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The 3'-Jα Region of the TCRα Locus Bears Gene Regulatory Activity in Thymic and Peripheral T Cells. PLoS One 2015; 10:e0132856. [PMID: 26177549 PMCID: PMC4503570 DOI: 10.1371/journal.pone.0132856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/18/2015] [Indexed: 11/19/2022] Open
Abstract
Much progress has been made in understanding the important cis-mediated controls on mouse TCRα gene function, including identification of the Eα enhancer and TCRα locus control region (LCR). Nevertheless, previous data have suggested that other cis-regulatory elements may reside in the locus outside of the Eα/LCR. Based on prior findings, we hypothesized the existence of gene regulatory elements in a 3.9-kb region 5’ of the Cα exons. Using DNase hypersensitivity assays and TCRα BAC reporter transgenes in mice, we detected gene regulatory activity within this 3.9-kb region. This region is active in both thymic and peripheral T cells, and selectively affects upstream, but not downstream, gene expression. Together, these data indicate the existence of a novel cis-acting regulatory complex that contributes to TCRα transgene expression in vivo. The active chromatin sites we discovered within this region would remain in the locus after TCRα gene rearrangement, and thus may contribute to endogenous TCRα gene activity, particularly in peripheral T cells, where the Eα element has been found to be inactive.
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Barkess G, West AG. Chromatin insulator elements: establishing barriers to set heterochromatin boundaries. Epigenomics 2012; 4:67-80. [PMID: 22332659 DOI: 10.2217/epi.11.112] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Epigenomic profiling has revealed that substantial portions of genomes in higher eukaryotes are organized into extensive domains of transcriptionally repressive chromatin. The boundaries of repressive chromatin domains can be fixed by DNA elements known as barrier insulators, to both shield neighboring gene expression and to maintain the integrity of chromosomal silencing. Here, we examine the current progress in identifying vertebrate barrier elements and their binding factors. We overview the design of the reporter assays used to define enhancer-blocking and barrier insulators. We look at the mechanisms vertebrate barrier proteins, such as USF1 and VEZF1, employ to counteract Polycomb- and heterochromatin-associated repression. We also undertake a critical analysis of whether CTCF could also act as a barrier protein. There is good evidence that barrier elements in vertebrates can form repressive chromatin domain boundaries. Future studies will determine whether barriers are frequently used to define repressive domain boundaries in vertebrates.
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Affiliation(s)
- Gráinne Barkess
- Institute of Cancer Sciences, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, Scotland, UK
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Ter-Minassian M, Wang Z, Asomaning K, Wu MC, Liu CY, Paulus JK, Liu G, Bradbury PA, Zhai R, Su L, Frauenhoffer CS, Hooshmand SM, De Vivo I, Lin X, Christiani DC, Kulke MH. Genetic associations with sporadic neuroendocrine tumor risk. Carcinogenesis 2011; 32:1216-22. [PMID: 21606320 DOI: 10.1093/carcin/bgr095] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genetic risk factors for sporadic neuroendocrine tumors (NET) are poorly understood. We tested risk associations in patients with sporadic NET and non-cancer controls, using a custom array containing 1536 single-nucleotide polymorphisms (SNPs) in 355 candidate genes. We identified 18 SNPs associated with NET risk at a P-value <0.01 in a discovery set of 261 cases and 319 controls. Two of these SNPs were found to be significantly associated with NET risk in an independent replication set of 235 cases and 113 controls, at a P value ≤0.05. An SNP in interleukin 12A (IL12A rs2243123), a gene implicated in inflammatory response, replicated with an adjusted odds ratio (95% confidence interval) (aOR) = 1.47 (1.03, 2.11) P-trend = 0.04. A second SNP in defender against cell death, (DAD1 rs8005354), a gene that modulates apoptosis, replicated at aOR = 1.43 (1.02, 2.02) P-trend = 0.04. Consistent with our observations, a pathway analysis, performed in the discovery set, suggested that genetic variation in inflammatory pathways or apoptosis pathways is associated with NET risk. Our findings support further investigation of the potential role of IL12A and DAD1 in the etiology of NET.
