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Liu GB, Yan H, Jiang YF, Chen R, Pettigrew JD, Zhao KN. The properties of CpG islands in the putative promoter regions of human immunoglobulin (Ig) genes. Gene 2005; 358:127-38. [PMID: 16112518 DOI: 10.1016/j.gene.2005.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Revised: 05/25/2005] [Accepted: 06/09/2005] [Indexed: 12/27/2022]
Abstract
CpG island is a GC-rich motif occurred in gene promoter region, which can play important roles in gene silencing and imprinting. Here, we present a set of discriminant functions that can recognize the structural and compositional features of CpG islands in the putative promoter regions (PPRs) of human and mouse immunoglobulin (Ig) genes. We showed that the PPRs of both human and mouse Ig genes irrespective of gene chromosomal localization are apparently CpG island poor, with a low percentage of the CpG islands overlapped with the transcription start site (TSS). The human Ig genes that have CpG islands in the PPRs show a very narrow range of CpG densities. 47% of the Ig genes fall in the range of 3.5-4 CpGs/100 bp. In contrast, the non-Ig genes examined have a wide range of the density of CpG island, with 10.5% having the density of 8.1-15 CpGs/100 bp. Meantime, five patterns of the CpG distributions within the CpG islands have been classified: Pat A, B, C, D, and E. 21.6% and 10.8% of the Ig genes fall into the Pat B and Pat D groups, respectively, which were significantly higher than the non-Ig genes examined (8.2% and 3.8%). Moreover, the length of CpG islands is shorter in human Ig genes than in non-Ig genes but is much longer than in mouse orthologues. These findings provide a clear picture of non-neutral and nonrandom occurrence of the CpG islands in the PPRs of human and mouse Ig genes, which facilitate rational recommendations regarding their nomenclature.
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Affiliation(s)
- Guang B Liu
- Vision, Touch and Hearing Research Centre, Faculty of Biomedical Sciences, The University of Queensland, Brisbane, Qld 4072, Australia.
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Kalmanovich G, Mehr R. Models for antigen receptor gene rearrangement. III. Heavy and light chain allelic exclusion. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:182-93. [PMID: 12496399 DOI: 10.4049/jimmunol.170.1.182] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The extent of allelic exclusion in Ig genes is very high, although not absolute. Thus far, it has not been clearly established whether rapid selection of the developing B cell as soon as it has achieved the first productively rearranged, functional heavy chain is the only mechanism responsible for allelic exclusion. Our computational models of Ag receptor gene rearrangement in B lymphocytes are hereby extended to calculate the expected fractions of heavy chain allelically included newly generated B cells as a function of the probability of heavy chain pairing with the surrogate light chain, and the probability that the cell would test this pairing immediately after the first rearrangement. The expected fractions for most values of these probabilities significantly exceed the levels of allelic inclusion in peripheral B cells, implying that in most cases productive rearrangement and subsequent cell surface expression of one allele of the heavy chain gene probably leads to prevention of rearrangement completion on the other allele, and that additional mechanisms, such as peripheral selection disfavoring cells with two productively rearranged heavy chain genes, may also play a role. Furthermore, we revisit light chain allelic exclusion by utilizing the first (to our knowledge) computational model which addresses and enumerates B cells maturing with two productively rearranged kappa light chain genes. We show that, assuming that there are no selection mechanisms responsible for abolishing cells expressing two light chains, the repertoire of newly generated B lymphocytes exiting the bone marrow must contain a significant fraction of such kappa double-productive B cells.
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Affiliation(s)
- Gil Kalmanovich
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Simon I, Tenzen T, Mostoslavsky R, Fibach E, Lande L, Milot E, Gribnau J, Grosveld F, Fraser P, Cedar H. Developmental regulation of DNA replication timing at the human beta globin locus. EMBO J 2001; 20:6150-7. [PMID: 11689454 PMCID: PMC125288 DOI: 10.1093/emboj/20.21.6150] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human beta globin locus replicates late in most cell types, but becomes early replicating in erythroid cells. Using FISH to map DNA replication timing around the endogenous beta globin locus and by applying a genetic approach in transgenic mice, we have demonstrated that both the late and early replication states are controlled by regulatory elements within the locus control region. These results also show that the pattern of replication timing is set up by mechanisms that work independently of gene transcription.
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Affiliation(s)
- Itamar Simon
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Toyoaki Tenzen
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Raul Mostoslavsky
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Eitan Fibach
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Laura Lande
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Eric Milot
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Joost Gribnau
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Frank Grosveld
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Peter Fraser
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
| | - Howard Cedar
- Department of Cellular Biochemistry and Department of Hematology, Hebrew University Medical School, Jerusalem, Israel 91120, Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka-ken, Japan 411-8540 and
MGC Department of Cell Biology and Genetics, Erasmus University, PO Box 1738, 3000 DR Rotterdam, The Netherlands Present address: Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Corresponding author e-mail: I.Simon and T.Tenzen contributed equally to this work
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