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Abstract
Gene regulation involves long-range communication between silencers, enhancers, and promoters. In Saccharomyces cerevisiae, silencers flank transcriptionally repressed genes to mediate regional silencing. Silencers recruit the Sir proteins, which then spread along chromatin to encompass the entire silenced domain. In this report we have employed a boundary trap assay, an enhancer activity assay, chromatin immunoprecipitations, and chromosome conformation capture analyses to demonstrate that the two HMR silencer elements are in close proximity and functionally communicate with one another in vivo. We further show that silencing is necessary for these long-range interactions, and we present models for Sir-mediated silencing based upon these results.
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303
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Freed WJ, Chen J, Bäckman CM, Schwartz CM, Vazin T, Cai J, Spivak CE, Lupica CR, Rao MS, Zeng X. Gene expression profile of neuronal progenitor cells derived from hESCs: activation of chromosome 11p15.5 and comparison to human dopaminergic neurons. PLoS One 2008; 3:e1422. [PMID: 18183302 PMCID: PMC2170519 DOI: 10.1371/journal.pone.0001422] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2007] [Accepted: 12/09/2007] [Indexed: 01/03/2023] Open
Abstract
Background We initiated differentiation of human embryonic stem cells (hESCs) into dopamine neurons, obtained a purified population of neuronal precursor cells by cell sorting, and determined patterns of gene transcription. Methodology Dopaminergic differentiation of hESCs was initiated by culturing hESCs with a feeder layer of PA6 cells. Differentiating cells were then sorted to obtain a pure population of PSA-NCAM-expressing neuronal precursors, which were then analyzed for gene expression using Massive Parallel Signature Sequencing (MPSS). Individual genes as well as regions of the genome which were activated were determined. Principal Findings A number of genes known to be involved in the specification of dopaminergic neurons, including MSX1, CDKN1C, Pitx1 and Pitx2, as well as several novel genes not previously associated with dopaminergic differentiation, were expressed. Notably, we found that a specific region of the genome located on chromosome 11p15.5 was highly activated. This region contains several genes which have previously been associated with the function of dopaminergic neurons, including the gene for tyrosine hydroxylase (TH), the rate-limiting enzyme in catecholamine biosynthesis, IGF2, and CDKN1C, which cooperates with Nurr1 in directing the differentiation of dopaminergic neurons. Other genes in this region not previously recognized as being involved in the functions of dopaminergic neurons were also activated, including H19, TSSC4, and HBG2. IGF2 and CDKN1C were also found to be highly expressed in mature human TH-positive dopamine neurons isolated from human brain samples by laser capture. Conclusions The present data suggest that the H19-IGF2 imprinting region on chromosome 11p15.5 is involved in the process through which undifferentiated cells are specified to become neuronal precursors and/or dopaminergic neurons.
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Affiliation(s)
- William J Freed
- Cellular Neurobiology Research Branch, Intramural Research Program (IRP), National Institute on Drug Abuse, National Institutes of Health (NIH), Baltimore, Maryland, USA.
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304
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Schneider R, Grosschedl R. Dynamics and interplay of nuclear architecture, genome organization, and gene expression. Genes Dev 2008; 21:3027-43. [PMID: 18056419 DOI: 10.1101/gad.1604607] [Citation(s) in RCA: 314] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression.
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305
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de Laat W, Klous P, Kooren J, Noordermeer D, Palstra RJ, Simonis M, Splinter E, Grosveld F. Three-dimensional organization of gene expression in erythroid cells. Curr Top Dev Biol 2008; 82:117-39. [PMID: 18282519 DOI: 10.1016/s0070-2153(07)00005-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The history of globin research is marked by a series of contributions seminal to our understanding of the genome, its function, and its relation to disease. For example, based on studies on hemoglobinopathies, it was understood that gene expression can be under the control of DNA elements that locate away from the genes on the linear chromosome template. Recent technological developments have allowed the demonstration that these regulatory DNA elements communicate with the genes through physical interaction, which loops out the intervening chromatin fiber. Subsequent studies showed that the spatial organization of the beta-globin locus dynamically changes in relation to differences in gene expression. Moreover, it was shown that the beta-globin locus adopts a different position in the nucleus during development and erythroid maturation. Here, we discuss the most recent insight into the three-dimensional organization of gene expression.
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Affiliation(s)
- Wouter de Laat
- Department of Cell Biology and Genetics, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands
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306
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Tuskan RG, Tsang S, Sun Z, Baer J, Rozenblum E, Wu X, Munroe DJ, Reilly KM. Real-time PCR analysis of candidate imprinted genes on mouse chromosome 11 shows balanced expression from the maternal and paternal chromosomes and strain-specific variation in expression levels. Epigenetics 2007; 3:43-50. [PMID: 18188004 DOI: 10.4161/epi.3.1.5469] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Imprinted genes are monoallelically expressed from either the maternal or paternal genome. Because cancer develops through genetic and epigenetic alterations, imprinted genes affect tumorigenesis depending on which parental allele undergoes alteration. We have shown previously in a mouse model of neurofibromatosis type 1 (NF1) that inheriting mutant alleles of Nf1 and Trp53 on chromosome 11 from the mother or father dramatically changes the tumor spectrum of mutant progeny, likely due to alteration in an imprinted gene(s) linked to Nf1 and Trp53. In order to identify imprinted genes on chromosome 11 that are responsible for differences in susceptibility, we tested candidate imprinted genes predicted by a bioinformatics approach and an experimental approach. We have tested 30 candidate genes (Havcr2, Camk2b, Ccdc85a, Cntnap1, Ikzf1, 5730522E02Rik, Gria1, Zfp39, Sgcd, Jup, Nxph3, Spnb2, Asb3, Rasd1, Map2k3, Map2k4, Trp53, Serpinf1, Crk, Rasl10b, Itga3, Hoxb5, Cbx1, Pparbp, Igfbp4, Smarce1, Stat3, Atp6v0a1, Nbr1 and Meox1), two known imprinted genes (Grb10 and Impact) and Nf1, which has not been previously identified as an imprinted gene. Although we confirmed the imprinting of Grb10 and Impact, we found no other genes imprinted in the brain. We did, however, find strain-biased expression of Camk2b, 5730522E02Rik, Havcr2, Map2k3, Serpinf1, Rasl10b, Itga3, Asb3, Trp53, Nf1, Smarce1, Stat3, Cbx1, Pparbp and Cntnap1. These results suggest that the prediction of imprinted genes is complicated and must be individually validated. This manuscript includes supplementary data listing primer sequences for Taqman assays and Ct values for Taqman PCR.
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Affiliation(s)
- Robert G Tuskan
- Mouse Cancer Genetics Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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307
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Higgs DR, Vernimmen D, Hughes J, Gibbons R. Using genomics to study how chromatin influences gene expression. Annu Rev Genomics Hum Genet 2007; 8:299-325. [PMID: 17506662 DOI: 10.1146/annurev.genom.8.080706.092323] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A postgenome challenge is to understand how the code in DNA is converted into the biological processes underlying various cell fates. By establishing the appropriate technical tools, we are moving from an era in which such questions have been asked by studying individual genes to one in which large domains, whole chromosomes, and the entire human genome can be investigated. These developments will allow us to study in parallel the transcriptional program and components of the epigenetic program (nuclear position, timing of replication, chromatin structure and modification, DNA methylation) to determine the hierarchy and order of events required to switch genes on and off during differentiation and development.
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Affiliation(s)
- Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom.
