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Chu JM, Pease NA, Kueh HY. In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation. Immunol Rev 2021; 300:134-151. [PMID: 33734444 PMCID: PMC8005465 DOI: 10.1111/imr.12946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022]
Abstract
Proper timing of gene expression is central to lymphocyte development and differentiation. Lymphocytes often delay gene activation for hours to days after the onset of signaling components, which act on the order of seconds to minutes. Such delays play a prominent role during the intricate choreography of developmental events and during the execution of an effector response. Though a number of mechanisms are sufficient to explain timing at short timescales, it is not known how timing delays are implemented over long timescales that may span several cell generations. Based on the literature, we propose that a class of cis-regulatory elements, termed "timing enhancers," may explain how timing delays are controlled over these long timescales. By considering chromatin as a kinetic barrier to state switching, the timing enhancer model explains experimentally observed dynamics of gene expression where other models fall short. In this review, we elaborate on features of the timing enhancer model and discuss the evidence for its generality throughout development and differentiation. We then discuss potential molecular mechanisms underlying timing enhancer function. Finally, we explore recent evidence drawing connections between timing enhancers and genetic risk for immunopathology. We argue that the timing enhancer model is a useful framework for understanding how cis-regulatory elements control the central dimension of timing in lymphocyte biology.
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Affiliation(s)
- Jonathan M Chu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
| | - Nicholas A Pease
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
| | - Hao Yuan Kueh
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA
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2
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Diao Y, Li B, Meng Z, Jung I, Lee AY, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B. A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening. Genome Res 2016; 26:397-405. [PMID: 26813977 PMCID: PMC4772021 DOI: 10.1101/gr.197152.115] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/20/2016] [Indexed: 01/01/2023]
Abstract
With <2% of the human genome coding for proteins, a major challenge is to interpret the function of the noncoding DNA. Millions of regulatory sequences have been predicted in the human genome through analysis of DNA methylation, chromatin modification, hypersensitivity to nucleases, and transcription factor binding, but few have been shown to regulate transcription in their native contexts. We have developed a high-throughput CRISPR/Cas9-based genome-editing strategy and used it to interrogate 174 candidate regulatory sequences within the 1-Mbp POU5F1 locus in human embryonic stem cells (hESCs). We identified two classical regulatory elements, including a promoter and a proximal enhancer, that are essential for POU5F1 transcription in hESCs. Unexpectedly, we also discovered a new class of enhancers that contribute to POU5F1 transcription in an unusual way: Disruption of such sequences led to a temporary loss of POU5F1 transcription that is fully restored after a few rounds of cell division. These results demonstrate the utility of high-throughput screening for functional characterization of noncoding DNA and reveal a previously unrecognized layer of gene regulation in human cells.
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Affiliation(s)
- Yarui Diao
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA
| | - Zhipeng Meng
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Inkyung Jung
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA
| | - Ah Young Lee
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA
| | - Jesse Dixon
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA; Medical Scientist Training Program, University of California, San Diego, La Jolla, California 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093, USA
| | - Lenka Maliskova
- Institute for Human Genetics and Department of Neurology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Yin Shen
- Institute for Human Genetics and Department of Neurology, University of California, San Francisco, San Francisco, California 94143, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, California 92093, USA; Department of Cellular and Molecular Medicine, Institute of Genomic Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, USA
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3
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Gallagher PG, Steiner LA, Liem RI, Owen AN, Cline AP, Seidel NE, Garrett LJ, Bodine DM. Mutation of a barrier insulator in the human ankyrin-1 gene is associated with hereditary spherocytosis. J Clin Invest 2010; 120:4453-65. [PMID: 21099109 DOI: 10.1172/jci42240] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 09/22/2010] [Indexed: 11/17/2022] Open
Abstract
Defects of the ankyrin-1 gene are the most common cause in humans of hereditary spherocytosis, an inherited anemia that affects patients of all ethnic groups. In some kindreds, linked -108/-153 nucleotide substitutions have been found in the upstream region of the ankyrin gene promoter that is active in erythroid cells. In vivo, the ankyrin erythroid promoter and its upstream region direct position-independent, uniform expression, a property of barrier insulators. Using human erythroid cell lines and primary cells and transgenic mice, here we have demonstrated that a region upstream of the erythroid promoter is a barrier insulator in vivo in erythroid cells. The region exhibited both functional and structural characteristics of a barrier, including prevention of gene silencing in an in vivo functional assay, appropriate chromatin configuration, and occupancy by barrier-associated proteins. Fragments with the -108/-153 spherocytosis-associated mutations failed to function as barrier insulators in vivo and demonstrated perturbations in barrier-associated chromatin configuration. In transgenic mice, flanking a mutant -108/-153 ankyrin gene promoter with the well-characterized chicken HS4 barrier insulator restored position-independent, uniform expression at levels comparable to wild-type. These data indicate that an upstream region of the ankyrin-1 erythroid promoter acts as a barrier insulator and identify disruption of the barrier element as a potential pathogenetic mechanism of human disease.
