1
|
Yeshaya J, Amir I, Rimon A, Freedman J, Shohat M, Avivi L. Microdeletion syndromes disclose replication timing alterations of genes unrelated to the missing DNA. Mol Cytogenet 2009; 2:11. [PMID: 19284877 PMCID: PMC2660353 DOI: 10.1186/1755-8166-2-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 03/14/2009] [Indexed: 11/26/2022] Open
Abstract
Background The temporal order of allelic replication is interrelated to the epigenomic profile. A significant epigenetic marker is the asynchronous replication of monoallelically-expressed genes versus the synchronous replication of biallelically-expressed genes. The present study sought to determine whether a microdeletion in the genome affects epigenetic profiles of genes unrelated to the missing segment. In order to test this hypothesis, we checked the replication patterns of two genes – SNRPN, a normally monoallelically expressed gene (assigned to 15q11.13), and the RB1, an archetypic biallelically expressed gene (assigned to 13.q14) in the genomes of patients carrying the 22q11.2 deletion (DiGeorge/Velocardiofacial syndrome) and those carrying the 7q11.23 deletion (Williams syndrome). Results The allelic replication timing was determined by fluorescence in situ hybridization (FISH) technology performed on peripheral blood cells. As expected, in the cells of normal subjects the frequency of cells showing asynchronous replication for SNRPN was significantly (P < 10-12) higher than the corresponding value for RB1. In contrast, cells of the deletion-carrying patients exhibited a reversal in this replication pattern: there was a significantly lower frequency of cells engaging in asynchronous replication for SNRPN than for RB1 (P < 10-4 and P < 10-3 for DiGeorge/Velocardiofacial and Williams syndromes, respectively). Accordingly, the significantly lower frequency of cells showing asynchronous replication for SNRPN than for RB1 is a new epigenetic marker distinguishing these deletion syndrome genotypes from normal ones. Conclusion In cell samples of each deletion-carrying individual, an aberrant, reversed pattern of replication is delineated, namely, where a monoallelic gene replicates more synchronously than a biallelic gene. This inverted pattern, which appears to be non-deletion-specific, clearly distinguishes cells of deletion-carriers from normal ones. As such, it offers a potential epigenetic marker for suspecting a hidden microdeletion that is too small to be detected by conventional karyotyping methods.
Collapse
Affiliation(s)
- Josepha Yeshaya
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Itay Amir
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ayelet Rimon
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Jane Freedman
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Mordechai Shohat
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Lydia Avivi
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
2
|
Amiel A, Drori G, Weinstein G, Fejgin MD. Molecular cytogenetic parameters in fibroblasts of ataxia telangiectasia carrier. ACTA ACUST UNITED AC 2004; 153:102-7. [PMID: 15350298 DOI: 10.1016/j.cancergencyto.2003.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 12/11/2003] [Accepted: 12/12/2003] [Indexed: 10/26/2022]
Abstract
Ataxia telangiectasia (AT) is a pleiotropic and rare (1:40,000 to 1:100,000) recessive disease. Laboratory investigations have failed to detect any consistent anomaly in cells from AT heterozygotes. To estimate random aneuploidy, we applied a fluorescence in situ hybridization technique with alpha-satellite probes for chromosomes 8 and 9 and replication pattern for RB-1, HER-2/neu, and the imprinted SNRPN loci on primary AT carrier fibroblasts. Higher random aneuploidy was not found in the carrier fibroblasts compared to control amniocytic cells. The asynchrony pattern was higher in the AT carrier cells with the RB-1 locus (P=0.057) and significantly higher with the HER-2/neu locus (P < 0.001) compared to control cells. As for the imprinted locus SNRPN, there was a significantly lower asynchrony rate in the AT carriers (P < 10(-5)) compared to the control group. Molecular cytogenetic parameters of random aneuploidy and replication pattern may reflect predisposition for the development of cancer. It is possible that in some AT carriers the genetic instability phenomena associated with the abnormal replication pattern may represent their potential for developing malignancies.
Collapse
Affiliation(s)
- A Amiel
- Genetic Institute, Meir Hospital, Kfar-Saba 44281, Israel.