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308
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Enhanced sensitivity to IGF-II signaling links loss of imprinting of IGF2 to increased cell proliferation and tumor risk. Proc Natl Acad Sci U S A 2007; 104:20926-31. [PMID: 18087038 DOI: 10.1073/pnas.0710359105] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Loss of imprinting (LOI) of the insulin-like growth factor-II gene (IGF2), leading to abnormal activation of the normally silent maternal allele, is a common human epigenetic population variant associated with a 5-fold increased frequency of colorectal neoplasia. Here, we show first that LOI leads specifically to increased expression of proliferation-related genes in mouse intestinal crypts. Surprisingly, LOI(+) mice also have enhanced sensitivity to IGF-II signaling, not simply increased IGF-II levels, because in vivo blockade with NVP-AEW541, a specific inhibitor of the IGF-II signaling receptor, showed reduction of proliferation-related gene expression to levels half that seen in LOI(-) mice. Signal transduction assays in microfluidic chips confirmed this enhanced sensitivity with marked augmentation of Akt/PKB signaling in LOI(+) cells at low doses of IGF-II, which was reduced in the presence of the inhibitor to levels below those found in LOI(-) cells, and was associated with increased expression of the IGF1 and insulin receptor genes. We exploited this increased IGF-II sensitivity to develop an in vivo chemopreventive strategy using the azoxymethane (AOM) mutagenesis model. LOI(+) mice treated with AOM showed a 60% increase in premalignant aberrant crypt foci (ACF) formation over LOI(-) mice. In vivo IGF-II blockade with NVP-AEW541 abrogated this effect, reducing ACF to a level 30% lower even than found in exposed LOI(-) mice. Thus, LOI increases cancer risk in a counterintuitive way, by increasing the sensitivity of the IGF-II signaling pathway itself, providing a previously undescribed epigenetic chemoprevention strategy in which cells with LOI are "IGF-II addicted" and undergo reduced tumorigenesis in the colon upon IGF-II pathway blockade.
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309
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Baudat F, de Massy B. Cis- and trans-acting elements regulate the mouse Psmb9 meiotic recombination hotspot. PLoS Genet 2007; 3:e100. [PMID: 17590084 PMCID: PMC1892046 DOI: 10.1371/journal.pgen.0030100] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 05/04/2007] [Indexed: 01/28/2023] Open
Abstract
In most eukaryotes, the prophase of the first meiotic division is characterized by a high level of homologous recombination between homologous chromosomes. Recombination events are not distributed evenly within the genome, but vary both locally and at large scale. Locally, most recombination events are clustered in short intervals (a few kilobases) called hotspots, separated by large intervening regions with no or very little recombination. Despite the importance of regulating both the frequency and the distribution of recombination events, the genetic factors controlling the activity of the recombination hotspots in mammals are still poorly understood. We previously characterized a recombination hotspot located close to the Psmb9 gene in the mouse major histocompatibility complex by sperm typing, demonstrating that it is a site of recombination initiation. With the goal of uncovering some of the genetic factors controlling the activity of this initiation site, we analyzed this hotspot in both male and female germ lines and compared the level of recombination in different hybrid mice. We show that a haplotype-specific element acts at distance and in trans to activate about 2,000-fold the recombination activity at Psmb9. Another haplotype-specific element acts in cis to repress initiation of recombination, and we propose this control to be due to polymorphisms located within the initiation zone. In addition, we describe subtle variations in the frequency and distribution of recombination events related to strain and sex differences. These findings show that most regulations observed act at the level of initiation and provide the first analysis of the control of the activity of a meiotic recombination hotspot in the mouse genome that reveals the interactions of elements located both in and outside the hotspot. In most sexually reproducing species, during meiosis a high level of recombination between homologous chromosomes is induced. These events are not evenly distributed in the genome but clustered in small regions called hotspots. The genetic factors controlling their activity in mammals are still poorly understood. We have performed experiments to identify factors that influence the recombination activity of a hotspot in the mouse genome. By detecting the recombination products by a PCR-based method, we show that the variation of hotspot activity (up to 2,000-fold) is mainly due to differences of initiation frequencies, rather than differences at later steps of recombination. In addition, we identify several levels of controls. First, the initiation of recombination is activated by a haplotype-specific element, localized outside the hotspot and acting in trans (when heterozygous, this element allows for recombination initiation on both homologous chromosomes). This suggests a unique type of regulation requiring the presence of a diffusible factor and/or of communications between homologous chromosomes before recombination. A second element represses the recombination initiation in cis, which might indicate the influence of local polymorphisms affecting initiation events. Our results provide the first functional analysis of the control of recombination initiation sites for meiotic recombination in mammals.
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Affiliation(s)
- Frédéric Baudat
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
| | - Bernard de Massy
- Institute of Human Genetics, Centre National de la Recherche Scientifique, Unité Propre de Recherche 1142, Montpellier, France
- * To whom correspondence should be addressed. E-mail:
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310
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GATA-1 modulates the chromatin structure and activity of the chicken alpha-globin 3' enhancer. Mol Cell Biol 2007; 28:575-86. [PMID: 17984219 DOI: 10.1128/mcb.00943-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Long-distance regulatory elements and local chromatin structure are critical for proper regulation of gene expression. Here we characterize the chromatin conformation of the chicken alpha-globin silencer-enhancer elements located 3' of the domain. We found a characteristic and erythrocyte-specific structure between the previously defined silencer and the enhancer, defined by two nuclease hypersensitive sites, which appear when the enhancer is active during erythroid differentiation. Fine mapping of these sites demonstrates the absence of a positioned nucleosome and the association of GATA-1. Functional analyses of episomal vectors, as well as stably integrated constructs, revealed that GATA-1 plays a major role in defining both the chromatin structure and the enhancer activity. We detected a progressive enrichment of histone acetylation on critical enhancer nuclear factor binding sites, in correlation with the formation of an apparent nucleosome-free region. On the basis of these results, we propose that the local chromatin structure of the chicken alpha-globin enhancer plays a central role in its capacity to differentially regulate alpha-globin gene expression during erythroid differentiation and development.
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311
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Bao L, Zhou M, Cui Y. CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Res 2007; 36:D83-7. [PMID: 17981843 PMCID: PMC2238977 DOI: 10.1093/nar/gkm875] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Recent studies on transcriptional control of gene expression have pinpointed the importance of long-range interactions and three-dimensional organization of chromatins within the nucleus. Distal regulatory elements such as enhancers may activate transcription over long distances; hence, their action must be restricted within appropriate boundaries to prevent illegitimate activation of non-target genes. Insulators are DNA elements with enhancer-blocking and/or chromatin-bordering functions. In vertebrates, the versatile transcription regulator CCCTC-binding factor (CTCF) is the only identified trans-acting factor that confers enhancer-blocking insulator activity. CTCF-binding sites were found to be commonly distributed along the vertebrate genomes. We have constructed a CTCF-binding site database (CTCFBSDB) to characterize experimentally identified and computationally predicted CTCF-binding sties. Biological knowledge and data from multiple resources have been integrated into the database, including sequence data, genetic polymorphisms, function annotations, histone methylation profiles, gene expression profiles and comparative genomic information. A web-based user interface was implemented for data retrieval, analysis and visualization. In silico prediction of CTCF-binding motifs is provided to facilitate the identification of candidate insulators in the query sequences submitted by users. The database can be accessed at http://insulatordb.utmem.edu/
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Affiliation(s)
- Lei Bao
- Department of Molecular Sciences, Center of Genomics and Bioinformatics, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN 38163, USA
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312
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Wallace JA, Felsenfeld G. We gather together: insulators and genome organization. Curr Opin Genet Dev 2007; 17:400-7. [PMID: 17913488 PMCID: PMC2215060 DOI: 10.1016/j.gde.2007.08.005] [Citation(s) in RCA: 310] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 07/20/2007] [Accepted: 08/17/2007] [Indexed: 12/21/2022]
Abstract
When placed between an enhancer and promoter, certain DNA sequence elements inhibit enhancer-stimulated gene expression. The best characterized of these enhancer-blocking insulators, gypsy in Drosophila and the CTCF-binding element in vertebrates and flies, stabilize contacts between distant genomic regulatory sites leading to the formation of loop domains. Current results show that CTCF mediates long-range contacts in the mouse beta-globin locus and at the Igf2/H19-imprinted locus. Recently described active chromatin hubs and transcription factories also involve long-range interactions; it is likely that CTCF interferes with their formation when acting as an insulator. The properties of CTCF, and its newly described genomic distribution, suggest that it may play an important role in large-scale nuclear architecture, perhaps mediated by the co-factors with which it interacts in vivo.