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Affiliation(s)
- Patrick G Gallagher
- Departments of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA.
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4
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An insulator with barrier-element activity promotes alpha-spectrin gene expression in erythroid cells. Blood 2008; 113:1547-54. [PMID: 19008453 DOI: 10.1182/blood-2008-06-164954] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Understanding mechanisms controlling expression of the alpha-spectrin gene is important for understanding erythropoiesis, membrane biogenesis, and spectrin-linked hemolytic anemia. We showed previously that a minimal alpha-spectrin promoter directed low levels of expression only in early erythroid development, indicating elements outside the promoter are required for expression in adult erythrocytes. Addition of noncoding exon 1' and intron 1' conferred a 10-fold increase in activity in reporter gene assays. In this report, we used a transgenic mouse model to show that addition of exon 1' and intron 1' to the alpha-spectrin promoter conferred tissue-specific expression of a linked (A)gamma-globin gene in erythroid cells at all developmental stages. Expression was nearly position-independent, as 21 of 23 lines expressed the transgene, and gamma-globin protein was present in 100% of erythrocytes, indicating uniform expression. Additional in vivo studies revealed that exon 1' functions as an insulator with barrier-element activity. Chromatin immunoprecipitation assays demonstrated that this region was occupied by the upstream stimulatory factors 1/2 (USF1/USF2), similar to the well-characterized chicken HS4 insulator. These data identify the first barrier element described in an erythrocyte membrane protein gene and indicate that exon 1' and intron 1' are excellent candidate regions for mutations in patients with spectrin-linked hemolytic anemia.
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5
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Morahan JM, Yu B, Trent RJ, Pamphlett R. Genetic susceptibility to environmental toxicants in ALS. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:885-90. [PMID: 17503480 DOI: 10.1002/ajmg.b.30543] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Environmental toxicants such as heavy metals, pesticides, and chemicals appear to be risk factors for sporadic amyotrophic lateral sclerosis (SALS). An impaired ability to break down these toxicants because of differences in detoxification genes could underlie some cases of this disease. We therefore examined the frequencies of single nucleotide polymorphisms (SNPs) in 186 SALS patients and 186 controls at the allele, genotype, and haplotype levels for the metallothionein (MT) family of genes, metal transcription factor-1 (MTF-1), and glutathione synthetase (GSS). Exposure to heavy metals, solvents/chemicals, and pesticides/herbicides was assessed by questionnaire, and gene-toxicant interactions were analyzed. An intronic SNP upstream of MT-Ie differed in SALS patients and controls at the allele and genotype levels. Haplotypes covering MT-I isoforms also differed between the two groups. Alleles and genotypes of one MTF-1 SNP differed in female SALS patients. One GSS haplotype interacted with both metals and solvents/chemicals to increase the risk of the disease. Differences in genes involved in handling toxicants, and interactions between toxicants and these genes, appear to be present in some patients with SALS. This suggests that impaired detoxification mechanisms play a role in SALS.
