1
|
Tan SN, Sim SP. Matrix association region/scaffold attachment region: the crucial player in defining the positions of chromosome breaks mediated by bile acid-induced apoptosis in nasopharyngeal epithelial cells. BMC Med Genomics 2019; 12:9. [PMID: 30646906 PMCID: PMC6334432 DOI: 10.1186/s12920-018-0465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/21/2018] [Indexed: 11/23/2022] Open
Abstract
Background It has been found that chronic rhinosinusitis (CRS) increases the risk of developing nasopharyngeal carcinoma (NPC). CRS can be caused by gastro-oesophageal reflux (GOR) that may reach nasopharynx. The major component of refluxate, bile acid (BA) has been found to be carcinogenic and genotoxic. BA-induced apoptosis has been associated with various cancers. We have previously demonstrated that BA induced apoptosis and gene cleavages in nasopharyngeal epithelial cells. Chromosomal cleavage occurs at the early stage of both apoptosis and chromosome rearrangement. It was suggested that chromosome breaks tend to cluster in the region containing matrix association region/scaffold attachment region (MAR/SAR). This study hypothesised that BA may cause chromosome breaks at MAR/SAR leading to chromosome aberrations in NPC. This study targeted the AF9 gene located at 9p22 because 9p22 is a deletion hotspot in NPC. Methods Potential MAR/SAR sites were predicted in the AF9 gene by using MAR/SAR prediction tools. Normal nasopharyngeal epithelial cells (NP69) and NPC cells (TWO4) were treated with BA at neutral and acidic pH. Inverse-PCR (IPCR) was used to identify chromosome breaks in SAR region (contains MAR/SAR) and non-SAR region (does not contain MAR/SAR). To map the chromosomal breakpoints within the AF9 SAR and non-SAR regions, DNA sequencing was performed. Results In the AF9 SAR region, the gene cleavage frequencies of BA-treated NP69 and TWO4 cells were significantly higher than those of untreated control. As for the AF9 non-SAR region, no significant difference in cleavage frequency was detected between untreated and BA-treated cells. A few breakpoints detected in the SAR region were mapped within the AF9 region that was previously reported to translocate with the mixed lineage leukaemia (MLL) gene in an acute lymphoblastic leukaemia (ALL) patient. Conclusions Our findings suggest that MAR/SAR may be involved in defining the positions of chromosomal breakages induced by BA. Our report here, for the first time, unravelled the relation of these BA-induced chromosomal breakages to the AF9 chromatin structure. Electronic supplementary material The online version of this article (10.1186/s12920-018-0465-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sang-Nee Tan
- Faculty of Medicine and Health Sciences, Department of Paraclinical Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Sai-Peng Sim
- Faculty of Medicine and Health Sciences, Department of Paraclinical Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia.
| |
Collapse
|
2
|
Abstract
In mouse and human, the genes encoding protamines PRM1, PRM2 and transition protein TNP2 are found clustered together on chromosome 16. In addition, these three genes lie in the same orientation to one another and are coordinately expressed in a haploid-specific manner during spermatogenesis. Previously, we have shown that the human PRM1 --> PRM2 --> TNP2 locus exists as a single chromatin domain bounded by two male germ cell-specific MARs, i.e. Matrix Attachment Regions. A third, somatic-specific MAR element lies immediately 3' of the PRM1 --> PRM2 --> TNP2 domain. This MAR maps to a conserved CpG island 5' of the human SOCS-1 gene. Similarly, two candidate MARs flank the mouse Prm1 --> Prm2 --> Tnp2 domain. Comparative analysis of the mouse and human promoter regions identified several conserved regulatory motifs for each of the genes of this cluster. This further establishes the synteny of this region. Global structural similarities and the functional relevance of the associated candidate regulatory elements are discussed.
