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Johanson TM, Coughlan HD, Lun ATL, Bediaga NG, Naselli G, Garnham AL, Harrison LC, Smyth GK, Allan RS. Genome-wide analysis reveals no evidence of trans chromosomal regulation of mammalian immune development. PLoS Genet 2018; 14:e1007431. [PMID: 29883495 PMCID: PMC6010296 DOI: 10.1371/journal.pgen.1007431] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/20/2018] [Accepted: 05/18/2018] [Indexed: 12/31/2022] Open
Abstract
It has been proposed that interactions between mammalian chromosomes, or transchromosomal interactions (also known as kissing chromosomes), regulate gene expression and cell fate determination. Here we aimed to identify novel transchromosomal interactions in immune cells by high-resolution genome-wide chromosome conformation capture. Although we readily identified stable interactions in cis, and also between centromeres and telomeres on different chromosomes, surprisingly we identified no gene regulatory transchromosomal interactions in either mouse or human cells, including previously described interactions. We suggest that advances in the chromosome conformation capture technique and the unbiased nature of this approach allow more reliable capture of interactions between chromosomes than previous methods. Overall our findings suggest that stable transchromosomal interactions that regulate gene expression are not present in mammalian immune cells and that lineage identity is governed by cis, not trans chromosomal interactions. It is a widely held belief that, in the darkness of the nucleus, strands of DNA that make up different chromosomes frequently meet to ‘kiss’. These kisses, or transchromosomal interactions, are thought to be important for the expression of genes and thus cell development. Here, we aimed to identify novel transchromosomal interactions in mouse and human immune cells by high-resolution genome-wide chromosome conformation capture methods. Although we readily identified stable interactions within chromosomes and also between centromeres and telomeres on different chromosomes, surprisingly we identified no gene regulatory transchromosomal interactions in either mouse or human cells, including those previously described. Overall our findings suggest that stable transchromosomal interactions that regulate gene expression are not present in mammalian immune cells and that chromosomes are doing far less kissing than was previously believed.
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Affiliation(s)
- Timothy M. Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Hannah D. Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Aaron T. L. Lun
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Naiara G. Bediaga
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Gaetano Naselli
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Alexandra L. Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Leonard C. Harrison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Gordon K. Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- * E-mail:
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2
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Imprinted genes in myeloid lineage commitment in normal and malignant hematopoiesis. Leukemia 2015; 29:1233-42. [PMID: 25703588 DOI: 10.1038/leu.2015.47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 01/27/2015] [Accepted: 02/16/2015] [Indexed: 12/12/2022]
Abstract
Genomic imprinting is characterized by the parent-of-origin monoallelic expression of several diploid genes because of epigenetic regulation. Imprinted genes (IGs) are key factors in development, supporting the ability of a genotype to produce phenotypes in response to environmental stimuli. IGs are highly expressed during prenatal stages but are downregulated after birth. They also affect aspects of life other than growth such as cognition, behavior, adaption to novel environments, social dominance and memory consolidation. Deregulated genomic imprinting leads to developmental disorders and is associated with solid and blood cancer as well. Several data have been published highlighting the involvement of IGs in as early as the very small embryonic-like stem cells stage and further during myeloid lineage commitment in normal and malignant hematopoiesis. Therefore, we have assembled the current knowledge on the topic, based mainly on recent findings, trying not to focus on a particular cluster but rather to have a global view of several different IGs in hematopoiesis.
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3
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Kawamura R, Tanabe H, Wada T, Saitoh S, Fukushima Y, Wakui K. Visualization of the spatial positioning of the SNRPN, UBE3A, and GABRB3 genes in the normal human nucleus by three-color 3D fluorescence in situ hybridization. Chromosome Res 2012; 20:659-72. [PMID: 22801776 PMCID: PMC3481056 DOI: 10.1007/s10577-012-9300-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 06/14/2012] [Accepted: 06/14/2012] [Indexed: 11/06/2022]
Abstract
The three-dimensional (3D) structure of the genome is organized non-randomly and plays a role in genomic function via epigenetic mechanisms in the eukaryotic nucleus. Here, we analyzed the spatial positioning of three target regions; the SNRPN, UBE3A, and GABRB3 genes on human chromosome 15q11.2–q12, a representative cluster of imprinted regions, in the interphase nuclei of B lymphoblastoid cell lines, peripheral blood cells, and skin fibroblasts derived from normal individuals to look for evidence of genomic organization and function. The positions of these genes were simultaneously visualized, and all inter-gene distances were calculated for each homologous chromosome in each nucleus after three-color 3D fluorescence in situ hybridization. None of the target genes were arranged linearly in most cells analyzed, and GABRB3 was positioned closer to SNRPN than UBE3A in a high proportion of cells in all cell types. This was in contrast to the genomic map in which GABRB3 was positioned closer to UBE3A than SNRPN. We compared the distances from SNRPN to UBE3A (SU) and from UBE3A to GABRB3 (UG) between alleles in each nucleus, 50 cells per subject. The results revealed that the gene-to-gene distance of one allele was longer than that of the other and that the SU ratio (longer/shorter SU distance between alleles) was larger than the UG ratio (longer/shorter UG distance between alleles). The UG distance was relatively stable between alleles; in contrast, the SU distance of one allele was obviously longer than the distance indicated by the genome size. The results therefore indicate that SNRPN, UBE3A, and GABRB3 have non-linear and non-random curved spatial positioning in the normal nucleus, with differences in the SU distance between alleles possibly representing epigenetic evidence of nuclear organization and gene expression.