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Affiliation(s)
- Julia M Morahan
- The Stacey MND Laboratory, Department of Pathology, The University of Sydney, Sydney, New South Wales 2006, Australia
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6
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Zhang Q, Andersen ME, Conolly RB. Binary gene induction and protein expression in individual cells. Theor Biol Med Model 2006; 3:18. [PMID: 16597340 PMCID: PMC1488830 DOI: 10.1186/1742-4682-3-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 04/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eukaryotic gene transcription is believed to occur in either a binary or a graded fashion. With binary induction, a transcription activator (TA) regulates the probability with which a gene template is switched from the inactive to the active state without affecting the rate at which RNA molecules are produced from the template. With graded, also called rheostat-like, induction the gene template has continuously varying levels of transcriptional activity, and the TA regulates the rate of RNA production. Support for each of these two mechanisms arises primarily from experimental studies measuring reporter proteins in individual cells, rather than from direct measurement of induction events at the gene template. METHODS AND RESULTS In this paper, using a computational model of stochastic gene expression, we have studied the biological and experimental conditions under which a binary induction mode operating at the gene template can give rise to differentially expressed "phenotypes" (i.e., binary, hybrid or graded) at the protein level. We have also investigated whether the choice of reporter genes plays a significant role in determining the observed protein expression patterns in individual cells, given the diverse properties of commonly-used reporter genes. Our simulation confirmed early findings that the lifetimes of active/inactive promoters and half-lives of downstream mRNA/protein products are important determinants of various protein expression patterns, but showed that the induction time and the sensitivity with which the expressed genes are detected are also important experimental variables. Using parameter conditions representative of reporter genes including green fluorescence protein (GFP) and beta-galactosidase, we also demonstrated that graded gene expression is more likely to be observed with GFP, a longer-lived protein with low detection sensitivity. CONCLUSION The choice of reporter genes may determine whether protein expression is binary, graded or hybrid, even though gene induction itself operates in an all-or-none fashion.
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Affiliation(s)
- Qiang Zhang
- Division of Computational Biology, CIIT Centers for Health Research, Research Triangle Park, NC 27709, USA
| | - Melvin E Andersen
- Division of Computational Biology, CIIT Centers for Health Research, Research Triangle Park, NC 27709, USA
| | - Rory B Conolly
- National Center for Computational Toxicology, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA
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7
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Ronai D, Berru M, Shulman MJ. The epigenetic stability of the locus control region-deficient IgH locus in mouse hybridoma cells is a clonally varying, heritable feature. Genetics 2005; 167:411-21. [PMID: 15166165 PMCID: PMC1470874 DOI: 10.1534/genetics.167.1.411] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cis-acting elements such as enhancers and locus control regions (LCRs) prevent silencing of gene expression. We have shown previously that targeted deletion of an LCR in the immunoglobulin heavy-chain (IgH) locus creates conditions in which the immunoglobulin micro heavy chain gene can exist in either of two epigenetically inherited states, one in which micro expression is positive and one in which micro expression is negative, and that the positive and negative states are maintained by a cis-acting mechanism. As described here, the stability of these states, i.e., the propensity of a cell to switch from one state to the other, varied among subclones and was an inherited, clonal feature. A similar variation in stability was seen for IgH loci that both lacked and retained the matrix attachment regions associated with the LCR. Our analysis of cell hybrids formed by fusing cells in which the micro expression had different stabilities indicated that stability was also determined by a cis-acting feature of the IgH locus. Our results thus show that a single-copy gene in the same chromosomal location and in the presence of the same transcription factors can exist in many different states of expression.
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Affiliation(s)
- Diana Ronai
- Immunology Department, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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8
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Pirone JR, Elston TC. Fluctuations in transcription factor binding can explain the graded and binary responses observed in inducible gene expression. J Theor Biol 2004; 226:111-21. [PMID: 14637060 DOI: 10.1016/j.jtbi.2003.08.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Inducible genes are expressed in the presence of an external stimulus. Individual cells may exhibit either a binary or graded response to such signals. It has been hypothesized that the chemical kinetics of transcription factor/DNA interactions can account for both these scenarios (EMBO J. 9(9) (1990) 2835; BioEssays 14(5) (1992) 341). To explore this question, we have conducted work based on the experimental results of Fiering et al. (Genes Dev. 4 (10) (1990) 1823). In these experiments, three upstream NF-AT binding sites control transcription of the lacZ gene, which codes for the enzyme beta-Galactosidase. The experimental data show a binary response for this system. We consider the effects of fluctuations in NF-AT binding on the response of the system. Our modeling results are in good qualitative agreement with the experimental data, and illustrate how the binary and graded responses can stem from the same underlying mechanism.
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Affiliation(s)
- Jason R Pirone
- Biomathematics Graduate Program and Department of Environmental and Molecular Toxicology, Campus Box 8203, North Carolina State University, Raleigh, NC 27695-8203, USA.