Collapse
Affiliation(s)
- Susan M Wykes
- Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Institute for Scientific Computing, Wayne State University, C.S. Mott Center, 275 E. Hancock, Detroit, MI 48201, USA
| | | |
Collapse
|
3
|
Klochkov DB, Gavrilov AA, Vassetzky YS, Razin SV. Early replication timing of the chicken alpha-globin gene domain correlates with its open chromatin state in cells of different lineages. Genomics 2009; 93:481-6. [PMID: 19187796 DOI: 10.1016/j.ygeno.2009.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 12/10/2008] [Accepted: 01/06/2009] [Indexed: 10/21/2022]
Abstract
The vertebrate alpha-globin gene domain is an open chromatin domain overlapping a neighboring house-keeping gene. The tissue-specific cluster of alpha-globin genes and the overlapping housekeeping gene share the same replication origin. We have studied the replication timing of chicken alpha-globin genes in cells of different lineages using the FISH-based approach and found that alpha-globin genes replicate early both in erythroid and in non-erythroid cells, i.e. regardless of their transcriptional activity. Early replication timing of chicken alpha-globin genes in cells of different lineages was in good correlation with the open chromatin configuration of the alpha-globin gene domain in both erythroid and non-erythroid cells. We propose that active transcription of the housekeeping gene overlapping the alpha-globin gene domain enables an access of Origin Recognition Complex (ORC) proteins to the replication origin resulting in early replication of alpha-globin genes even in non-erythroid cells.
Collapse
Affiliation(s)
- Denis B Klochkov
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov Street 34/5, 119334 Moscow, Russia
| | | | | | | |
Collapse
|
4
|
Gavrilov AA, Razin SV. Study of spatial organization of chicken α-globin gene domain by 3c technique. BIOCHEMISTRY (MOSCOW) 2008; 73:1192-9. [DOI: 10.1134/s0006297908110047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Gavrilov AA, Razin SV. Spatial configuration of the chicken alpha-globin gene domain: immature and active chromatin hubs. Nucleic Acids Res 2008; 36:4629-40. [PMID: 18621783 PMCID: PMC2504291 DOI: 10.1093/nar/gkn429] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The spatial configuration of the chicken α-globin gene domain in erythroid and lymphoid cells was studied by using the Chromosome Conformation Capture (3C) approach. Real-time PCR with TaqMan probes was employed to estimate the frequencies of cross-linking of different restriction fragments within the domain. In differentiated cultured erythroblasts and in 10-day chick embryo erythrocytes expressing ‘adult’ αA and αD globin genes the following elements of the domain were found to form an ‘active’ chromatin hub: upstream Major Regulatory Element (MRE), −9 kb upstream DNase I hypersensitive site (DHS), −4 kb upstream CpG island, αD gene promoter and the downstream enhancer. The αA gene promoter was not present in the ‘active’ chromatin hub although the level of αA gene transcription exceeded that of the αD gene. Formation of the ‘active’ chromatin hub was preceded by the assembly of multiple incomplete hubs containing MRE in combination with either −9 kb DHS or other regulatory elements of the domain. These incomplete chromatin hubs were present in proliferating cultured erythroblasts which did not express globin genes. In lymphoid cells only the interaction between the αD promoter and the CpG island was detected.
Collapse
Affiliation(s)
- Alexey A Gavrilov
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 34/5 Vavilov Street, 119334 Moscow, Russia
| | | |
Collapse
|
6
|
Ioudinkova ES, Petrov AV, Vassetzky YS, Razin SV. Spatial Organization of the Chicken α-Globin Gene Domain in Cells of Different Origins. Mol Biol 2005. [DOI: 10.1007/s11008-005-0105-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
7
|
Rincón-Arano H, Valadez-Graham V, Guerrero G, Escamilla-Del-Arenal M, Recillas-Targa F. YY1 and GATA-1 interaction modulate the chicken 3'-side alpha-globin enhancer activity. J Mol Biol 2005; 349:961-75. [PMID: 15913647 DOI: 10.1016/j.jmb.2005.04.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 04/11/2005] [Accepted: 04/19/2005] [Indexed: 11/21/2022]
Abstract
Studying the chicken alpha-globin domain as a model system of gene regulation, we have previously identified contiguous silencer-enhancer elements located on the 3'-side of the domain. To better characterize the enhancer we performed a systematic functional analysis to define its expression influence range and the ubiquitous and stage-specific transcriptional regulators interacting with this control element. In contrast to previous reports, we found that, in addition to a core element that includes three GATA-1 binding sites, the enhancer incorporates a 120 base-pair DNA fragment where EKLF, NF-E2 and a fourth GATA-1 factor could interact. Functional experiments demonstrate that the enhancer activity over the adult alpha(D) promoter is differentially regulated. We found that the transcriptional factor Ying Yang 1 (YY1) binds to the 120 base-pair DNA fragment and its effect over the enhancer activity is GATA-1-dependent. In addition, we characterize a novel physical interaction between GATA-1 and YY1 that influences the enhancer function. Experiments using a histone deacetylation inhibitor indicate that, in pre-erythroblasts, the enhancer down-regulation could be influenced by a closed chromatin conformation. Our observations show that the originally defined enhancer possesses a more complex composition than previously assumed. We propose that its activity is modulated through differential nuclear factor interactions and chromatin modifications at distinct erythroid stages.