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Affiliation(s)
- Monica Ter-Minassian
- Environmental and Occupational Medicine and Epidemiology Program, Department of Environmental Health, Harvard School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.
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Knirr S, Gomos-Klein J, Andino BE, Harrow F, Erhard KF, Kovalovsky D, Sant'Angelo DB, Ortiz BD. Ectopic T cell receptor-α locus control region activity in B cells is suppressed by direct linkage to two flanking genes at once. PLoS One 2010; 5:e15527. [PMID: 21124935 PMCID: PMC2989920 DOI: 10.1371/journal.pone.0015527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/06/2010] [Indexed: 11/18/2022] Open
Abstract
The molecular mechanisms regulating the activity of the TCRα gene are required for the production of the circulating T cell repertoire. Elements of the mouse TCRα locus control region (LCR) play a role in these processes. We previously reported that TCRα LCR DNA supports a gene expression pattern that mimics proper thymus-stage, TCRα gene-like developmental regulation. It also produces transcription of linked reporter genes in peripheral T cells. However, TCRα LCR-driven transgenes display ectopic transcription in B cells in multiple reporter gene systems. The reasons for this important deviation from the normal TCRα gene regulation pattern are unclear. In its natural locus, two genes flank the TCRα LCR, TCRα (upstream) and Dad1 (downstream). We investigated the significance of this gene arrangement to TCRα LCR activity by examining transgenic mice bearing a construct where the LCR was flanked by two separate reporter genes. Surprisingly, the presence of a second, distinct, reporter gene downstream of the LCR virtually eliminated the ectopic B cell expression of the upstream reporter observed in earlier studies. Downstream reporter gene activity was unaffected by the presence of a second gene upstream of the LCR. Our findings indicate that a gene arrangement in which the TCRα LCR is flanked by two distinct transcription units helps to restrict its activity, selectively, on its 5′-flanking gene, the natural TCRα gene position with respect to the LCR. Consistent with these findings, a TCRα/Dad1 locus bacterial artificial chromosome dual-reporter construct did not display the ectopic upstream (TCRα) reporter expression in B cells previously reported for single TCRα transgenes.
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Affiliation(s)
- Stefan Knirr
- Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States of America
| | - Janette Gomos-Klein
- Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States of America
| | - Blanca E. Andino
- Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States of America
| | - Faith Harrow
- Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States of America
| | - Karl F. Erhard
- Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States of America
| | - Damian Kovalovsky
- Division of Immunology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Derek B. Sant'Angelo
- Division of Immunology, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Benjamin D. Ortiz
- Department of Biological Sciences, City University of New York, Hunter College, New York, New York, United States of America
- * E-mail:
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Kulke MH, Freed E, Chiang DY, Philips J, Zahrieh D, Glickman JN, Shivdasani RA. High-resolution analysis of genetic alterations in small bowel carcinoid tumors reveals areas of recurrent amplification and loss. Genes Chromosomes Cancer 2008; 47:591-603. [DOI: 10.1002/gcc.20561] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Gomos-Klein J, Harrow F, Alarcón J, Ortiz BD. CTCF-Independent, but Not CTCF-Dependent, Elements Significantly Contribute to TCR-α Locus Control Region Activity. THE JOURNAL OF IMMUNOLOGY 2007; 179:1088-95. [PMID: 17617601 DOI: 10.4049/jimmunol.179.2.1088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mouse TCRalpha/TCRdelta/Dad1 gene locus bears a locus control region (LCR) that drives high-level, position-independent, thymic transgene expression in chromatin. It achieves this through DNA sequences that enhance transcription and protect transgene expression from integration site-dependent position effects. The former activity maps to a classical enhancer region (Ealpha). In contrast, the elements supporting the latter capacity that suppresses position effects are incompletely understood. Such elements likely play important roles in their native locus and may resemble insulator/boundary sequences. Insulators support enhancer blocking and/or chromatin barrier activity. Most vertebrate enhancer-blocking insulators are dependent on the CTCF transcription factor and its cognate DNA binding site. However, studies have also revealed CTCF-independent enhancer blocking and barrier insulator activity in the vertebrate genome. The TCRalpha LCR contains a CTCF-dependent and multiple CTCF-independent enhancer-blocking regions whose roles in LCR activity are unknown. Using randomly integrated reporter transgenes in mice, we find that the CTCF region plays a very minor role in LCR function. In contrast, we report the in vivo function of two additional downstream elements located in the region of the LCR that supports CTCF-independent enhancer-blocking activity in cell culture. Internal deletion of either of these elements significantly impairs LCR activity. These results reveal that the position-effect suppression region of the TCRalpha LCR harbors an array of CTCF-independent, positive-acting gene regulatory elements, some of which share characteristics with barrier-type insulators. These elements may help manage the separate regulatory programs of the TCRalpha and Dad1 genes.