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Affiliation(s)
- Rie Kawamura
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
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4
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Sinclair P, Bian Q, Plutz M, Heard E, Belmont AS. Dynamic plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions. ACTA ACUST UNITED AC 2010; 190:761-76. [PMID: 20819934 PMCID: PMC2935575 DOI: 10.1083/jcb.200912167] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Interphase chromatin compaction well above the 30-nm fiber is well documented, but the structural motifs underlying this level of chromatin folding remain unknown. Taking a reductionist approach, we analyzed in mouse embryonic stem (ES) cells and ES-derived fibroblasts and erythroblasts the folding of 10-160-megabase pair engineered chromosome regions consisting of tandem repeats of bacterial artificial chromosomes (BACs) containing approximately 200 kilobases of mammalian genomic DNA tagged with lac operator (LacO) arrays. Unexpectedly, linear mitotic and interphase chromatid regions formed from noncontiguously folded DNA topologies. Particularly, in ES cells, these model chromosome regions self-organized with distant sequences segregating into functionally distinct, compact domains. Transcriptionally active and histone H3K27me3-modified regions positioned toward the engineered chromosome subterritory exterior, with LacO repeats and the BAC vector backbone localizing within an H3K9me3, HP1-enriched core. Differential compaction of Dhfr and alpha- and beta-globin transgenes was superimposed on dramatic, lineage-specific reorganization of large-scale chromatin folding, demonstrating a surprising plasticity of large-scale chromatin organization.
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Affiliation(s)
- Paul Sinclair
- Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA
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5
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Philimonenko AA, Janacek J, Snyers L, Almeder M, Berger W, Schmidt W, Schöfer C, Hozák P, Weipoltshammer K. Chromosomal dynamics of cell cycle regulator gene p21 during transcriptional activation. J Struct Biol 2010; 173:382-90. [PMID: 20974257 DOI: 10.1016/j.jsb.2010.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 10/19/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
Abstract
The radial position of a gene within its chromosome territory (CT) in the interphase nucleus is thought to depend on the transcriptional activity of the gene and on transcriptional activity, gene density, and conformation of the chromosomal surrounding. In this study we analyzed the position of the cell cycle regulator gene p21 within the CT of human chromosome 6 (HSA6) upon transcriptional activation. Whereas the majority of active p21 genes is located in the interior of the CT of HSA6, induction of p21 transcription correlates with increased variation of gene localization within the CT and with a higher percentage of p21 genes located at the periphery of the CT. Additionally it demonstrates once more that transcription can take place throughout CTs. Comparison of the p21 locus with two non-coding regions on HSA6 showed that both non-coding sequences are located more frequently in the interior of the CT than p21 genes although they are situated in chromosomal neighborhoods with widely differing gene density and regional transcriptional activity. Thus our data support models describing an influence of the transcriptional activity of a gene on the localization within its CT. However, our data also indicate that additional factors such as chromatin remodeling are implicated in the positioning of genes within the respective chromosome territory.
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Affiliation(s)
- Anatoly A Philimonenko
- Department of the Biology of the Cell Nucleus, Institute of Molecular Genetics, vvi, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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6
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Kocanova S, Kerr EA, Rafique S, Boyle S, Katz E, Caze-Subra S, Bickmore WA, Bystricky K. Activation of estrogen-responsive genes does not require their nuclear co-localization. PLoS Genet 2010; 6:e1000922. [PMID: 20421946 PMCID: PMC2858706 DOI: 10.1371/journal.pgen.1000922] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 03/24/2010] [Indexed: 01/06/2023] Open
Abstract
The spatial organization of the genome in the nucleus plays a role in the regulation of gene expression. Whether co-regulated genes are subject to coordinated repositioning to a shared nuclear space is a matter of considerable interest and debate. We investigated the nuclear organization of estrogen receptor alpha (ERalpha) target genes in human breast epithelial and cancer cell lines, before and after transcriptional activation induced with estradiol. We find that, contrary to another report, the ERalpha target genes TFF1 and GREB1 are distributed in the nucleoplasm with no particular relationship to each other. The nuclear separation between these genes, as well as between the ERalpha target genes PGR and CTSD, was unchanged by hormone addition and transcriptional activation with no evidence for co-localization between alleles. Similarly, while the volume occupied by the chromosomes increased, the relative nuclear position of the respective chromosome territories was unaffected by hormone addition. Our results demonstrate that estradiol-induced ERalpha target genes are not required to co-localize in the nucleus.
