved in establishing heterochromatin and gene silencing are notably absent from the Barr Body despite being localized generally elsewhere throughout the nucleus, indicating that the Barr Body represents a discrete subnuclear compartment that is not freely accessible to most chromatin proteins. A similar dichotomous pattern of association or exclusion describes the spatial relationship of a number of specific histone methylation patterns in relation to the Barr Body. Notably, though, several methylated forms of histone H3 that are deficient in Xi chromatin generally are present at a region near the macrosatellite repeat DXZ4, as are the chromatin proteins CTCF and SAP30, indicating a distinctive chromatin state in this region of the Xi. Taken together, our data imply that the Xi adopts a distinct chromatin configuration in interphase nuclei and are consistent with a mechanism by which HP1, through histone H3 lysine-9 methylation, recognizes and assists in maintaining heterochromatin and gene silencing at the human Xi.
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chromatin of the Barr Body histone and non histone proteins associated with or excluded from the inactive x chromosome
Human Molecular Genetics, 2003Co-Authors: Brian P Chadwick, Huntington F WillardAbstract:The Barr Body has long been recognized as the cytological manifestation of the inactive X chromosome (Xi)in interphase nuclei. Despite being known for over 50 years, relatively few components of the Barr Body havebeen identified. In this study, we have screened over 30 histone variants, modified histones and non-histoneproteins for their association with or exclusion from the Barr Body. We demonstrate that, similar to thehistone variant macroH2A, heterochromatin protein-1 (HP1), histone H1 and the high mobility group proteinHMG-I/Y are elevated at the territory of the Xi in interphase in human cell lines, but only when the Xi chromatinis heteropycnotic, implicating each as a component of the Barr Body. Surprisingly, however, virtually all othercandidate proteins involved in establishing heterochromatin and gene silencing are notably absent from theBarr Body despite being localized generally elsewhere throughout the nucleus, indicating that the Barr Bodyrepresents a discrete subnuclear compartment that is not freely accessible to most chromatin proteins. Asimilar dichotomous pattern of association or exclusion describes the spatial relationship of a number ofspecific histone methylation patterns in relation to the Barr Body. Notably, though, several methylated formsof histone H3 that are deficient in Xi chromatin generally are present at a region near the macrosatellite repeatDXZ4, as are the chromatin proteins CTCF and SAP30, indicating a distinctive chromatin state in this regionof the Xi. Taken together, our data imply that the Xi adopts a distinct chromatin configuration in interphasenuclei and are consistent with a mechanism by which HP1, through histone H3 lysine-9 methylation,recognizes and assists in maintaining heterochromatin and gene silencing at the human Xi.INTRODUCTIONEarly in mammalian development, X-inactivation transcrip-tionally silences all but one X chromosome per cell in order toequalize the levels of X-linked gene expression between thesexes (1). The Barr Body has long been recognized as thecytological manifestation of the inactive X chromosome (Xi)in interphase nuclei (2). However, what accounts for theformation of a Barr Body is uncertain, as one is visible in only asubset of female cells (3) and as it is not a feature of the Xi inmouse cultured cells (4). Since its discovery over 50 yearsago (2), the constituents of the Barr Body remain largelyunknown.A critical component of the X-inactivation process is a largenon-coding but functional RNA, the Xi-specific transcript(XIST), that is expressed from and associates in cis with the Xias part of the Barr Body (5,6). Other features of the Xi and ofthe Barr Body include enrichment for the H2A variantmacroH2A (7–9) and several general characteristics ofconstitutive heterochromatin such as DNA methylation(10,11) and replication in late S-phase (12,13).Notably, chromatin of the Xi is marked by a distinctiveconfiguration of histone modifications. Certain amino acidresidues within the tail regions of core histones have thepotential of acquiring a range of covalent modifications,including acetylation, methylation and phosphorylation (14).A specific combination of modifications confers a particularproperty to the local chromatin, referred to as the ‘histonecode’ (15). Histone tails of the Xi are hypoacetylated (16–19),and histone H3 is both hypomethylated at lysine-4 (20) andhypermethylated at lysine residues 9 (20,21) and 27 (22,23).How the histone code at the Xi determines or influences
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histone h2a variants and the inactive x chromosome identification of a second macroh2a variant
Human Molecular Genetics, 2001Co-Authors: Brian P Chadwick, Huntington F WillardAbstract:MacroH2A1 is an unusual variant of the core histone H2A which is enriched in chromatin on the inactive X chromosome of female mammals. The N-terminal third of the protein shares 65% amino acid identity with core histone H2A, while the remaining two-thirds of the protein are novel, with a small stretch of basic amino acids and a putative leucine zipper motif. We have now cloned a second macroH2A gene, encoding macroH2A2 which shares 80% amino acid identity with macroH2A1. Despite mapping to different chromosomes, the genomic organization of the macroH2A2 and macroH2A1 genes are nearly identical. The leucine zipper motif of macroH2A1 is not conserved in macroH2A2. Like macroH2A1, macroH2A2 forms a Macro Chromatin Body in the nuclei of female cells which is coincident with an X chromosome and co-localizes with macroH2A1. To address the distribution of other histone H2A variants in relation to macroH2A and the inactive X chromosome, we constructed a series of epitope-tagged versions of other histone H2A variants. Like the recently described H2A-Bbd (Barr Body-deficient) variant, the histone variant H2A.Z was found to be deficient in chromatin on the inactive X chromosome in a significant proportion of female nuclei. This study provides further information about the nucleosomal composition of chromatin on the inactive X chromosome and indicates that a number of H2A variants are non-randomly distributed on the active and inactive X chromosomes.