Collapse
Affiliation(s)
- Héctor Rincón-Arano
- Instituto de Fisiología Celular, Departamento de Genética Molecular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, México D.F. 04510, México
| | | | | | | | | |
Collapse
|
8
|
Razin SV, Farrell CM, Recillas-Targa F. Genomic domains and regulatory elements operating at the domain level. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 226:63-125. [PMID: 12921236 DOI: 10.1016/s0074-7696(03)01002-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The sequencing of the complete genomes of several organisms, including humans, has so far not contributed much to our understanding of the mechanisms regulating gene expression in the course of realization of developmental programs. In this so-called "postgenomic" era, we still do not understand how (if at all) the long-range organization of the genome is related to its function. The domain hypothesis of the eukaryotic genome organization postulates that the genome is subdivided into a number of semiindependent functional units (domains) that may include one or several functionally related genes, with these domains having well-defined borders, and operate under the control of special (domain-level) regulatory systems. This hypothesis was extensively discussed in the literature over the past 15 years. Yet it is still unclear whether the hypothesis is valid or not. There is evidence both supporting and questioning this hypothesis. The most conclusive data supporting the domain hypothesis come from studies of avian and mammalian beta-globin domains. In this review we will critically discuss the present state of the studies on these and other genomic domains, paying special attention to the domain-level regulatory systems known as locus control regions (LCRs). Based on this discussion, we will try to reevaluate the domain hypothesis of the organization of the eukaryotic genome.
Collapse
Affiliation(s)
- Sergey V Razin
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 117334 Moscow, Russia
| | | | | |
Collapse
|
9
|
Razin SV, Rynditch A, Borunova V, Ioudinkova E, Smalko V, Scherrer K. The 33 kb transcript of the chicken ?-globin gene domain is part of the nuclear matrix. J Cell Biochem 2004; 92:445-57. [PMID: 15156557 DOI: 10.1002/jcb.20066] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Giant nuclear transcripts, and in particular the RNAs of the globin gene domains which are much larger than their canonical pre-mRNAs, have been an enigma for many years. We show here that in avian erythroblastosis virus (AEV)-transformed chicken erythroleukaemic cells, where globin gene expression is abortive, the whole domain of alpha-globin genes is transcribed for about 33 kb in the globin direction and that this RNA is part of the nuclear matrix. Northern blot hybridisation with strand-specific riboprobes, recognising genes and intergenic sequences, and RT-PCR with downstream primers, show that the continuous full domain transcript (FDT) starts in the vicinity of a putative LCR and includes all the genes as well as known regulatory sites, the replication origin, and the DNA loop anchorage region in the upstream area. Absent in chicken fibroblasts, the globin FDT overlaps the major part of the ggPRX housekeeping gene that is transcribed in the opposite direction. RT-PCR and in situ hybridisation with genic and extra-genic globin probes demonstrated that the globin FDT is a component of the nuclear matrix. We suggest that the globin FDTs keep the domain in an active state, and the globin RNAs on the processing pathway are a component of the nuclear matrix. They may take part in the dynamic nuclear architecture when productively processed, or turn over slowly when globins are not synthesised.