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Affiliation(s)
- Julie A Wallace
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892-0540, United States
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313
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Chromosome kissing. Curr Opin Genet Dev 2007; 17:443-50. [PMID: 17933509 DOI: 10.1016/j.gde.2007.08.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 07/27/2007] [Accepted: 08/31/2007] [Indexed: 11/23/2022]
Abstract
Eukariotic chromosomes occupy distinct territories in the cell nucleus. These territories intermingle little with other chromosomes. Nevertheless, several contacts between different chromosomal loci have been documented, a phenomenon called chromosome kissing. Some of these contacts may arise simply because of preferred chromosome neighborhoods and of the sharing of transcriptional machineries, while others seem to have exquisite regulatory functions. Recent approaches that allow to detect chromosome kissing events in an unbiased manner suggest that chromatin folding is such that cis contacts with neighboring elements are most frequent, but contacts with remote parts of the same chromosome or with different chromosomes are possible. These contacts are modulated by specific chromatin features of each locus, and they may play important roles in the regulation of gene expression. Chromosome kissing events may also be at the origin of chromosomal rearrangements.
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314
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Xu N, Donohoe ME, Silva SS, Lee JT. Evidence that homologous X-chromosome pairing requires transcription and Ctcf protein. Nat Genet 2007; 39:1390-6. [PMID: 17952071 DOI: 10.1038/ng.2007.5] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 08/15/2007] [Indexed: 12/11/2022]
Abstract
X-chromosome inactivation (XCI) ensures the equality of X-chromosome dosages in male and female mammals by silencing one X in the female. To achieve the mutually exclusive designation of active X (Xa) and inactive X (Xi), the process necessitates that two Xs communicate in trans through homologous pairing. Pairing depends on a 15-kb region within the genes Tsix and Xite. Here, we dissect molecular requirements and find that pairing can be recapitulated by 1- to 2-kb subfragments of Tsix or Xite with little sequence similarity. However, a common denominator among them is the presence of the protein Ctcf, a chromatin insulator that we find to be essential for pairing. By contrast, the Ctcf-interacting partner, Yy1 (ref. 8), is not required. Pairing also depends on transcription. Transcriptional inhibition prevents new pair formation but does not perturb existing pairs. The kinetics suggest a pairing half-life of <1 h. We propose that pairing requires Ctcf binding and co-transcriptional activity of Tsix and Xite.
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Affiliation(s)
- Na Xu
- Howard Hughes Medical Institute Department of Molecular Biology, Massachusetts General Hospital Department of Genetics, Harvard Medical School Boston, Massachusetts 02114, USA
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315
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Activation-dependent intrachromosomal interactions formed by the TNF gene promoter and two distal enhancers. Proc Natl Acad Sci U S A 2007; 104:16850-5. [PMID: 17940009 DOI: 10.1073/pnas.0708210104] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Here we provide a mechanism for specific, efficient transcription of the TNF gene and, potentially, other genes residing within multigene loci. We identify and characterize highly conserved noncoding elements flanking the TNF gene, which undergo activation-dependent intrachromosomal interactions. These elements, hypersensitive site (HSS)-9 and HSS+3 (9 kb upstream and 3 kb downstream of the TNF gene, respectively), contain DNase I hypersensitive sites in naive, T helper 1, and T helper 2 primary T cells. Both HSS-9 and HSS+3 inducibly associate with acetylated histones, indicative of chromatin remodeling, bind the transcription factor nuclear factor of activated T cells (NFAT)p in vitro and in vivo, and function as enhancers of NFAT-dependent transactivation mediated by the TNF promoter. Using the chromosome conformation capture assay, we demonstrate that upon T cell activation intrachromosomal looping occurs in the TNF locus. HSS-9 and HSS+3 each associate with the TNF promoter and with each other, circularizing the TNF gene and bringing NFAT-containing nucleoprotein complexes into close proximity. TNF gene regulation thus reveals a mode of intrachromosomal interaction that combines a looped gene topology with interactions between enhancers and a gene promoter.
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316
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Teller K, Solovei I, Buiting K, Horsthemke B, Cremer T. Maintenance of imprinting and nuclear architecture in cycling cells. Proc Natl Acad Sci U S A 2007; 104:14970-5. [PMID: 17848516 PMCID: PMC1986597 DOI: 10.1073/pnas.0704285104] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Indexed: 12/16/2022] Open
Abstract
Dynamic gene repositioning has emerged as an additional level of epigenetic gene regulation. An early example was the report of a transient, spatial convergence (< or =2 microm) of oppositely imprinted regions ("kissing"), including the Angelman syndrome/Prader-Willi syndrome (AS/PWS) locus and the Beckwith-Wiedemann syndrome locus in human lymphocytes during late S phase. It was argued that kissing is required for maintaining opposite imprints in cycling cells. Employing 3D-FISH with a BAC contig covering the AS/PWS region, light optical, serial sectioning, and quantitative 3D-image analysis, we observed that both loci always retained a compact structure and did not form giant loops. Three-dimensional distances measured among various, homologous AS/PWS segments in 393 human lymphocytes, 132 human fibroblasts, and 129 lymphoblastoid cells from Gorilla gorilla revealed a wide range of distances at any stage of interphase and in G(0). At late S phase, 4% of nuclei showed distances < or =2 microm, 49% showed distances >6 microm, and 18% even showed distances >8 microm. A similar distance variability was found for Homo sapiens (HSA) 15 centromeres in a PWS patient with a deletion of the maternal AS/PWS locus and for the Beckwith-Wiedemann syndrome loci in human lymphocytes. A transient kiss during late S phase between loci widely separated at other stages of the cell cycle seems incompatible with known global constraints of chromatin movements in cycling cells. Further experiments suggest that the previously observed convergence of AS/PWS loci during late S phase was most likely a side effect of the convergence of nucleolus organizer region-bearing acrocentric human chromosomes, including HSA 15.
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Affiliation(s)
- Kathrin Teller
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Irina Solovei
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Karin Buiting
- Institut für Humangenetik, Universitaetsklinikum Essen, Hufelandstrasse 55, 45122 Essen, Germany; and
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitaetsklinikum Essen, Hufelandstrasse 55, 45122 Essen, Germany; and
| | - Thomas Cremer
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
- Munich Center for Integrated Protein Science, 81377 Munich, Germany
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317
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Fuss SH, Omura M, Mombaerts P. Local and cis effects of the H element on expression of odorant receptor genes in mouse. Cell 2007; 130:373-84. [PMID: 17662950 DOI: 10.1016/j.cell.2007.06.023] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2007] [Revised: 03/08/2007] [Accepted: 06/13/2007] [Indexed: 12/18/2022]
Abstract
From the approximately 1,200 odorant receptor (OR) genes in the mouse genome, an olfactory sensory neuron is thought to express only one gene. The mechanisms of OR gene choice are not understood. A 2.1 kilobase region (the H element) adjacent to a cluster of seven OR genes has been proposed as a trans- and pan-enhancer for OR gene expression. Here, we deleted the H element by gene targeting in mice. The deletion abolishes expression of a family of three OR genes proximal to H, and H operates in cis on these genes. Deletion of H has a graded effect on expression of a distal group of four OR genes, commensurate with genomic distance. There is no demonstrable effect on expression of OR genes located outside the cluster. Our findings are not consistent with the hypothesis of H as an essential trans-acting enhancer for genome-wide regulation of OR gene expression.