| | | | | | | |
Collapse
|
3
|
Amiel A, Peretz G, Slor H, Weinstein G, Fejgin MD. Molecular cytogenetic parameters in fibroblasts from patients and carriers of xeroderma pigmentosum. ACTA ACUST UNITED AC 2004; 149:154-60. [PMID: 15036891 DOI: 10.1016/j.cancergencyto.2003.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2003] [Revised: 07/25/2003] [Accepted: 07/30/2003] [Indexed: 11/22/2022]
Abstract
Xeroderma pigmentosum (XP) is a rare autosomal recessive syndrome. Laboratory investigations have failed to detect any consistent anomaly in cells from XP heterozygotic subjects, although examples of behavior intermediate between normal and XP cells have been reported. To estimate random aneuploidy we applied fluorescence in situ hybridization (FISH) with alpha-satellite probes for chromosomes 8 and 9 and replication pattern for TP53 (p53), ERBB2 (HER-2/neu), and MYCN (N-MYC) loci and for the imprinted SNRPN locus. A significantly higher rate of aneuploidy rate was observed in XP patients and carriers than in controls. The asynchrony pattern was significantly higher in XP carriers and patients with all three coding loci analyzed and significantly lower in XP patients and carriers with the imprinted locus SNRPN than in the control group. Molecular cytogenetic parameters such as random aneuploidy and replication pattern, which are known to reflect chromosomal instability, may be part of the tumorigenesis process. In XP patients and carriers, this genetic instability may represent a potential for developing malignancies.
Collapse
Affiliation(s)
- A Amiel
- Sackler School of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel.
| | | | | | | | | |
Collapse
|
4
|
Reish O, Orlovski A, Mashevitz M, Sher C, Libman V, Rosenblat M, Avivi L. Modified allelic replication in lymphocytes of patients with neurofibromatosis type 1. CANCER GENETICS AND CYTOGENETICS 2003; 143:133-9. [PMID: 12781447 DOI: 10.1016/s0165-4608(02)00858-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Transcription activity of genes is related to their replication timing, accordingly gene activation is coupled with a shift from late replication to early replication and vice versa. The relationship between replication timing and gene expression is best manifested by monoallelically expressed genes which show an asynchronous pattern of allelic replication, with the active allele replicating earlier than the inactive counterpart. Biallelically expressed genes, which normally replicate highly synchronously, when present in lymphocytes derived from patients with various types of malignancies or premalignancies, replicate highly asynchronously, similar to monoallelically expressed genes. Since neurofibromatosis-type 1 (NF1) patients are at an increased risk to develop malignancies, we used the fluorescence in situ hybridization (FISH) replication assay and evaluated the level of replication synchrony of three cancer-implicated genes (RB1, AML1, and CMYC) in lymphocytes derived from patients with NF1 without malignancy. Each gene, which normally displayed synchrony in allelic replication, in the patients' cells displayed loss of synchrony. The loss of replication synchrony, of each gene, in the patients' cells was achieved by an advanced replication of a single allele, which replicated remarkably earlier than its normal scheduled timing. In addition, the second allele showed slightly earlier replication timing than that normal for the gene. Thus, it is assumed that the NF1 condition is associated with activation of cancer-implicated genes that may be the cause for increased risk of patients to develop malignancies. As loss of synchrony in allelic replication timing differentiates well between NF1 patients and control subjects, this marker may have a potential use for identification of presymptomatic carriers of NF1 disorders.
Collapse
Affiliation(s)
- Orit Reish
- Genetic Institute, Assaf Harofeh Medical Center, Zerifin, Israel.
| | | | | | | | | | | | | |
Collapse
|
5
|
Bacolla A, Pradhan S, Larson JE, Roberts RJ, Wells RD. Recombinant human DNA (cytosine-5) methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the fragile X CGG.CCG sequence. J Biol Chem 2001; 276:18605-13. [PMID: 11359795 DOI: 10.1074/jbc.m100404200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Steady-state kinetic analyses revealed that the methylation reaction of the human DNA (cytosine-5) methyltransferase 1 (DNMT1) is repressed by the N-terminal domain comprising the first 501 amino acids, and that repression is relieved when methylated DNA binds to this region. DNMT1 lacking the first 501 amino acids retains its preference for hemimethylated DNA. The methylation reaction proceeds by a sequential mechanism, and either substrate (S-adenosyl-l-methionine and unmethylated DNA) may be the first to bind to the active site. However, initial binding of S-adenosyl-l-methionine is preferred. The binding affinities of DNA for both the regulatory and the catalytic sites increase in the presence of methylated CpG dinucleotides and vary considerably (more than one hundred times) according to DNA sequence. DNA topology strongly influences the reaction rates, which increased with increasing negative superhelical tension. These kinetic data are consistent with the role of DNMT1 in maintaining the methylation patterns throughout development and suggest that the enzyme may be involved in the etiology of fragile X, a syndrome characterized by de novo methylation of a greatly expanded CGG.CCG triplet repeat sequence.