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Affiliation(s)
- Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse - UPS, Toulouse, France
- LBME, CNRS, Toulouse, France
| | - Elizabeth A. Kerr
- The Breakthrough Breast Cancer Research Unit, Edinburgh, United Kingdom
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sehrish Rafique
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Shelagh Boyle
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Elad Katz
- The Breakthrough Breast Cancer Research Unit, Edinburgh, United Kingdom
| | - Stephanie Caze-Subra
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse - UPS, Toulouse, France
- LBME, CNRS, Toulouse, France
| | - Wendy A. Bickmore
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse - UPS, Toulouse, France
- LBME, CNRS, Toulouse, France
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7
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Benetatos L, Hatzimichael E, Dasoula A, Dranitsaris G, Tsiara S, Syrrou M, Georgiou I, Bourantas KL. CpG methylation analysis of the MEG3 and SNRPN imprinted genes in acute myeloid leukemia and myelodysplastic syndromes. Leuk Res 2010; 34:148-53. [PMID: 19595458 DOI: 10.1016/j.leukres.2009.06.019] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 06/12/2009] [Accepted: 06/15/2009] [Indexed: 11/25/2022]
Abstract
Methylation is now established as a fundamental regulator of gene transcription. To investigate this in haematologic malignancies, we evaluated the aberrant promoter methylation of two imprinted genes (MEG3 and SNRPN) in 43 MDS and 42 AML patients. MEG3 hypermethylation occurred in 15 MDS patients (34.9%), and in 20 AML patients (47.6%). SNRPN hypermethylation was observed in 15 MDS patients (34.9%), and in 21 AML patients (50%). There were no significant correlations between WHO subtype, WPSS score, karyotype, haemoglobin levels, white blood cell count, platelet count and CpG methylation of any gene. MEG3 hypermethylation was associated with significantly reduced overall survival in individuals with AML (HR=1.98, p=0.04), while SNRPN CpG methylation was not associated with survival (HR=0.94, p=0.87). In addition, no association between survival and aberrant MEG3 (HR=2.15, p=0.072) or SNRPN methylation (HR=1.08, p=0.85) was observed in patients MDS. Our findings suggest that these genes are abnormally methylated in AML and MDS patients, and methylation of MEG3 confers worse overall prognosis. The MEG3 methylation status may serve as a useful biomarker in leukemia.
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Affiliation(s)
- Leonidas Benetatos
- Department of Hematology, University Hospital of Ioannina, Niarchos Avenue, 45500 Ioannina, Greece.
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8
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Mahmud M, Stebbing J. Epigenetic modifications in AML and MDS. Leuk Res 2010; 34:139-40. [DOI: 10.1016/j.leukres.2009.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 07/11/2009] [Accepted: 07/13/2009] [Indexed: 10/20/2022]
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9
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Vitali P, Royo H, Marty V, Bortolin-Cavaillé ML, Cavaillé J. Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J Cell Sci 2010; 123:70-83. [DOI: 10.1242/jcs.054957] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The imprinted Snurf-Snrpn domain, also referred to as the Prader-Willi syndrome region, contains two ∼100-200 kb arrays of repeated small nucleolar (sno)RNAs processed from introns of long, paternally expressed non-protein-coding RNAs whose biogenesis and functions are poorly understood. We provide evidence that C/D snoRNAs do not derive from a single transcript as previously envisaged, but rather from (at least) two independent transcription units. We show that spliced snoRNA host-gene transcripts accumulate near their transcription sites as structurally constrained RNA species that are prevented from diffusing, as well as multiple stable nucleoplasmic RNA foci dispersed in the entire nucleus but not in the nucleolus. Chromatin structure at these repeated arrays displays an outstanding parent-of-origin-specific higher-order organization: the transcriptionally active allele is revealed as extended DNA FISH signals whereas the genetically identical, silent allele is visualized as singlet DNA FISH signals. A similar allele-specific chromatin organization is documented for snoRNA gene arrays at the imprinted Dlk1-Dio3 domain. Our findings have repercussions for understanding the spatial organization of gene expression and the intra-nuclear fate of non-coding RNAs in the context of nuclear architecture.