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Affiliation(s)
- Stefan H Fuss
- The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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318
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Williams BR, Bateman JR, Novikov ND, Wu CT. Disruption of topoisomerase II perturbs pairing in drosophila cell culture. Genetics 2007; 177:31-46. [PMID: 17890361 PMCID: PMC2013714 DOI: 10.1534/genetics.107.076356] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 06/22/2007] [Indexed: 12/16/2022] Open
Abstract
Homolog pairing refers to the alignment and physical apposition of homologous chromosomal segments. Although commonly observed during meiosis, homolog pairing also occurs in nonmeiotic cells of several organisms, including humans and Drosophila. The mechanism underlying nonmeiotic pairing, however, remains largely unknown. Here, we explore the use of established Drosophila cell lines for the analysis of pairing in somatic cells. Using fluorescent in situ hybridization (FISH), we assayed pairing at nine regions scattered throughout the genome of Kc167 cells, observing high levels of homolog pairing at all six euchromatic regions assayed and variably lower levels in regions in or near centromeric heterochromatin. We have also observed extensive pairing in six additional cell lines representing different tissues of origin, different ploidies, and two different species, demonstrating homolog pairing in cell culture to be impervious to cell type or culture history. Furthermore, by sorting Kc167 cells into G1, S, and G2 subpopulations, we show that even progression through these stages of the cell cycle does not significantly change pairing levels. Finally, our data indicate that disrupting Drosophila topoisomerase II (Top2) gene function with RNAi and chemical inhibitors perturbs homolog pairing, suggesting Top2 to be a gene important for pairing.
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Affiliation(s)
- Benjamin R Williams
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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319
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Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One 2007; 2:e807. [PMID: 17726537 PMCID: PMC1950076 DOI: 10.1371/journal.pone.0000807] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/24/2007] [Indexed: 01/07/2023] Open
Abstract
Background Transcription factors (TF) regulate expression by binding to specific DNA sequences. A binding event is functional when it affects gene expression. Functionality of a binding site is reflected in conservation of the binding sequence during evolution and in over represented binding in gene groups with coherent biological functions. Functionality is governed by several parameters such as the TF-DNA binding strength, distance of the binding site from the transcription start site (TSS), DNA packing, and more. Understanding how these parameters control functionality of different TFs in different biological contexts is a must for identifying functional TF binding sites and for understanding regulation of transcription. Methodology/Principal Findings We introduce a novel method to screen the promoters of a set of genes with shared biological function (obtained from the functional Gene Ontology (GO) classification) against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. More than 8000 human (and 23,000 mouse) genes, were assigned to one of 134 GO sets. Their promoters were searched (from 200 bp downstream to 1000 bp upstream the TSS) for 414 known DNA motifs. We optimized the sequence similarity score threshold, independently for every location window, taking into account nucleotide heterogeneity along the promoters of the target genes. The method, combined with binding sequence and location conservation between human and mouse, identifies with high probability functional binding sites for groups of functionally-related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were tested experimentally. Conclusions/Significance We identified reliably functional TF binding sites. This is an essential step towards constructing regulatory networks. The promoter region proximal to the TSS is of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.
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Affiliation(s)
- Yuval Tabach
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Ran Brosh
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yossi Buganim
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Anat Reiner
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Or Zuk
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Mark Koudritsky
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Eytan Domany
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail:
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320
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Rincón-Arano H, Furlan-Magaril M, Recillas-Targa F. Protection against telomeric position effects by the chicken cHS4 beta-globin insulator. Proc Natl Acad Sci U S A 2007; 104:14044-9. [PMID: 17715059 PMCID: PMC1955792 DOI: 10.1073/pnas.0704999104] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Indexed: 12/26/2022] Open
Abstract
Epigenetic silencing of genes relocated near telomeres, termed telomeric position effect, has been extensively studied in yeast and more recently in vertebrates. However, protection of a transgene against telomeric position effects by chromatin insulators has not yet been addressed. In this work we investigated the capacity of the chicken beta-globin insulator cHS4 to shield a transgene against silencing by telomeric heterochromatin. Using telomeric repeats, we targeted transgene integration into telomeres of the chicken cell line HD3. When the chicken cHS4 insulator is incorporated to the transgene, we observe a sustained gene expression of single-copy integrants that can be maintained for >100 days of continuous culture. However, uninsulated single-copy clones showed an accelerated gene expression extinction profile. Unexpectedly, telomeric silencing was not reversed with trichostatin A or nicotidamine. In contrast, significant reactivation was obtained with 5-aza-2'-deoxycytidine, consistent with the subtelomeric DNA methylation status. Strikingly, insulated transgenes integrated into telomeric regions were enriched in histone methylation, such as H3K4me2 and H3K79me2, but not in histone acetylation. Furthermore, the cHS4 insulator counteracts telomeric position effects in an upstream stimulatory factor-independent manner. Our results suggest that this insulator has the capacity to adapt to different chromatin propagation signals in distinct insertional epigenome environments.
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Affiliation(s)
- Héctor Rincón-Arano
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510 México, D.F., México
| | - Mayra Furlan-Magaril
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510 México, D.F., México
| | - Félix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510 México, D.F., México
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321
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Chuang CH, Belmont AS. Moving chromatin within the interphase nucleus-controlled transitions? Semin Cell Dev Biol 2007; 18:698-706. [PMID: 17905613 PMCID: PMC2117624 DOI: 10.1016/j.semcdb.2007.08.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2007] [Accepted: 08/22/2007] [Indexed: 12/17/2022]
Abstract
The past decade has seen an increasing appreciation for nuclear compartmentalization as an underlying determinant of interphase chromosome nuclear organization. To date, attention has focused primarily on describing differential localization of particular genes or chromosome regions as a function of differentiation, cell cycle position, and/or transcriptional activity. The question of how exactly interphase chromosome compartmentalization is established and in particular how interphase chromosomes might move during changes in nuclear compartmentalization has received less attention. Here we review what is known concerning chromatin mobility in relationship to physiologically regulated changes in nuclear interphase chromosome organization.
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Affiliation(s)
| | - Andrew S. Belmont
- * Corresponding author Andrew Belmont, Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, B107 CLSL, 601 S. Goodwin Ave., Urbana, IL 61801 USA, tel: +1 217-244-2311, fax: +1 217-244-1648, email address:
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322
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Ciavatta D, Rogers S, Magnuson T. Drosophila CTCF is required for Fab-8 enhancer blocking activity in S2 cells. J Mol Biol 2007; 373:233-9. [PMID: 17825318 PMCID: PMC2694738 DOI: 10.1016/j.jmb.2007.07.065] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 07/23/2007] [Accepted: 07/25/2007] [Indexed: 10/23/2022]
Abstract
CTCF is a conserved transcriptional regulator with binding sites in DNA insulators identified in vertebrates and invertebrates. The Drosophila Abdominal-B locus contains CTCF binding sites in the Fab-8 DNA insulator. Previous reports have shown that Fab-8 has enhancer blocking activity in Drosophila transgenic assays. We now confirm the enhancer blocking capability of the Fab-8 insulator in stably transfected Drosophila S2 cells and show this activity depends on the Fab-8 CTCF binding sites. Furthermore, knockdown of Drosophila CTCF by RNAi in our stable cell lines demonstrates that CTCF itself is critical for Fab-8 enhancer blocking.
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Affiliation(s)
- Dominic Ciavatta
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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323
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Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc 2007; 2:988-1002. [PMID: 17446898 DOI: 10.1038/nprot.2007.116] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genomic elements separated by large genomic distances can physically interact to mediate long-range gene regulation and other chromosomal processes. Interactions between genomic elements can be detected using the chromosome conformation capture (3C) technology. We recently developed a high-throughput adaptation of 3C, 3C-carbon copy (5C), that is used to measure networks of millions of chromatin interactions in parallel. As in 3C, cells are treated with formaldehyde to cross-link chromatin interactions. The chromatin is solubilized, digested with a restriction enzyme and ligated at low DNA concentration to promote intra-molecular ligation of cross-linked DNA fragments. Ligation products are subsequently purified to generate a 3C library. The 5C technology then employs highly multiplexed ligation-mediated amplification (LMA) to detect and amplify 3C ligation junctions. The resulting 5C library of ligated primers is analyzed using either microarray detection or ultra-high-throughput DNA sequencing. The 5C protocol described here can be completed in 13 d.