Collapse
Affiliation(s)
- A Bacolla
- Institute of Biosciences and Technology, Center for Genome Research, Texas A & M University System Health Science Center, Texas Medical Center, Houston, Texas 77030-3303, USA
| | | | | | | | | |
Collapse
|
6
|
Amiel A, Kitay-Cohen Y, Fejgin MD, Lishner M. Replication status as a marker for predisposition for lymphoma in patients with chronic hepatitis C with and without cryoglobulinemia. Exp Hematol 2000; 28:156-60. [PMID: 10706071 DOI: 10.1016/s0301-472x(99)00140-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Essential mixed cryoglobulinemia (EMC) type II is associated with hepatitis C virus (HCV) in 90% of the patients with this disorder. A significant subset of these patients is at risk to develop non-Hodgkin lymphoma (NHL). The objective of this study was to examine whether the presence of EMC, a presumably premalignant step of lymphoproliferation, is associated with changes in the replication state of normal structural genes. MATERIALS AND METHODS The study group included three subgroups: (1) seven patients with HCV without EMC; (2) eight patients with HCV associated with EMC. 3. Seven patients with follicular lymphoma; and (3) six healthy individuals served as control group. Monocolor fluorescent in situ hybridization (FISH) with probes to p53, RB-1, and 21q22 was applied to leukocytes nuclei for the evaluation of replication timing. RESULTS Asynchronous replication (SD) rate was similar in patients with NHL and those with HCV associated with EMC and both are significantly higher when compared to patients with HCV without EMC and to normal controls (p < 0.01) for each comparison. This held true for all studied loci (21q22, RB-1, and p53). Patients infected by HCV (but without EMC) had a significantly higher rate of asynchronous pattern in comparison with healthy controls (p < 0.01). CONCLUSIONS Patients with a "premalignant" clinical condition HCV with EMC already demonstrate asynchronous type of replication which is similar to patients who already have an established malignant disease (i.e., NHL). In the future, replication may be used to assess the risk of malignant transformation in patients with "benign" proliferation.
Collapse
MESH Headings
- Adult
- Aged
- Biomarkers, Tumor
- Cell Division
- Chromosomes, Human, Pair 21
- Cryoglobulinemia/complications
- Cryoglobulinemia/genetics
- Cryoglobulinemia/pathology
- DNA Replication
- Genes, p53
- Hepatitis C, Chronic/complications
- Hepatitis C, Chronic/genetics
- Hepatitis C, Chronic/pathology
- Humans
- Lymphocytes/pathology
- Lymphoma, Non-Hodgkin/etiology
- Lymphoma, Non-Hodgkin/genetics
- Lymphoma, Non-Hodgkin/pathology
- Male
- Middle Aged
- Predictive Value of Tests
- Retinoblastoma Protein/genetics
Collapse
Affiliation(s)
- A Amiel
- Genetic Institute, Meir Hospital and Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | | | | | | |
Collapse
|
7
|
Amiel A, Litmanovitch T, Lishner M, Mor A, Gaber E, Tangi I, Fejgin M, Avivi L. Temporal differences in replication timing of homologous loci in malignant cells derived from CML and lymphoma patients. Genes Chromosomes Cancer 1998; 22:225-31. [PMID: 9624534 DOI: 10.1002/(sici)1098-2264(199807)22:3<225::aid-gcc8>3.0.co;2-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A close association usually exists between replication timing of a given locus and its transcriptional activity: expressed loci replicate early whereas silent ones replicate late. Accordingly, alleles that show concomitant expression replicate synchronously, while those displaying an allele-specific mode of expression show temporal differences in their replication timing, i.e., they replicate asynchronously. We aimed in our study to see whether the cancer phenotype is accompanied by a relaxation in the temporal control of allelic replication. Fluorescence in situ hybridization (FISH) was used to determine the level of synchronization in replication timing of four pairs of homologous loci in samples of malignant cells derived from patients with chronic myeloid leukemia (CML) and lymphoma and in samples from healthy individuals. Four loci, HER2 mapped to 17q11.2-q12, a locus at 21q22, TP53 mapped to 17q13.1, and MYC mapped to 8q24 were studied. In each sample we analyzed two chromosomal regions, either 17q11.2-q12 and 21q22 or 17p13.1 and 8q24. The results showed distinct differences between healthy individuals and CML/lymphoma patients: all samples derived from noncancerous subjects showed high levels of synchrony in replication timing of alleles, whereas those of cancer patients displayed a large temporal difference in replication timing, indicating early and late replicating alleles. Thus, as judged by four unrelated loci, malignancy is associated with changes in the replication pattern of homologous loci.
Collapse
MESH Headings
- Alleles
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 8/genetics
- DNA Replication
- DNA, Neoplasm/biosynthesis
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Lymphoma/genetics
- Sequence Homology, Nucleic Acid
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- A Amiel
- Genetic Institute, Meir Hospital, Kfar Saba, Israel
| | | | | | | | | | | | | | | |
Collapse
|