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Affiliation(s)
- Janette Gomos-Klein
- Department of Biological Sciences, City University of New York, Hunter College, New York, NY 10021, USA
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Harrow F, Ortiz BD. The TCRalpha locus control region specifies thymic, but not peripheral, patterns of TCRalpha gene expression. THE JOURNAL OF IMMUNOLOGY 2006; 175:6659-67. [PMID: 16272321 DOI: 10.4049/jimmunol.175.10.6659] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The molecular mechanisms ensuring the ordered expression of TCR genes are critical for proper T cell development. The mouse TCR alpha-chain gene locus contains a cis-acting locus control region (LCR) that has been shown to direct integration site-independent, lymphoid organ-specific expression of transgenes in vivo. However, the fine cell type specificity and developmental timing of TCRalpha LCR activity are both still unknown. To address these questions, we established a transgenic reporter model of TCRalpha LCR function that allows for analysis of LCR activity in individual cells by the use of flow cytometry. In this study we report the activation of TCRalpha LCR activity at the CD4-CD8-CD25-CD44- stage of thymocyte development that coincides with the onset of endogenous TCRalpha gene rearrangement and expression. Surprisingly, TCRalpha LCR activity appears to decrease in peripheral T cells where TCRalpha mRNA is normally up-regulated. Furthermore, LCR-linked transgene activity is evident in gammadelta T cells and B cells. These data show that the LCR has all the elements required to reliably reproduce a developmentally correct TCRalpha-like expression pattern during thymic development and unexpectedly indicate that separate gene regulatory mechanisms are acting on the TCRalpha gene in peripheral T cells to ensure its high level and fine cell type-specific expression.
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Affiliation(s)
- Faith Harrow
- Department of Biological Sciences, City University of New York, Hunter College, New York, NY 10021, USA
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Abstract
Coregulation of lymphoid-specific gene sets is achieved by a series of epigenetic mechanisms. Association with higher-order chromosomal structures (nuclear subcompartments repressing or favouring gene expression) and locus control regions affects recombination and transcription of clonotypic antigen receptors and expression of a series of other lymphoid-specific genes. Locus control regions can regulate DNA methylation patterns in their vicinity. They may induce tissue- and site-specific DNA demethylation and affect, thereby, accessibility to recombination-activating proteins, transcription factors, and enzymes involved in histone modifications. Both DNA methylation and the Polycomb group of proteins (PcG) function as alternative systems of epigenetic memory in lymphoid cells. Complexes of PcG proteins mark their target genes by covalent histone tail modifications and influence lymphoid development and rearrangement of IgH genes. Ectopic expression of protein noncoding microRNAs may affect the generation of B-lineage cells, too, by guiding effector complexes to sites of heterochromatin assembly. Coregulation of lymphoid and viral promoters is also possible. EBNA 2, a nuclear protein encoded by episomal Epstein-Barr virus genomes, binds to the cellular protein CBF1 (C promoter binding factor 1) and operates, thereby, a regulatory network to activate latent viral promoters and cellular promoters associated with CBF1 binding sites.Key words : lymphoid cells, coregulation of gene batteries, epigenetic regulation, nuclear subcompartment switch, locus control region, DNA methylation, Polycomb group of proteins, histone modifications, microRNA, Epstein-Barr virus, EBNA 2, regulatory network.