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Affiliation(s)
- Patrice Vitali
- Université de Toulouse, UPS; Laboratoire de Biologie Moléculaire Eucaryote, F-31000 Toulouse, France
- CNRS; LBME, F-31000 Toulouse, France
| | - Hélène Royo
- Université de Toulouse, UPS; Laboratoire de Biologie Moléculaire Eucaryote, F-31000 Toulouse, France
- CNRS; LBME, F-31000 Toulouse, France
| | - Virginie Marty
- Université de Toulouse, UPS; Laboratoire de Biologie Moléculaire Eucaryote, F-31000 Toulouse, France
- CNRS; LBME, F-31000 Toulouse, France
| | - Marie-Line Bortolin-Cavaillé
- Université de Toulouse, UPS; Laboratoire de Biologie Moléculaire Eucaryote, F-31000 Toulouse, France
- CNRS; LBME, F-31000 Toulouse, France
| | - Jérôme Cavaillé
- Université de Toulouse, UPS; Laboratoire de Biologie Moléculaire Eucaryote, F-31000 Toulouse, France
- CNRS; LBME, F-31000 Toulouse, France
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10
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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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11
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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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Sugimura K, Takebayashi SI, Ogata S, Taguchi H, Okumura K. Non-denaturing fluorescence in situ hybridization to find replication origins in a specific genome region on the DNA fiber. Biosci Biotechnol Biochem 2007; 71:627-32. [PMID: 17284819 DOI: 10.1271/bbb.60662] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a useful method of determining the replication timing of specific genomic loci in mammals and of delineating replicon structures on DNA fibers in combination with in vivo replication labeling. In the case of simultaneous detection of a FISH probe and replicated forks, however, the DNA fibers are damaged by the DNA denaturation step for FISH detection, and the resulting fragmented fluorescence signals prevent analysis at high resolution. Here we found that hybridization of the probe to the genomic DNA was possible even under non-denaturing condition, but only at the time its genomic region replicated. Using the method designated non-denaturing FISH, we determined the replication timing of a specific BAC clone and the standard clones, and found that at least one replication origin exists within the genomic region covered by its BAC clone as an example.
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Affiliation(s)
- Kazuto Sugimura
- Laboratory of Molecular and Cellular Biology, Graduate School of Bioresources, Mie University, Tsu, Mie, Japan
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13
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Zubair M, Ishihara S, Oka S, Okumura K, Morohashi KI. Two-step regulation of Ad4BP/SF-1 gene transcription during fetal adrenal development: initiation by a Hox-Pbx1-Prep1 complex and maintenance via autoregulation by Ad4BP/SF-1. Mol Cell Biol 2006; 26:4111-21. [PMID: 16705164 PMCID: PMC1489093 DOI: 10.1128/mcb.00222-06] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The orphan nuclear receptor Ad4BP/SF-1 (adrenal 4 binding protein/steroidogenic factor 1) is essential for the proper development and function of reproductive and steroidogenic tissues. Although the expression of Ad4BP/SF-1 is specific for those tissues, the mechanisms underlying this tissue-specific expression remain unknown. In this study, we used transgenic mouse assays to examine the regulation of the tissue-specific expression of Ad4BP/SF-1. An investigation of the entire Ad4BP/SF-1 gene locus revealed a fetal adrenal enhancer (FAdE) in intron 4 containing highly conserved binding sites for Pbx-Prep, Pbx-Hox, and Ad4BP/SF-1. Transgenic assays revealed that the Ad4 sites, together with Ad4BP/SF-1, develop an autoregulatory loop and thereby maintain transcription, while the Pbx/Prep and Pbx/Hox sites initiate transcription prior to the establishment of the autoregulatory loop. Indeed, a limited number of Hox family members were found to be expressed in the adrenal primordia. Whether a true fetal-type adrenal cortex is present in mice remained controversial, and this argument was complicated by the postnatal development of the so-called X zone. Using transgenic mice with lacZ driven by the FAdE, we clearly identified a fetal adrenal cortex in mice, and the X zone is the fetal adrenal cells accumulated at the juxtamedullary region after birth.
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Affiliation(s)
- Mohamad Zubair
- Division of Sex Differentiation, National Institute for Basic Biology, Myodaiji-cho, Okazaki 444-8787, Japan
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14
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Clemson CM, Hall LL, Byron M, McNeil J, Lawrence JB. The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences. Proc Natl Acad Sci U S A 2006; 103:7688-93. [PMID: 16682630 PMCID: PMC1472506 DOI: 10.1073/pnas.0601069103] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Indexed: 11/18/2022] Open
Abstract
We investigated whether genes escape X chromosome inactivation by positioning outside of the territory defined by XIST RNA. Results reveal an unanticipated higher order organization of genes and noncoding sequences. All 15 X-linked genes, regardless of activity, position on the border of the XIST RNA territory, which resides outside of the DAPI-dense Barr body. Although more strictly delineated on the inactive X chromosome (Xi), all genes localized predominantly to the outer rim of the Xi and active X chromosome. This outer rim is decorated only by X chromosome DNA paints and is excluded from both the XIST RNA and dense DAPI staining. The only DNA found well within the Barr body and XIST RNA territory was centromeric and Cot-1 DNA; hence, the core of the X chromosome essentially excludes genes and is composed primarily of noncoding repeat-rich DNA. Moreover, we show that this core of repetitive sequences is expressed throughout the nucleus yet is silenced throughout Xi, providing direct evidence for chromosome-wide regulation of "junk" DNA transcription. Collective results suggest that the Barr body, long presumed to be the physical manifestation of silenced genes, is in fact composed of a core of silenced noncoding DNA. Instead of acting at a local gene level, XIST RNA appears to interact with and silence core architectural elements to effectively condense and shut down the Xi.