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Affiliation(s)
- Josée Dostie
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Room 519, Worcester, Massachusetts 01605-4321, USA
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324
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Abstract
Much work has been published on the cis-regulatory elements that affect gene function locally, as well as on the biochemistry of the transcription factors and chromatin- and histone-modifying complexes that influence gene expression. However, surprisingly little information is available about how these components are organized within the three-dimensional space of the nucleus. Technological advances are now helping to identify the spatial relationships and interactions of genes and regulatory elements in the nucleus and are revealing an unexpectedly extensive network of communication within and between chromosomes. A crucial unresolved issue is the extent to which this organization affects gene function, rather than just reflecting it.
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Affiliation(s)
- Peter Fraser
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Cambridge CB2 4AT, UK.
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325
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Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007; 128:1231-45. [PMID: 17382889 PMCID: PMC2572726 DOI: 10.1016/j.cell.2006.12.048] [Citation(s) in RCA: 791] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 11/23/2006] [Accepted: 12/28/2006] [Indexed: 12/31/2022]
Abstract
Insulator elements affect gene expression by preventing the spread of heterochromatin and restricting transcriptional enhancers from activation of unrelated promoters. In vertebrates, insulator's function requires association with the CCCTC-binding factor (CTCF), a protein that recognizes long and diverse nucleotide sequences. While insulators are critical in gene regulation, only a few have been reported. Here, we describe 13,804 CTCF-binding sites in potential insulators of the human genome, discovered experimentally in primary human fibroblasts. Most of these sequences are located far from the transcriptional start sites, with their distribution strongly correlated with genes. The majority of them fit to a consensus motif highly conserved and suitable for predicting possible insulators driven by CTCF in other vertebrate genomes. In addition, CTCF localization is largely invariant across different cell types. Our results provide a resource for investigating insulator function and possible other general and evolutionarily conserved activities of CTCF sites.
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Affiliation(s)
- Tae Hoon Kim
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653
- To whom correspondence should be addressed,
,
| | - Ziedulla K. Abdullaev
- National Institutes of Allergy and Infectious Disease, 5640 Fishers Lane, Rockville, MD 20852
| | - Andrew D. Smith
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724
| | - Keith A. Ching
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653
| | - Dmitri I. Loukinov
- National Institutes of Allergy and Infectious Disease, 5640 Fishers Lane, Rockville, MD 20852
| | | | - Michael Q. Zhang
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724
| | - Victor V. Lobanenkov
- National Institutes of Allergy and Infectious Disease, 5640 Fishers Lane, Rockville, MD 20852
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653
- To whom correspondence should be addressed,
,
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326
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Abstract
DNA segments that are separated from the promoter region of a gene by many thousands of bases may nonetheless regulate the transcriptional activity of that gene. This finding has led to the investigation of mechanisms underlying long-range chromatin interactions. In intermitotic cells, chromosomes decondense, filling the nucleus with distinct chromosome territories that interdigitate and intercalate with neighboring and even more distant chromosome territories. Both intrachromosomal and interchromosomal long-range associations have been demonstrated, and DNA binding proteins have been implicated in the maintenance of these interactions. A single gene may have interactions with many distant DNA segments. Genes that are monoallelically expressed, such as imprinted genes and odorant receptors, are frequently found to be regulated by these long-range interactions. These findings emphasize the importance of studying the geography and architecture of the nucleus as an important factor in the regulation of gene transcription.
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327
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de Laat W. Long-range DNA contacts: romance in the nucleus? Curr Opin Cell Biol 2007; 19:317-20. [PMID: 17467258 DOI: 10.1016/j.ceb.2007.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Accepted: 04/12/2007] [Indexed: 12/22/2022]
Abstract
Recent studies show that genes far apart on the same chromosome or even on different chromosomes can come together in the nuclear space. It has been hypothesized that functionally related genes 'kiss' at transcription factories to coordinate their expression. Novel high-throughput methods, such as 4C technology, that study DNA interactions in an unbiased manner should uncover the generality of this romantic concept of nuclear architecture.
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Affiliation(s)
- Wouter de Laat
- Department of Cell Biology, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.
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328
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Ohlsson R, Göndör A. The 4C technique: the 'Rosetta stone' for genome biology in 3D? Curr Opin Cell Biol 2007; 19:321-5. [PMID: 17466501 DOI: 10.1016/j.ceb.2007.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 04/13/2007] [Indexed: 01/22/2023]
Abstract
Despite considerable efforts, the spatial link between the nuclear architecture and the genome remains enigmatic. The 4C method, independently innovated in four different laboratories, might in combination with other methods change that. As this method is based on the unbiased identification of sequences interacting with specific baits, there are unique opportunities for unravelling the secrets of how the genome functions in 3D.
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Affiliation(s)
- Rolf Ohlsson
- Department of Development & Genetics, Norbyvägen 18A, Evolution Biology Centre, Uppsala University, S-752 36 Uppsala, Sweden.
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329
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De La Rosa-Velázquez IA, Rincón-Arano H, Benítez-Bribiesca L, Recillas-Targa F. Epigenetic regulation of the human retinoblastoma tumor suppressor gene promoter by CTCF. Cancer Res 2007; 67:2577-85. [PMID: 17363576 DOI: 10.1158/0008-5472.can-06-2024] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Epigenetic misregulation is a more common feature in human cancer than previously anticipated. In the present investigation, we identified CCCTC-binding factor (CTCF), the multivalent 11-zinc-finger nuclear factor, as a regulator that favors a particular local chromatin conformation of the human retinoblastoma gene promoter. We show that its binding contributes to Rb gene promoter epigenetic stability. Ablation of the CTCF binding site from the human Rb gene promoter induced a rapid epigenetic silencing of reporter gene expression in an integrated genome context. CTCF DNA binding is methylation sensitive, and the methylated Rb-CTCF site is recognized by the Kaiso methyl-CpG-binding protein. This is the first evidence suggesting that CTCF protects the Rb gene promoter, a classic CpG island, against DNA methylation, and when such control region is abnormally methylated Kaiso, and probably its associated repressor complex, induce epigenetic silencing of the promoter. Our results identify CTCF as a novel epigenetic regulator of the human retinoblastoma gene promoter.
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Affiliation(s)
- Inti A De La Rosa-Velázquez
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, México D.F., México
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330
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Day L, Chau CM, Nebozhyn M, Rennekamp AJ, Showe M, Lieberman PM. Chromatin profiling of Epstein-Barr virus latency control region. J Virol 2007; 81:6389-401. [PMID: 17409162 PMCID: PMC1900095 DOI: 10.1128/jvi.02172-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) escapes host immunity by the reversible and epigenetic silencing of immunogenic viral genes. We previously presented evidence that a dynamic chromatin domain, which we have referred to as the latency control region (LCR), contributes to the reversible repression of EBNA2 and LMP1 gene transcription. We now explore the protein-DNA interaction profiles for a few known regulatory factors and histone modifications that regulate LCR structure and activity. A chromatin immunoprecipitation assay combined with real-time PCR analysis was used to analyze protein-DNA interactions at approximately 500-bp intervals across the first 60,000 bp of the EBV genome. We compared the binding patterns of EBNA1 with those of the origin recognition complex protein ORC2, the chromatin boundary factor CTCF, the linker histone H1, and several histone modifications. We analyzed three EBV-positive cell lines (MutuI, Raji, and LCL3459) with distinct transcription patterns reflecting different latency types. Our findings suggest that histone modification patterns within the LCR are complex but reflect differences in each latency type. The most striking finding was the identification of CTCF sites immediately upstream of the Qp, Cp, and EBER transcription initiation regions in all three cell types. In transient assays, CTCF facilitated EBNA1-dependent transcription activation of Cp, suggesting that CTCF coordinates interactions between different chromatin domains. We also found that histone H3 methyl K4 clustered with CTCF and EBNA1 at sites of active transcription or DNA replication initiation. Our findings support a model where CTCF delineates multiple domains within the LCR and regulates interactions between these domains that correlate with changes in gene expression.