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Affiliation(s)
- Ildikó Györy
- Microbiological Research Group, National Center for Epidemiology, Budapest, Hungary
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Krangel MS, Carabana J, Abbarategui I, Schlimgen R, Hawwari A. Enforcing order within a complex locus: current perspectives on the control of V(D)J recombination at the murine T-cell receptor alpha/delta locus. Immunol Rev 2004; 200:224-32. [PMID: 15242408 DOI: 10.1111/j.0105-2896.2004.00155.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
V(D)J recombination proceeds according to defined developmental programs at T-cell receptor (TCR) and immunoglobulin loci as a function of cell lineage and stage of differentiation. Although the molecular details are still lacking, such regulation is thought to occur at the level of accessibility of chromosomal recombination signal sequences to the recombinase. The unique and complex organization of the TCRalpha/delta locus poses intriguing regulatory challenges in this regard: embedded TCRalpha and TCRdelta gene segments rearrange at distinct stages of thymocyte development, there is a highly regulated progression of primary followed by secondary rearrangements involving Jalpha segments, and there are important developmental constraints on V gene segment usage. The locus therefore provides a fascinating laboratory in which to explore the basic mechanisms underlying developmental control. We provide here a current view of cis-acting mechanisms that enforce the TCRalpha/delta locus developmental program, and we emphasize the unresolved issues that command the attention of our and other laboratories.
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Affiliation(s)
- Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.
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Magdinier F, Yusufzai TM, Felsenfeld G. Both CTCF-dependent and -independent Insulators Are Found between the Mouse T Cell Receptor α and Dad1 Genes. J Biol Chem 2004; 279:25381-9. [PMID: 15082712 DOI: 10.1074/jbc.m403121200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The T cell rearrangement of the T cell receptor (TCR) genes TCRalpha and delta is specifically regulated by a complex interplay between enhancer elements and chromatin structure. The alpha enhancer is active in T cells and drives TCRalpha recombination in collaboration with a locus control region-like element located downstream of the Calpha gene on mouse chromosome 14. Twelve kb further down-stream lies another gene, Dad1, with a program of expression different from that of TCRalpha. The approximately 6-kb locus control region element lying between them contains multiple regulatory sites with a variety of roles in regulating the two genes. Previous evidence has indicated that among these there are widely distributed regions with enhancer blocking (insulating) activity. We have shown in this report that one of these sites, not previously examined, strongly binds the insulator protein CCTC-binding factor (CTCF) in vitro and in vivo and can function in an enhancer blocking assay. However, other regions within the 6-kb element that also can block enhancers clearly do not harbor CTCF sites and thus must reflect the presence of a previously undetected and distinct vertebrate insulator activity.
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Affiliation(s)
- Frédérique Magdinier
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0504, USA
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Harrow F, Amuta JU, Hutchinson SR, Akwaa F, Ortiz BD. Factors Binding a Non-classical Cis-element Prevent Heterochromatin Effects on Locus Control Region Activity. J Biol Chem 2004; 279:17842-9. [PMID: 14966120 DOI: 10.1074/jbc.m401258200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A locus control region (LCR) is a cis-acting gene-regulatory element capable of transferring the expression characteristics of its gene locus of origin to a linked transgene. Furthermore, it can do this independently of the site of integration in the genome of transgenic mice. Although most LCRs contain subelements with classical transcriptional enhancer function, key aspects of LCR activity are supported by cis-acting sequences devoid of the ability to act as direct transcriptional enhancers. Very few of these "non-enhancer" LCR components have been characterized. Consequently, the sequence requirements and molecular bases for their functions, as well as their roles in LCR activity, are poorly understood. We have investigated these questions using the LCR from the mouse T cell receptor (TCR) alpha/Dad1 gene locus. Here we focus on DNase hypersensitive site (HS) 6 of the TCRalpha LCR. HS6 does not support classical enhancer activity, yet has gene regulatory activity in an in vivo chromatin context. We have identified three in vivo occupied factor-binding sites within HS6, two of which interact with Runx1 and Elf-1 factors. Deletion of these sites from the LCR impairs its activity in vivo. This mutation renders the transgene locus abnormally inaccessible in chromatin, preventing the normal function of other LCR subelements and reducing transgene mRNA levels. These data show these factor-binding sites are required for preventing heterochromatin formation and indicate that they function to maintain an active TCRalpha LCR assembly in vivo.