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Affiliation(s)
- Christine Moulton Clemson
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655
| | - Lisa L. Hall
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655
| | - Meg Byron
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655
| | - John McNeil
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655
| | - Jeanne Bentley Lawrence
- Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655
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15
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Abstract
The mouse jerky gene and its human orthologue, JRK/JH8, encode a putative DNA-binding protein with homology to the CENP-B (centromere-binding protein B). Disruption of the mouse jerky gene by transgene insertion causes generalized recurrent seizures reminiscent of human idiopathic generalized epilepsy. In addition (and similar to a cenp-b null mouse) jerky null mice exhibit postnatal weight loss and reduced fertility. Using fluorescence confocal microscopy, the cellular localization of a JRK-GFP fusion (where GFP stands for green fluorescent protein) was investigated in HeLa cells. JRK-GFP has a dynamic expression pattern in the interphase nucleus, localizing in a small number of punctate nuclear foci and in the nucleolus. The JRK-GFP foci number changes during the cell cycle, but a distinct pattern of three JRK-GFP foci is observed at G(2). The endogenous protein behaves in a similar manner to the GFP-fusion protein. JRK-GFP was found to co-localize with CREST antigens (which recognize the centromere-binding proteins, CENP-A, -B and -C) through S and G(2) phases of interphase and co-localized completely with a subset of PML nuclear bodies at G(2). We speculate that JRK protein associates with a specific chromosomal centromeric locus in G(2), where it associates fully with PML bodies. Research is underway to identify this locus.
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Affiliation(s)
- R Waldron
- Department of Biochemistry, Biosciences Institute, University College Cork, Ireland
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16
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Dehghani H, Dellaire G, Bazett-Jones DP. Organization of chromatin in the interphase mammalian cell. Micron 2005; 36:95-108. [PMID: 15629642 DOI: 10.1016/j.micron.2004.10.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 10/11/2004] [Accepted: 10/12/2004] [Indexed: 12/13/2022]
Abstract
The use of imaging techniques has become an essential tool in cell biology. In particular, advances in fluorescence microscopy and conventional transmission electron microscopy have had a major impact on our understanding of chromatin structure and function. In this review we attempt to chart the conceptual evolution of models describing the organization and function of chromatin in higher eukaryotic cells, in parallel with the advances in light and electron microscopy over the past 50 years. In the last decade alone, the application of energy filtered transmission electron microscopy (EFTEM), also referred to as electron spectroscopic imaging (ESI), has provided many new insights into the organization of chromatin in the interphase nucleus. Based on ESI imaging of chromatin in situ, we propose a 'lattice' model for the organization of chromatin in interphase cells. In this model, the chromatin fibers of 10 and 30nm diameter observed by ESI, produce a meshwork that accommodates an extensive and distributed interchromosomal (IC) space devoid of chromatin. The functional implications of this model for nuclear activity are discussed.
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Affiliation(s)
- Hesam Dehghani
- Programme in Cell Biology, The Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, Ont., Canada M5G 1X8
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17
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Kim SH, McQueen PG, Lichtman MK, Shevach EM, Parada LA, Misteli T. Spatial genome organization during T-cell differentiation. Cytogenet Genome Res 2005; 105:292-301. [PMID: 15237218 DOI: 10.1159/000078201] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2003] [Accepted: 10/17/2003] [Indexed: 11/19/2022] Open
Abstract
The spatial organization of genomes within the mammalian cell nucleus is non-random. The functional relevance of spatial genome organization might be in influencing gene expression programs as cells undergo changes during development and differentiation. To gain insight into the plasticity of genomes in space and time and to correlate the activity of specific genes with their nuclear position, we systematically analyzed the spatial genome organization in differentiating mouse T-cells. We find significant global reorganization of centromeres, chromosomes and gene loci during the differentiation process. Centromeres were repositioned from a preferentially internal distribution in undifferentiated cells to a preferentially peripheral position in differentiated CD4+ and CD8+ cells. Chromosome 6, containing the differentially expressed T-cell markers CD4 and CD8, underwent differential changes in position depending on whether cells differentiated into CD4+ or CD8+ thymocytes. Similarly, the two marker loci CD4 and CD8 showed distinct behavior in their position relative to the chromosome 6 centromere at various stages of differentiation. Our results demonstrate that significant spatial genome reorganization occurs during differentiation and indicate that the relationship between dynamic genome topology and single gene regulation is highly complex.