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Affiliation(s)
- Latasha Day
- The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA
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331
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Giadrossi S, Dvorkina M, Fisher AG. Chromatin organization and differentiation in embryonic stem cell models. Curr Opin Genet Dev 2007; 17:132-8. [PMID: 17336511 DOI: 10.1016/j.gde.2007.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Accepted: 02/19/2007] [Indexed: 01/31/2023]
Abstract
Embryonic stem cells derived from mammalian embryos represent indispensable tools for mammalian genetics. Their key features--self-renewal and pluripotency--enable them, on the one hand, to be propagated in culture almost indefinitely and, on the other, to be used to study the molecular details of cell commitment and differentiation. In the past few years, it has become clear that chromatin and epigenetic modifications have a central role in maintaining the gene expression programs that are important for both self-renewal and cell commitment. Therefore, studies focused on the chromatin profiles of embryonic stem cells are likely to be very informative for understanding pluripotency and the process of differentiation, and ultimately for using embryonic stem cells as a tool for cell replacement therapy or as models for the study of genetic diseases, cancer progression or drug testing.
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Affiliation(s)
- Sara Giadrossi
- Lymphocytes Development Group, MRC Clinical Sciences Centre, Imperial College Faculty of Medicine, Hammersmith Hospital Campus, Du Cane Road, W12 0NN, London, UK
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332
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Abstract
At certain evolutionary junctures, two or more mutations participating in the build-up of a new complex function may be required to become available simultaneously in the same individuals. How could this happen in higher organisms whose populations are small compared to those of microbes, and in which chances of combined nearly simultaneous highly specific favorable mutations are correspondingly low? The question can in principle be answered for regulatory evolution, one of the basic processes of evolutionary change. A combined resetting of transcription rates in several genes could occur in the same individual. It is proposed that, in eukaryotes, changes in epigenetic trends and epigenetically transforming encounters between alternative chromatin structures could arise frequently enough so as to render probable particular conjunctions of changed transcription rates. Such conjunctions could involve mutational changes with low specificity requirements in gene-associated regions of non-protein-coding sequences. The effects of such mutations, notably when they determine the use of histone variants and covalent modifications of histones, can be among those that migrate along chromatin. Changes in chromatin structure are often cellularly inheritable over at least a limited number of generations of cells, and of individuals when the germ line is involved. SINEs and LINEs, which have been considered "junk DNA", are among the repeat sequences that would appear liable to have teleregulatory effects on the function of a nearby promoter, through changes in their numbers and distribution. There may also be present preexisting unstably inheritable epigenetic trends leading to cellular variegation, trends endemic in a cell population based on DNA sequences previously established in the neighborhood. Either way, epigenetically conditioned teleregulatory trends may display only limited penetrance. The imposition at a distance of new chromatin structures with regulatory impact can occur in cis as well as in trans, and is examined as intrachromosomally spreading teleregulation and interchromosomal "gene kissing". The chances for two or more particular epigenetically determined regulatory trends to occur together in a cell are increased thanks to the proposed low specificity requirements for most of the pertinent sequence changes in intergenic and intronic DNA or in the distribution of middle repetitive sequences that have teleregulatory impact. Inheritable epigenetic changes ("epimutations") with effects at a distance would then perdure over the number of generations required for "assimilation" of the several regulatory novelties through the occurrence and selection, gene by gene, of specific classical mutations. These mutations would have effects similar to the epigenetic effects, yet would provide stability and penetrance. The described epigenetic/genetic partnership may well at times have opened the way toward certain complex new functions. Thus, the presence of "junk DNA", through co-determining the (higher or lower) order and the variants of chromatin structure with regulatory effects at a distance, might make an important contribution to the evolution of complex organisms.
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Affiliation(s)
- Emile Zuckerkandl
- Department of Biological Sciences, Stanford University, Stanford, California 94305, USA
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333
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Abstract
Genomes are more than linear sequences. In vivo they exist as elaborate physical structures, and their functional properties are strongly determined by their cellular organization. I discuss here the functional relevance of spatial and temporal genome organization at three hierarchical levels: the organization of nuclear processes, the higher-order organization of the chromatin fiber, and the spatial arrangement of genomes within the cell nucleus. Recent insights into the cell biology of genomes have overturned long-held dogmas and have led to new models for many essential cellular processes, including gene expression and genome stability.
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Affiliation(s)
- Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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334
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Abstract
Mammalian X inactivation, imprinting, and allelic exclusion are classic examples of monoallelic gene expression. Two emerging themes are thought to be critical for monoallelic expression: (1) noncoding, often antisense, transcription linked to differential chromatin marks on otherwise homologous alleles and (2) physical segregation of alleles to separate domains within the nucleus. Here, we highlight recent progress in identifying these phenomena as possible key regulatory mechanisms of monoallelic expression.
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Affiliation(s)
- Pok Kwan Yang
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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335
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Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 2007; 8:104-15. [PMID: 17230197 DOI: 10.1038/nrg2041] [Citation(s) in RCA: 585] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The regulation of gene expression is mediated by interactions between chromatin and protein complexes. The importance of where and when these interactions take place in the nucleus is currently a subject of intense investigation. Increasing evidence indicates that gene activation or silencing is often associated with repositioning of the locus relative to nuclear compartments and other genomic loci. At the same time, however, structural constraints impose limits on chromatin mobility. Understanding how the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is therefore essential to our overall understanding of gene regulation.
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Affiliation(s)
- Christian Lanctôt
- Department Biologie II, Ludwig-Maximilians Universität, Grosshadernerstr. 2, Planegg-Martinsried, Germany.
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336
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Abstract
Transcriptional insulators are specialized cis-acting elements that protect promoters from inappropriate activation by distal enhancers. The H19 imprinting control region (ICR) functions as a CTCF-dependent, methylation-sensitive transcriptional insulator. We analyzed several insertional mutations and demonstrate that the ICR can function as a methylation-regulated maternal chromosome-specific insulator in novel chromosomal contexts. We used chromosome conformation capture and chromatin immunoprecipitation assays to investigate the configuration of cis-acting elements at these several insertion sites. By comparing maternal and paternal organizations on wild-type and mutant chromosomes, we hoped to identify mechanisms for ICR insulator function. We found that promoter and enhancer elements invariably associate to form DNA loop domains at transcriptionally active loci. Conversely, active insulators always prevent these promoter-enhancer interactions. Instead, the ICR insulator forms novel loop domains by associating with the blocked promoters and enhancers. We propose that these associations are fundamental to insulator function.
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Affiliation(s)
- Young Soo Yoon
- Laboratory of Mammalian Genes and Development, NICHD, NIH, Bethesda, MD 20892, USA
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337
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Unneberg P, Claverie JM. Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data. PLoS One 2007; 2:e254. [PMID: 17330142 PMCID: PMC1804257 DOI: 10.1371/journal.pone.0000254] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Accepted: 02/06/2007] [Indexed: 11/18/2022] Open
Abstract
Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes in transcription factories. This spatial proximity of actively transcribing genes could provide a means for RNA interaction at the transcript level. We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal interactions. We suggest that chimeric transcripts may be the result of close encounters of active genes, either as functional products or "noise" in the transcription process, and that they could be used as probes for chromosome interactions. We have found a total of 5,614 chimeric ESTs and 587 chimeric mRNAs that meet our selection criteria. Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology.