Collapse
Affiliation(s)
- Sergey V Razin
- Institut J Monod, 2, Place Jussieu, 75251 Paris, Cedex 05, France.
| | | | | | | | | | | |
Collapse
|
10
|
Zhang Y, Strissel P, Strick R, Chen J, Nucifora G, Le Beau MM, Larson RA, Rowley JD. Genomic DNA breakpoints in AML1/RUNX1 and ETO cluster with topoisomerase II DNA cleavage and DNase I hypersensitive sites in t(8;21) leukemia. Proc Natl Acad Sci U S A 2002; 99:3070-5. [PMID: 11867721 PMCID: PMC122474 DOI: 10.1073/pnas.042702899] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The translocation t(8;21)(q22;q22) is one of the most frequent chromosome translocations in acute myeloid leukemia (AML). AML1/RUNX1 at 21q22 is involved in t(8;21), t(3;21), and t(16;21) in de novo and therapy-related AML and myelodysplastic syndrome as well as in t(12;21) in childhood B cell acute lymphoblastic leukemia. Although DNA breakpoints in AML1 and ETO (at 8q22) cluster in a few introns, the mechanisms of DNA recombination resulting in t(8;21) are unknown. The correlation of specific chromatin structural elements, i.e., topoisomerase II (topo II) DNA cleavage sites, DNase I hypersensitive sites, and scaffold-associated regions, which have been implicated in chromosome recombination with genomic DNA breakpoints in AML1 and ETO in t(8;21) is unknown. The breakpoints in AML1 and ETO were clustered in the Kasumi 1 cell line and in 31 leukemia patients with t(8;21); all except one had de novo AML. Sequencing of the breakpoint junctions revealed no common DNA motif; however, deletions, duplications, microhomologies, and nontemplate DNA were found. Ten in vivo topo II DNA cleavage sites were mapped in AML1, including three in intron 5 and seven in intron 7a, and two were in intron 1b of ETO. All strong topo II sites colocalized with DNase I hypersensitive sites and thus represent open chromatin regions. These sites correlated with genomic DNA breakpoints in both AML1 and ETO, thus implicating them in the de novo 8;21 translocation.
Collapse
MESH Headings
- Adult
- Aged
- Binding Sites
- Child
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Cloning, Molecular
- Core Binding Factor Alpha 2 Subunit
- DNA Topoisomerases, Type II/metabolism
- DNA, Neoplasm/metabolism
- DNA-Binding Proteins/genetics
- Deoxyribonuclease I/metabolism
- Female
- Humans
- Leukemia, Myeloid/genetics
- Male
- Middle Aged
- Multigene Family
- Neoplasm Proteins/genetics
- Proto-Oncogene Proteins/genetics
- RUNX1 Translocation Partner 1 Protein
- Transcription Factors/genetics
- Translocation, Genetic
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- Yanming Zhang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Preferential damage to defined regions of genomic DNA by AT-specific anticancer drugs. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s1067-568x(02)80003-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
12
|
Razin SV, Ioudinkova ES, Scherrer K. Extensive methylation of a part of the CpG island located 3.0-4.5 kbp upstream to the chicken alpha-globin gene cluster may contribute to silencing the globin genes in non-erythroid cells. J Mol Biol 2000; 299:845-52. [PMID: 10843840 DOI: 10.1006/jmbi.2000.3775] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here, we show that in the chicken genome, the domain of alpha-globin genes is preceded by a CpG island of which the downstream part ( approximately 0.65 kbp) is heavily methylated in lymphoid cells; it is either non-methylated or undermethylated in erythroid cells. Recombinant plasmids were constructed with the corresponding DNA fragment (called "uCpG") placed upstream to a reporter CAT gene expressed from the promoter of the alpha(D) chicken globin gene. Selective methylation of CpG dinucleotides within the uCpG fragment suppressed fivefold the expression of the CAT gene, when neither this gene itself nor the alpha(D) promoter were methylated. Methylation of CpG dinucleotides within the alpha(D) gene promoter did not modify the suppression effect exerted by methylated uCpG. We interpret these results within the frame of the hypothesis postulating, that methylation of the upstream CpG island of the chicken alpha-globin gene domain may play an essential role in silencing the alpha-globin genes in non-erythroid cells.
Collapse
Affiliation(s)
- S V Razin
- Institut J. Monod CNRS/Université Paris 7;, 2 Place Jussieu-tour 43, Paris, Cedex 05, 75251, France
| | | | | |
Collapse
|