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Affiliation(s)
- S H Kim
- National Cancer Institute, NIH, Bethesda, MD 20892, USA
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18
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Scheuermann MO, Tajbakhsh J, Kurz A, Saracoglu K, Eils R, Lichter P. Topology of genes and nontranscribed sequences in human interphase nuclei. Exp Cell Res 2005; 301:266-79. [PMID: 15530862 DOI: 10.1016/j.yexcr.2004.08.031] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Revised: 07/03/2004] [Indexed: 01/29/2023]
Abstract
Knowledge about the functional impact of the topological organization of DNA sequences within interphase chromosome territories is still sparse. Of the few analyzed single copy genomic DNA sequences, the majority had been found to localize preferentially at the chromosome periphery or to loop out from chromosome territories. By means of dual-color fluorescence in situ hybridization (FISH), immunolabeling, confocal microscopy, and three-dimensional (3D) image analysis, we analyzed the intraterritorial and nuclear localization of 10 genomic fragments of different sequence classes in four different human cell types. The localization of three muscle-specific genes FLNA, NEB, and TTN, the oncogene BCL2, the tumor suppressor gene MADH4, and five putatively nontranscribed genomic sequences was predominantly in the periphery of the respective chromosome territories, independent from transcriptional status and from GC content. In interphase nuclei, the noncoding sequences were only rarely found associated with heterochromatic sites marked by the satellite III DNA D1Z1 or clusters of mammalian heterochromatin proteins (HP1alpha, HP1beta, HP1gamma). However, the nontranscribed sequences were found predominantly at the nuclear periphery or at the nucleoli, whereas genes tended to localize on chromosome surfaces exposed to the nuclear interior.
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Affiliation(s)
- Markus O Scheuermann
- Division of Molecular Genetics, Deutsches Krebsforschungszentrum, D-69120 Heidelberg, Germany
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19
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Takebayashi SI, Sugimura K, Saito T, Sato C, Fukushima Y, Taguchi H, Okumura K. Regulation of replication at the R/G chromosomal band boundary and pericentromeric heterochromatin of mammalian cells. Exp Cell Res 2004; 304:162-74. [PMID: 15707583 DOI: 10.1016/j.yexcr.2004.10.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2004] [Revised: 10/17/2004] [Accepted: 10/27/2004] [Indexed: 10/26/2022]
Abstract
Mammalian chromosomes consist of multiple replicons; however, in contrast to yeast, the details of this replication process (origin firing, fork progression and termination) relative to specific chromosomal domains remain unclear. Using direct visualization of DNA fibers, here we show that the rate of replication fork movement typically decreases in the early-mid S phase when the replication fork proceeds through the R/G chromosomal band boundary and pericentromeric heterochromatin. To support this, fluorescence in situ hybridization (FISH)-based replication profiles at the human 1q31.1 (R-band)-32.1 (G-band) regions revealed that replication timing switched around at the putative R/G chromosomal band boundary predicted by marked changes in GC content at the sequence level. Thus, the slowdown of replication fork movement is thought to be the general property of the band boundaries separating the functionally different chromosomal domains. By simultaneous visualization of replication fork movement and pericentromeric heterochromatin sequences on DNA fibers, we observed that this region is duplicated by many replication forks, some of which proceed unidirectionally, that originate from clustered replication origins. We showed that histone hyperacetylation is tightly associated with changes in the replication timing of pericentromeric heterochromatin induced by 5-aza-2'-deoxycytidine treatment. These results suggest that, similar to the yeast system, histone modification is involved in controlling the timing of origin firing in mammals.
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Affiliation(s)
- Shin-Ichiro Takebayashi
- Laboratory of Molecular and Cellular Biology, Faculty of Bioresources, Mie University, Tsu, Mie 514-8507, Japan.
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20
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Tsai TF, Bressler J, Jiang YH, Beaudet AL. Disruption of the genomic imprint in trans with homologous recombination at Snrpn in ES cells. Genesis 2004; 37:151-61. [PMID: 14666508 DOI: 10.1002/gene.10237] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In gene targeting studies of the Prader-Willi syndrome (PWS)/Angelman syndrome (AS) domain in mouse ES cells, we recovered only recombinants with the paternal allele for constructs at exons 2 or 3 of the imprinted, maternally silenced Snurf-Snrpn gene. These sites lie close to the imprinting center (IC) for this domain. In contrast, recombinants for Ube3a within the same imprinted domain were recovered with equal frequency on the maternal and paternal alleles. In addition, gene targeting of the paternal allele for Snurf-Snrpn resulted in partial or complete demethylation in trans with activation of expression for the previously silenced maternal allele. The imprint switching of the maternal allele in trans is not readily explained by competition for trans-acting factors and adds to a growing body of evidence indicating homologous association of oppositely imprinted chromatin domains in somatic mammalian cells.