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9
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Bondarenko VA, Liu YV, Jiang YI, Studitsky VM. Communication over a large distance: enhancers and insulators. Biochem Cell Biol 2003; 81:241-51. [PMID: 12897858 DOI: 10.1139/o03-051] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Enhancers are regulatory DNA sequences that can work over a large distance. Efficient enhancer action over a distance clearly requires special mechanisms for facilitating communication between the enhancer and its target. While the chromatin looping model can explain the majority of the observations, some recent experimental findings suggest that a chromatin scanning mechanism is used to establish the loop. These new findings help to understand the mechanism of action of the elements that can prevent enhancer-promoter communication (insulators).
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Affiliation(s)
- Vladimir A Bondarenko
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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10
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McBurney MW, Mai T, Yang X, Jardine K. Evidence for repeat-induced gene silencing in cultured Mammalian cells: inactivation of tandem repeats of transfected genes. Exp Cell Res 2002; 274:1-8. [PMID: 11855851 DOI: 10.1006/excr.2001.5443] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Foreign DNA can be readily integrated into the genomes of mammalian embryonic cells by retroviral infection, DNA microinjection, and transfection protocols. However, the transgenic DNA is frequently not expressed or is expressed at levels far below expectation. In a number of organisms such as yeast, plants, Drosophila, and nematodes, silencing of transfected genes is triggered by the interaction between adjacent or dispersed copies of genes of identical sequence. We set out to determine whether a mechanism similar to repeat-induced gene silencing (RIGS) is responsible for the silencing of transgenes in murine embryonal carcinoma stem cells. We compared the expression of identical reporter gene constructs in cells carrying single or multiple copies and found that the level of expression per integrated copy was more than 10-fold higher in single-copy integrants. In cells carrying tandem copies of the transgene, many copies were methylated and clones frequently failed to express both copies of near-identical integrated alleles. Addition of extra copies of the reporter gene coding sequence reduced the level of expression from the same reporter driven by a eukaryotic promoter. We also found that inhibitors of histone deacetylase such as trichostatin A forestall the silencing of multicopy transgenes, suggesting that chromatin mediates the silencing of transfected genes. This evidence is consistent with the idea that RIGS does occur in mammalian embryonic stem cells although silencing of single-copy transgenes also occurs, suggesting that RIGS is only one of the mechanisms responsible for triggering transgene silencing.
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Affiliation(s)
- Michael W McBurney
- Department of Medicine, University of Ottawa, Ottawa Regional Cancer Centre, 503 Smyth Road, Ottawa, Ontario, K1H 1C4, Canada.
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11
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Abstract
Cosuppression, the silencing of dispersed homologous genes triggered by high copy number, may have evolved in eukaryotic organisms to control molecular parasites such as viruses and transposons. Ty1 retrotransposons are dispersed gene repeats in Saccharomyces cerevisiae, where no cosuppression has been previously observed. Ty1 elements are seemingly expressed undeterred to a level as high as 10% of total mRNA. Using Ty1-URA3 reporters and negative selection with 5-fluoroorotic acid, it is shown that Ty1 genes can undergo transcriptional cosuppression that is independent of DNA methylation and polycomb-mediated repression. Expression of Ty1-related genes was shown to be in one of two states, the coexpressed state with all Ty1-related genes transcribed or the cosuppressed state with all Ty1-related genes shut off, without uncoordinated or mosaic expression in any individual cell. Rapid switches between the two states were observed. A high copy number of Ty1 elements was shown to be required for the initiation of Ty1 homology-dependent gene silencing, implying that Ty1 gene expression is under negative feedback control. Ty1 transcriptional repressors facilitated the onset of Ty1 cosuppression, and the native Ty1 promoters were required for Ty1 cosuppression, indicating that Ty1 cosuppression occurs at the transcriptional level.
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Affiliation(s)
- Yi Wei Jiang
- Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, College Station, Texas 77843-1114, USA.
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12
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Abstract
Transcriptional control is generally thought to operate as a binary switch, a behavior that might explain observations such as monoallelic gene expression, stochastic phenotypic changes and bimodal gene activation kinetics. By measuring the activity of the single-copy GAL1 promoter in single cells, we found that changes in the activities of either the transcriptional activator, Gal4 (by simple recruitment with synthetic ligands), or the transcriptional repressor, Mig1, generated graded (non-binary) changes in gene expression that were proportional to signal intensity. However, in the context of the endogenous glucose-responsive signaling pathway, these transcription factors formed part of a binary transcriptional response. Genetic studies demonstrated that this binary response resulted from regulation of a second repressor, Gal80, whereas regulation of Mig1 by a distinct signaling pathway generated graded changes in GAL1 promoter activity. Surprisingly, isogenetic cells can respond to glucose with either binary or graded changes in gene expression, depending on growth conditions. Our studies demonstrate that a given promoter can adapt either binary or graded behavior, and identify the Mig1 and Gal80 genes as necessary for binary versus graded behavior of the Gal1 promoter.