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Affiliation(s)
- Per Unneberg
- Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique (CNRS) UPR-2589, Institut de Biologie Structurale et Microbiologie, Marseille, France.
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338
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Lanctôt C, Kaspar C, Cremer T. Positioning of the mouse Hox gene clusters in the nuclei of developing embryos and differentiating embryoid bodies. Exp Cell Res 2007; 313:1449-59. [PMID: 17346703 DOI: 10.1016/j.yexcr.2007.01.027] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 01/15/2007] [Accepted: 01/21/2007] [Indexed: 02/06/2023]
Abstract
Expression of Hox genes located on different chromosomes is precisely regulated and synchronized during development. In order to test the hypothesis that the Hox loci might cluster in nuclear space in order to share regulatory components, we performed 3D FISH on cryosections of developing mouse embryos and differentiating embryoid bodies. We did not observe any instances of co-localization of 4 different Hox alleles. Instances of 2 different alleles touching each other were found in 20-47% of nuclei depending on the tissue. The frequency of such "kissing" events was not significantly different in cells expressing a high proportion of the Hox clusters when compared to cells expressing none or only a few Hox genes. We found that the HoxB and HoxC clusters, which are located in gene-rich regions, were involved more frequently in gene kissing in embryonic nuclei. In the case of HoxB, this observation correlated with the positioning of the corresponding chromosome towards the interior of the nucleus. Our results indicate that co-regulation of the different Hox clusters is not associated with co-localization of the loci at a single regulatory compartment and that the chromosomal context may influence the extent to which they contact each other in the nucleus.
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Affiliation(s)
- Christian Lanctôt
- Department Biology II, Ludwig-Maximilians University Munich, Grosshadernerstr. 2, Planegg-Martinsried, 82152, Germany.
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339
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Kyrchanova O, Toshchakov S, Parshikov A, Georgiev P. Study of the functional interaction between Mcp insulators from the Drosophila bithorax complex: effects of insulator pairing on enhancer-promoter communication. Mol Cell Biol 2007; 27:3035-43. [PMID: 17283051 PMCID: PMC1899939 DOI: 10.1128/mcb.02203-06] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Boundary elements have been found in the Abd-B 3' cis-regulatory region, which is subdivided into a series of iab domains. Previously, a 340-bp insulator-like element, M(340), was identified in one such 755-bp Mcp fragment linked to the PcG-dependent silencer. In this study, we identified a 210-bp core that was sufficient for pairing of sequence-remote Mcp elements. In two-gene transgenic constructs with two Mcp insulators (or their cores) surrounding yellow, the upstream yeast GAL4 sites were able to activate the distal white only if the insulators were in the opposite orientations (head-to-head or tail-to-tail), which is consistent with the looping/bypass model. The same was true for the efficiency of the cognate eye enhancer, while yellow thus isolated in the loop from its enhancers was blocked more strongly. These results indicate that the relative placement and orientation of insulator-like elements can determine proper enhancer-promoter communication.
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Affiliation(s)
- Olga Kyrchanova
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
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340
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Liu D, Bischerour J, Siddique A, Buisine N, Bigot Y, Chalmers R. The human SETMAR protein preserves most of the activities of the ancestral Hsmar1 transposase. Mol Cell Biol 2007; 27:1125-32. [PMID: 17130240 PMCID: PMC1800679 DOI: 10.1128/mcb.01899-06] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2006] [Revised: 11/06/2006] [Accepted: 11/10/2006] [Indexed: 12/11/2022] Open
Abstract
Transposons have contributed protein coding sequences to a unexpectedly large number of human genes. Except for the V(D)J recombinase and telomerase, all remain of unknown function. Here we investigate the activity of the human SETMAR protein, a highly expressed fusion between a histone H3 methylase and a mariner family transposase. Although SETMAR has demonstrated methylase activity and a DNA repair phenotype, its mode of action and the role of the transposase domain remain obscure. As a starting point to address this problem, we have dissected the activity of the transposase domain in the context of the full-length protein and the isolated transposase domain. Complete transposition of an engineered Hsmar1 transposon by the transposase domain was detected, although the extent of the reaction was limited by a severe defect for cleavage at the 3' ends of the element. Despite this problem, SETMAR retains robust activity for the other stages of the Hsmar1 transposition reaction, namely, site-specific DNA binding to the transposon ends, assembly of a paired-ends complex, cleavage of the 5' end of the element in Mn(2+), and integration at a TA dinucleotide target site. SETMAR is unlikely to catalyze transposition in the human genome, although the nicking activity may have a role in the DNA repair phenotype. The key activity for the mariner domain is therefore the robust DNA-binding and looping activity which has a high potential for targeting the histone methylase domain to the many thousands of specific binding sites in the human genome provided by copies of the Hsmar1 transposon.
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Affiliation(s)
- Danxu Liu
- University of Oxford, Department of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
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341
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Meaburn KJ, Misteli T, Soutoglou E. Spatial genome organization in the formation of chromosomal translocations. Semin Cancer Biol 2007; 17:80-90. [PMID: 17137790 PMCID: PMC1805052 DOI: 10.1016/j.semcancer.2006.10.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 10/17/2006] [Indexed: 10/24/2022]
Abstract
Chromosomal translocations and genomic instability are universal hallmarks of tumor cells. While the molecular mechanisms leading to the formation of translocations are rapidly being elucidated, a cell biological understanding of how chromosomes undergo translocations in the context of the cell nucleus in vivo is largely lacking. The recent realization that genomes are non-randomly arranged within the nuclear space has profound consequences for mechanisms of chromosome translocations. We review here the emerging principles of spatial genome organization and discuss the implications of non-random spatial genome organization for the genesis and specificity of cancerous chromosomal translocations.
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Affiliation(s)
- Karen J Meaburn
- National Cancer Institute, NIH, Bethesda, MD 20892, United States.
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342
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Rossi DJ, Bryder D, Weissman IL. Hematopoietic stem cell aging: mechanism and consequence. Exp Gerontol 2007; 42:385-90. [PMID: 17275237 PMCID: PMC1892213 DOI: 10.1016/j.exger.2006.11.019] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 11/28/2006] [Indexed: 12/15/2022]
Abstract
Advancing age is frequented by the onset of a variety of hematological conditions characterized by diminished homeostatic control of blood cell production. The fact that upstream hematopoietic stem and progenitor cells are obligate mediators of homeostatic control of all blood lineages, has implicated the involvement of these cells in the pathophysiology of these conditions. Indeed, evidence from our group and others has suggested that two of the most clinically significant age-associated hematological conditions, namely, the diminution of the adaptive immune system and the elevated incidence of myeloproliferative diseases, have their origin in cell autonomous changes in the functional capacity of hematopoietic stem cells.
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Affiliation(s)
- Derrick J Rossi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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343
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Recillas-Targa F, De La Rosa-Velázquez IA, Soto-Reyes E, Benítez-Bribiesca L. Epigenetic boundaries of tumour suppressor gene promoters: the CTCF connection and its role in carcinogenesis. J Cell Mol Med 2007; 10:554-68. [PMID: 16989720 PMCID: PMC3933142 DOI: 10.1111/j.1582-4934.2006.tb00420.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genetic and epigenetic regulations are essential mechanisms that ensure proper early and subsequent mammalian programming of diverse cellular processes. These mechanisms affect transcriptional regulation, stem cell determination and cell cycle control, including senescence and aging. It is not surprising that perturbation of the exquisite balance between genetic and epigenetic regulation can lead to diverse diseases, including cancer. Histone covalent modifications and DNA methylation do not explain all epigenetic phenomena. We describe a previously unsuspected epigenetic factor and propose the incorporation of the 11-zinc finger CCCTC-binding factor, known as CTCF as a novel and multifunctional epigenetic regulator.