Saadi Khochbin - One of the best experts on this subject based on the ideXlab platform.
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higher concentrations of histone macroh2a in the Barr Body are correlated with higher nucleosome density
Current Biology, 2000Co-Authors: Pierreyves Perche, Claire Vourch, Lara Konecny, Catherine Souchier, Michel Robertnicoud, Stefan Dimitrov, Saadi KhochbinAbstract:Histone macroH2A, which is a subtype of histone H2A, possesses a histone H2A-like portion fused to a relatively long non-histone portion. MacroH2A has been shown to associate preferentially with the inactive X chromosome [1]. To investigate the specificity of this association, the nuclear distribution of macroH2A was compared with that of regular core histones. In normal human female fibroblasts, all anti-histone antibodies that were tested (including anti-macroH2A antiBody) preferentially labeled the inactive X chromosome. Moreover, when expressed as green fluorescent protein (GFP) fusions, both histone H2A and macroH2A were concentrated in the Barr Body. These data clearly show the presence of a higher density of nucleosomes in the inactive X chromosome. Accordingly, the specificity of the macroH2A association with the inactive X chromosome should be reconsidered. While investigating the role of macroH2A, we found that the proximity of the non-histone region of macroH2A to a promoter could lead to a specific repression of transcription, suggesting that the incorporation of macroH2A into chromatin might help to establish the stable pattern of gene expression in differentiated cells.
Michel Robertnicoud - One of the best experts on this subject based on the ideXlab platform.
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higher concentrations of histone macroh2a in the Barr Body are correlated with higher nucleosome density
Current Biology, 2000Co-Authors: Pierreyves Perche, Claire Vourch, Lara Konecny, Catherine Souchier, Michel Robertnicoud, Stefan Dimitrov, Saadi KhochbinAbstract:Histone macroH2A, which is a subtype of histone H2A, possesses a histone H2A-like portion fused to a relatively long non-histone portion. MacroH2A has been shown to associate preferentially with the inactive X chromosome [1]. To investigate the specificity of this association, the nuclear distribution of macroH2A was compared with that of regular core histones. In normal human female fibroblasts, all anti-histone antibodies that were tested (including anti-macroH2A antiBody) preferentially labeled the inactive X chromosome. Moreover, when expressed as green fluorescent protein (GFP) fusions, both histone H2A and macroH2A were concentrated in the Barr Body. These data clearly show the presence of a higher density of nucleosomes in the inactive X chromosome. Accordingly, the specificity of the macroH2A association with the inactive X chromosome should be reconsidered. While investigating the role of macroH2A, we found that the proximity of the non-histone region of macroH2A to a promoter could lead to a specific repression of transcription, suggesting that the incorporation of macroH2A into chromatin might help to establish the stable pattern of gene expression in differentiated cells.
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three dimensional reconstruction of painted human interphase chromosomes active and inactive x chromosome territories have similar volumes but differ in shape and surface structure
Journal of Cell Biology, 1996Co-Authors: Roland Eils, Michel Robertnicoud, Steffen Dietzel, Etienne Bertin, Evelin Schrock, Michael R Speicher, Thomas Ried, Christoph Cremer, Thomas CremerAbstract:This study provides a three-dimensional (3D) analysis of differences between the 3D morphology of active and inactive human X interphase chromosomes (Xa and Xi territories). Chromosome territories were painted in formaldehyde-fixed, three-dimensionally intact human diploid female amniotic fluid cell nuclei (46, XX) with X-specific whole chromosome compositive probes. The colocalization of a 4,6-diamidino-2-phenylindole dihydrochloride-stained Barr Body with one of the two painted X territories allowed the unequivocal discrimination of the inactive X from its active counterpart. Light optical serial sections were obtained with a confocal laser scanning microscope. 3D-reconstructed Xa territories revealed a flatter shape and exhibited a larger and more irregular surface when compared to the apparently smoother surface and rounder shape of Xi territories. The relationship between territory surface and volume was quantified by the determination of a dimensionless roundness factor (RF). RF and surface area measurements showed a highly significant difference between Xa and Xi territories (P 0.1). For comparison with an autosome of similar DNA content, chromosome 7 territories were additionally painted. The 3D morphology of the chromosome 7 territories was similar to the Xa territory but differed strongly from the Xi territory with respect to RF and surface area (P < 0.001).