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Affiliation(s)
- Ting-Fen Tsai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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21
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Loidl J. Chromosomes of the budding yeast Saccharomyces cerevisiae. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 222:141-96. [PMID: 12503849 DOI: 10.1016/s0074-7696(02)22014-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mitotic chromosomes of the baker's yeast, Saccharomyces cerevisiae, cannot be visualized by standard cytological methods. Only the study of meiotic bivalents and the synaptonemal complex and the visualization of chromosome-sized DNA molecules on pulsed-field gels have provided some insight into chromosome structure and behavior. More recently, advanced techniques such as in situ hybridization, the illumination of chromosomal loci by GFP-tagged DNA-binding proteins, and immunostaining of chromosomal proteins have promoted our knowledge about yeast chromosomes. These novel cytological approaches in combination with the yeast's advanced biochemistry and genetics have produced a great wealth of information on the interplay between molecular and cytological processes and have strengthened the role of yeast as a leading cell biological model organism. Recent cytological studies have revealed much about the chromosomal organization in interphase nuclei and have contributed significantly to our current understanding of chromosome condensation, sister chromatid cohesion, and centromere orientation in mitosis. Moreover, important details about the biochemistry and ultrastructure of meiotic pairing and recombination have been revealed by combined cytological and molecular approaches. This article covers several aspects of yeast chromosome structure, including their organization within interphase nuclei and their behavior during mitosis and meiosis.
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Affiliation(s)
- Josef Loidl
- Institute of Botany, University of Vienna, A-1030 Vienna, Austria
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22
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Abstract
With the sequence of the human genome now complete, studies must focus on how the genome is functionally organized within the confines of the cell nucleus and the dynamic interplay between the genome and its regulatory factors to effectively control gene expression and silencing. In this review I describe our current state of knowledge with regard to the organization of chromosomes within the nucleus and the positioning of active versus inactive genes. In addition, I discuss studies on the dynamics of chromosomes and specific genetic loci within living cells and its relationship to gene activity and the cell cycle. Furthermore, our current understanding of the distribution and dynamics of RNA polymerase II transcription factors is discussed in relation to chromosomal loci and other nuclear domains.
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Affiliation(s)
- David L Spector
- Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York 11724, USA.
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23
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Mahy NL, Perry PE, Gilchrist S, Baldock RA, Bickmore WA. Spatial organization of active and inactive genes and noncoding DNA within chromosome territories. J Cell Biol 2002; 157:579-89. [PMID: 11994314 PMCID: PMC2173868 DOI: 10.1083/jcb.200111071] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The position of genes within the nucleus has been correlated with their transcriptional activity. The interchromosome domain model of nuclear organization suggests that genes preferentially locate at the surface of chromosome territories. Conversely, high resolution analysis of chromatin fibers suggests that chromosome territories do not present accessibility barriers to transcription machinery. To clarify the relationship between the organization of chromosome territories and gene expression, we have used fluorescence in situ hybridization to analyze the spatial organization of a contiguous approximately 1 Mb stretch of the Wilms' tumor, aniridia, genitourinary anomalies, mental retardation syndrome region of the human genome and the syntenic region in the mouse. These regions contain constitutively expressed genes, genes with tissue-restricted patterns of expression, and substantial regions of intergenic DNA. We find that there is a spatial organization within territories that is conserved between mouse and humans: certain sequences do preferentially locate at the periphery of the chromosome territories in both species. However, we do not detect genes necessarily at the periphery of chromosome territories or at the surface of subchromosomal domains. Intraterritory organization is not different among cell types that express different combinations of the genes under study. Our data demonstrate that transcription of both ubiquitous and tissue-restricted genes is not confined to the periphery of chromosome territories, suggesting that the basal transcription machinery and transcription factors can readily gain access to the chromosome interior.
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Affiliation(s)
- Nicola L Mahy
- Medical Research Council Human Genetics Unit, Edinburgh EH4 2XU, United Kingdom
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24
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Kagotani K, Takebayashi SI, Kohda A, Taguchi H, Paulsen M, Walter J, Reik W, Okumura K. Replication timing properties within the mouse distal chromosome 7 imprinting cluster. Biosci Biotechnol Biochem 2002; 66:1046-51. [PMID: 12092814 DOI: 10.1271/bbb.66.1046] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Genomic imprinting is characterized by allele-specific expression of genes within chromosomal domains. Here we show, using fluorescence in situ hybridization (FISH) analysis, that the large chromosomal domain of the mouse distal chromosome 7 imprinting cluster, approximately 1 Mb in length between p57Kip2 and H19 genes, replicates asynchronously between the two alleles during S-phase. At the telomeric side of this domain, we found a transition from asynchronous replication at the imprinted p57Kip2 gene to synchronous replication at the Nap2 gene. Two-color FISH suggested that the paternal allele of this whole domain replicates earlier than its maternal allele. Treatment of the cells with a histone deacetylase inhibitor abolished this allele-specific feature accompanied with accelerated replication of the later-replicating allele at a domain level. Allele-specific asynchronous replication was observed even in ES cells. These results suggest that this imprinting cluster consists of a large replication domain which is already found at the early stage in development.