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Affiliation(s)
- Felix Recillas-Targa
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, México.
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344
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Abstract
It has long been recognized that imprinted genes often act in common developmental or physiological pathways. A new knockout of the gene Zac1 reveals just how extensive the transcriptional network of imprinted genes may be.
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Affiliation(s)
- Guillaume Smits
- Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge CB22 3AT, United Kingdom
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345
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Chromosome organization: new facts, new models. Trends Cell Biol 2007; 17:127-34. [PMID: 17197184 DOI: 10.1016/j.tcb.2006.12.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Accepted: 12/19/2006] [Indexed: 02/05/2023]
Abstract
The study of nuclear organization has radically changed the way we envision gene regulation, imposing a paradigm shift from a seemingly featureless nucleus to a highly compartmentalized and complex organelle. The positioning of genes, regulatory sequences and transcription factors in relation to each other and to landmarks in the nucleus, such as nuclear bodies and the lamina, is important in determining which genes are transcribed at any one time. Investigating chromatin organization during interphase is therefore essential to the understanding of gene expression. The recent discovery of interactions between distal chromatin segments that occur within the same chromosome or across different chromosomes, and that have a role in transcription regulation, suggests a re-evaluation of current models of chromosome organization and the development of new ones.
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346
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Abstract
Recent advances in studying long-range chromatin interactions have shifted focus from the transcriptional regulation by nearby regulatory elements to recognition of the role of higher-order chromatin organization within the nucleus. These advances have also suggested that CCCTC-binding factor (CTCF), a known chromatin insulator protein, may play a central role in mediating long-range chromatin interactions, directing DNA segments into transcription factories and/or facilitating interactions with other DNA regions. Several models that describe possible mechanisms for multiple functions of CTCF in establishment and maintenance of epigenetic programs are now emerging. Epigenetics plays an important role in normal development and disease including cancer. CTCF involvement in multiple aspects of epigenetic regulation, including regulation of genomic imprinting and X-chromosome inactivation, has been well established. More recently, CTCF was found to play a role in regulation of noncoding transcription and establishing local chromatin structure at the repetitive elements in mammalian genomes, suggesting a new epigenetic basis for several repeat-associated genetic disorders. Emerging evidence also points to the role of CTCF deregulation in the epigenetic imbalance in cancer. These studies provide some of the important missing links in our understanding of epigenetic control of both development and cancer.
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Affiliation(s)
- Galina N Filippova
- Human Biology Division, Fred Hutchinson Cancer Research Center Seattle, Washington 98109, USA
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347
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Nuclear organization and splicing control. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:1-13. [PMID: 18380337 DOI: 10.1007/978-0-387-77374-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although major splicing regulatory mechanisms rely on the presence of cis-acting sequence elements in the precursor messenger RNA (pre-mRNA) to which specific protein and factors bind, splice choices are also influenced by transcription kinetics, promoter-dependent loading of RNA-binding proteins and nucleo-cytoplasmic distribution of splicing regulators. Within the highly crowded eukaryotic nucleus, molecular machines required for gene expression create specialized microenvironments that favor some interactions while repressing others. Genes located far apart in a chromosome or even in different chromosomes come together in the nucleus for coordinated transcription and splicing. Emerging tools to dissect gene expression pathways in living cells promise to provide more detailed insight as to how spatial confinement contributes to splicing control.
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348
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Abstract
The epigenetic events that occur during the development of the mammalian embryo are essential for correct gene expression and cell-lineage determination. Imprinted genes are expressed from only one parental allele due to differential epigenetic marks that are established during gametogenesis. Several theories have been proposed to explain the role that genomic imprinting has played over the course of mammalian evolution, but at present it is not clear if a single hypothesis can fully account for the diversity of roles that imprinted genes play. In this review, we discuss efforts to define the extent of imprinting in the mouse genome, and suggest that different imprinted loci may have been wrought by distinct evolutionary forces. We focus on a group of small imprinted domains, which consist of paternally expressed genes embedded within introns of multiexonic transcripts, to discuss the evolution of imprinting at these loci.
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349
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Sparago A, Russo S, Cerrato F, Ferraiuolo S, Castorina P, Selicorni A, Schwienbacher C, Negrini M, Ferrero GB, Silengo MC, Anichini C, Larizza L, Riccio A. Mechanisms causing imprinting defects in familial Beckwith-Wiedemann syndrome with Wilms' tumour. Hum Mol Genet 2006; 16:254-64. [PMID: 17158821 DOI: 10.1093/hmg/ddl448] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The imprinted expression of the IGF2 and H19 genes is controlled by the Imprinting Centre 1 (IC1) at chromosome 11p15.5. This is a methylation-sensitive chromatin insulator that works by binding the zinc-finger protein CTCF in a parent-specific manner. Microdeletions abolishing some of the CTCF target sites (CTSs) of IC1 have been associated with the Beckwith-Wiedemann syndrome (BWS). However, the link between these mutations and the molecular and clinical phenotypes was debated. We have identified two novel families with IC1 deletions, in which individuals with the clinical features of the BWS are present in multiple generations. By analysing the methylation pattern at the IGF2-H19 locus together with the clinical phenotypes in the individuals with maternal and those with paternal transmission of five different deletions, we demonstrate that maternal transmission of 1.4-1.8 kb deletions in the IC1 region co-segregates with the hypermethylation of the residual CTSs and BWS phenotype with complete penetrance, whereas normal phenotype is observed upon paternal transmission. Although gene expression could not be assayed in all cases, the methylation detected at the IGF2 DMR2 and H19 promoter suggests that IC1 hypermethylation is consistently associated with biallelic activation of IGF2 and biallelic silencing of H19. Comparison of these deletions with a 2.2 kb one previously reported by another group indicates that the spacing of the CTSs on the deleted allele is critical for the gain of the abnormal methylation and penetrance of the clinical phenotype. Furthermore, we observe that the hypermethylation resulting from the deletions is always mosaic, suggesting that the epigenetic defect at the IGF2-H19 locus is established post-zygotically and may cause body asymmetry and heterogeneity of the clinical phenotype. Finally, the IC1 microdeletions are associated with a high incidence of Wilms' tumour, making their molecular diagnosis particularly important for genetic counselling and tumour surveillance at follow-up.
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Affiliation(s)
- Angela Sparago
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy
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350
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Vadakkan KI, Li B, De Boni U. Trend towards varying combinatorial centromere association in morphologically identical clusters in Purkinje neurons. CELL & CHROMOSOME 2006; 5:1. [PMID: 17156432 PMCID: PMC1702546 DOI: 10.1186/1475-9268-5-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2006] [Accepted: 12/07/2006] [Indexed: 01/15/2023]
Abstract
Neurons with similar morphology and neurotransmitter content located at a specific brain region may be part of the same or functionally separate networks. To address the question whether morphologically similar neurons have similar structural architecture at the chromosomal level, we studied Purkinje neurons in the cerebellum. Previous studies have shown that in Purkinje neurons centromeres of several chromosomes form clusters and that the number and size of these clusters remain stable in the adult brain. We examined whether the same set of centromeres form clusters in all the Purkinje neurons. Fluorescent in situ hybridization (FISH) with chromosome-specific para-centromeric probes provided an indirect evidence for a trend towards varying contributions from different chromosomes forming the centromeric clusters in adjacent Purkinje neurons. The results of the study indicate that the individual Purkinje neurons are likely unique in inter-chromosomal spatial associations.
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Affiliation(s)
- Kunjumon I Vadakkan
- Department of Physiology and Collaborative Program in Neuroscience, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Baoxiang Li
- Department of Physiology and Collaborative Program in Neuroscience, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Umberto De Boni
- Department of Physiology and Collaborative Program in Neuroscience, Faculty of Medicine, University of Toronto, Toronto, ON, M5S1A8, Canada
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