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Affiliation(s)
- Faith Harrow
- Department of Biological Sciences, City University of New York, Hunter College, New York, New York 10021, USA
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Felsenfeld G, Burgess-Beusse B, Farrell C, Gaszner M, Ghirlando R, Huang S, Jin C, Litt M, Magdinier F, Mutskov V, Nakatani Y, Tagami H, West A, Yusufzai T. Chromatin boundaries and chromatin domains. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 69:245-50. [PMID: 16117655 DOI: 10.1101/sqb.2004.69.245] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Affiliation(s)
- G Felsenfeld
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0540, USA
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Xu L, Tsuji K, Mostowski H, Candotti F, Rosenberg A. Evidence that the mouse 3' kappa light chain enhancer confers position-independent transgene expression in T- and B-lineage cells. Hum Gene Ther 2003; 14:1753-64. [PMID: 14670126 DOI: 10.1089/104303403322611764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the major obstacles for successful application of murine leukemia virus (MLV) vectors to genetic therapy of lymphocyte disorders is low levels of transgene expression or the eventual loss of expression. To overcome this problem, an improved retroviral vector was constructed utilizing the myeloproliferative sarcoma virus (MPSV) long terminal repeat (LTR), which provided a significantly higher level of transgene expression in human lymphoid cells than did MLV vectors. Nevertheless, transgene expression remained low in a large percentage of transduced cells. To address whether lymphocyte enhancer elements might improve transgene expression mediated by retroviral vectors in lymphocytes, we cloned the mouse immunoglobulin 3' kappa light chain enhancer gene (mE3') into the MPSV vector. We found that the mE3' conferred a higher, more uniform and sustained level of expression in transduced T- and B-cell lines, and in primary T cells, than did the control vector lacking this element. Integration sites were diverse and a single copy of the proviral genome was present in all examined transduced cells. The mE3' failed to enhance transgene expression in most nonlymphoid cells, indicating it is relatively lineage-specific. Taken together, these results provide strong evidence that the mE3' functions as a locus control region (LCR) in conferring enhanced integration-site-independent expression of a retroviral transgene.
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Affiliation(s)
- Lai Xu
- Division of Therapeutic Proteins, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA
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Bulger M, Schübeler D, Bender MA, Hamilton J, Farrell CM, Hardison RC, Groudine M. A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus. Mol Cell Biol 2003; 23:5234-44. [PMID: 12861010 PMCID: PMC165715 DOI: 10.1128/mcb.23.15.5234-5244.2003] [Citation(s) in RCA: 139] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In order to create an extended map of chromatin features within a mammalian multigene locus, we have determined the extent of nuclease sensitivity and the pattern of histone modifications associated with the mouse beta-globin genes in adult erythroid tissue. We show that the nuclease-sensitive domain encompasses the beta-globin genes along with several flanking olfactory receptor genes that are inactive in erythroid cells. We describe enhancer-blocking or boundary elements on either side of the locus that are bound in vivo by the transcription factor CTCF, but we found that they do not coincide with transitions in nuclease sensitivity flanking the locus or with patterns of histone modifications within it. In addition, histone hyperacetylation and dimethylation of histone H3 K4 are not uniform features of the nuclease-sensitive mouse beta-globin domain but rather define distinct subdomains within it. Our results reveal a complex chromatin landscape for the active beta-globin locus and illustrate the complexity of broad structural changes that accompany gene activation.
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Affiliation(s)
- Michael Bulger
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Abstract
Locus control regions (LCRs) are operationally defined by their ability to enhance the expression of linked genes to physiological levels in a tissue-specific and copy number-dependent manner at ectopic chromatin sites. Although their composition and locations relative to their cognate genes are different, LCRs have been described in a broad spectrum of mammalian gene systems, suggesting that they play an important role in the control of eukaryotic gene expression. The discovery of the LCR in the beta-globin locus and the characterization of LCRs in other loci reinforces the concept that developmental and cell lineage-specific regulation of gene expression relies not on gene-proximal elements such as promoters, enhancers, and silencers exclusively, but also on long-range interactions of various cis regulatory elements and dynamic chromatin alterations.
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Affiliation(s)
- Qiliang Li
- Division of Medical Genetics, Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
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