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Affiliation(s)
- Kazuhiro Kagotani
- Laboratory of Molecular and Cellular Biology, Faculty of Bioresources, Mie University, Tsu, Japan
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25
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Kagotani K, Nabeshima H, Kohda A, Nakao M, Taguchi H, Okumura K. Visualization of transcription-dependent association of imprinted genes with the nuclear matrix. Exp Cell Res 2002; 274:189-96. [PMID: 11900479 DOI: 10.1006/excr.2002.5478] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genomic imprinting is characterized by allele-specific gene expression as a biological phenomenon. To analyze the participation of the nuclear matrix in the expression of imprinted genes, we first examined the allelic expression state of genes by simultaneously visualizing their primary transcripts and the gene sequences in individual cell nuclei using fluorescence in situ hybridization (FISH). We confirmed that each imprinted gene, SNRPN and UBE3A in human lymphocytes and Igf2 and H19 in mouse embryonic fibroblasts, mainly expressed from one allele, although some nuclei showed biallelic expression. We next visualized the gene sequences on the nuclear matrix by FISH with a tyramide signal amplification technique. Interestingly, we predominantly observed one DNA signal of imprinted genes on the nuclear matrix preparation, closely correlated with their expression patterns. Using patient cells, we confirmed that both the transcription and the binding to the nuclear matrix of the SNRPN gene occurred at the paternal allele. Our results suggest that the nuclear matrix plays an important role in gene expression, including imprinted genes, and that the FISH technique used here allows us to visualize the behaviors of genes at an individual cell level.
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Affiliation(s)
- Kazuhiro Kagotani
- Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Japan
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26
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Takebayashi SI, Manders EM, Kimura H, Taguchi H, Okumura K. Mapping sites where replication initiates in mammalian cells using DNA fibers. Exp Cell Res 2001; 271:263-8. [PMID: 11716538 DOI: 10.1006/excr.2001.5389] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA replication in mammalian chromosomes takes place as a unit of replicon clusters. Here we show a powerful method to detect replication origins and fork movement on DNA fibers from mammalian cells. Cells were loaded with nucleotide analogs, DNA fibers were prepared, and replicated DNA was detected. Using this approach, we could detect origins as close as 10 kb apart and found that the average size of replicon is smaller ( approximately 46 kb) than previously estimated. In addition, the procedure visualizes the complex structure of replicon clusters, e.g. sequential activation of origins in a cluster and flexible initiation sites in different cell cycles. Combined with fluorescence in situ hybridization, replication origins can be mapped in genomic loci including repetitive DNA and a single-copy gene.
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Affiliation(s)
- S I Takebayashi
- Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, 514-8507, Japan
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27
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Takebayashi S, Nakao M, Fujita N, Sado T, Tanaka M, Taguchi H, Okumura K. 5-Aza-2'-deoxycytidine induces histone hyperacetylation of mouse centromeric heterochromatin by a mechanism independent of DNA demethylation. Biochem Biophys Res Commun 2001; 288:921-6. [PMID: 11688997 DOI: 10.1006/bbrc.2001.5863] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
5-Aza-2'-deoxycytidine (5-azadC) is widely used as a potent inhibitor of DNA methyltransferase. Cells treated with this drug show various phenomena such as the reactivation of repressed genes, change in replication timing, and decondensation of heterochromatin. A number of studies using this drug have been reported so far but it is still controversial whether such changes are due to 5-azadC-induced demethylation itself or the side effects of the drug. Here we report that 5-azadC treatment induces histone hyperacetylation in mouse centromeric heterochromatin which normally contains methylated DNA and hypoacetylated histones. Treatment also affects the intranuclear distribution of histone deacetylase 2 (HDAC2). However, histone hyperacetylation was not observed in DNA methyltransferase 1-deficient cells with a reduced level of genomic DNA methylation. Our results suggest that 5-azadC-induced histone hyperacetylation is independent of DNA demethylation and that DNA methylation is not essential for the maintenance of the histone hypoacetylated state in centromeric heterochromatin.
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Affiliation(s)
- S Takebayashi
- Faculty of Bioresources, Mie University, 1515 Kamihama, Tsu, Mie, 514-8507, Japan.
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28
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Kohda A, Taguchi H, Okumura K. Visualization of biallelic expression of the imprinted SNRPN gene induced by inhibitors of DNA methylation and histone deacetylation. Biosci Biotechnol Biochem 2001; 65:1236-9. [PMID: 11440148 DOI: 10.1271/bbb.65.1236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have adapted a fluorescence in situ hybridization (FISH) method to detect nascent RNA molecules of the imprinted SNRPN gene at the initial transcription sites in nuclei of human HL60 and WI38 cells. Simultaneous detection of RNA and DNA of SNRPN by FISH using the cosmid probe confirmed its monoallelic expression in these cell lines. Treatment of both cells by inhibitors of DNA methylation and histone deacetylation resulted in time-dependent increase of the cell population with the biallelic expression of SNRPN.
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Affiliation(s)
- A Kohda
- Laboratory of Molecular and Cellular Biology, Faculty of Bioresources, Mie University, Tsu, Japan
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