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Affiliation(s)
| | - Gerald R. Crabtree
- Department of Developmental Biology, Howard Hughes Medical Institute, Room B211, Beckman Center, 279 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305-5323, USA
Corresponding author e-mail:
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13
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Ishii H. A statistical-mechanical model for regulation of long-range chromatin structure and gene expression. J Theor Biol 2000; 203:215-28. [PMID: 10716906 DOI: 10.1006/jtbi.2000.1081] [Citation(s) in RCA: 8] [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
In eukaryotic organisms, organization of chromatin is considered to play a role in transcriptional regulation by limiting the accessibility of a gene to the transcription machinery. It is not fully understood, however, how chromatin around a particular locus can be specifically altered to allow transcription. This paper introduces a statistical-mechanical model of chromatin to illustrate a potential mechanism. The model, which is mathematically equivalent to the one-dimensional Ising model of magnetic systems, explains how gene regulatory DNA sequences can affect the chromatin structure over a long distance in cis. The main assumption of the model is cooperativity of histone H1 in binding to the nucleosome array. This cooperativity results in a long-range correlation of histone H1 distribution along the chromatin. Due to this long-range correlation, a gene regulatory element, such as a transcriptional enhancer, may lead to depletion of histone H1 over a large region of chromatin thereby increasing the accessibility of the gene. The model provides a mechanism for a sensitive genetic switch and explains several aspects of gene regulation and chromatin structure.
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Affiliation(s)
- H Ishii
- Graduate Program in Biophysics and Structural Biology, MS 008, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA
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14
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Abstract
Transcriptional enhancers are traditionally considered to regulate the rate at which a linked promoter transcribes mRNA, but recent experiments suggest a reevaluation of this model is necessary. Single-cell assays of transgenes reveal that enhancers increase the probability that a reporter gene will be active, but have little or no effect on the transcription rate once a gene has been activated. These results raise the question of how enhancers affect gene expression in their native contexts. A simple interpretation is that enhancers act in a stochastic fashion to increase the probability that a regulated gene will be transcribed; such a model is compatible with programs of cell differentiation in which multiple similar cells subject to similar environmental stimuli do not respond uniformly.
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Affiliation(s)
- S Fiering
- Department of Microbiology, Dartmouth Medical Center, Lebanon, NH, USA
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15
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Ronai D, Berru M, Shulman MJ. Variegated expression of the endogenous immunoglobulin heavy-chain gene in the absence of the intronic locus control region. Mol Cell Biol 1999; 19:7031-40. [PMID: 10490640 PMCID: PMC84698 DOI: 10.1128/mcb.19.10.7031] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/1999] [Accepted: 07/25/1999] [Indexed: 11/20/2022] Open
Abstract
The expression of chromosomally integrated transgenes usually varies greatly among independent transfectants. This variability in transgene expression has led to the definition of locus control regions (LCRs) as elements which render expression consistent. Analyses of expression in single cells revealed that the expression of transgenes which lack an LCR is often variegated, i.e., on in some cells and off in others. In many cases, transgenes which show variegated expression were found to have inserted near the centromere. These observations have suggested that the LCR prevents variegation by blocking the inhibitory effect of heterochromatin and other repetitive-DNA-containing structures at the insertion site and have raised the question of whether the LCR plays a similar role in endogenous genes. To address this question, we have examined the effects of deleting the LCR from the immunoglobulin heavy-chain locus of a mouse hybridoma cell line in which expression of the immunoglobulin mu heavy-chain gene is normally highly stable. Our analysis of mu expression in single cells shows that deletion of this LCR resulted in variegated expression of the mu gene. That is, in the absence of the LCR, expression of the mu gene in the recombinant locus could be found in either of two epigenetically maintained, metastable states, in which transcription occurred either at the normal rate or not at all. In the absence of the LCR, the on state had a half-life of approximately 100 cell divisions, while the half-life of the off state was approximately 40,000 cell divisions. For recombinants with an intact LCR, the half-life of the on state exceeded 50,000 cell divisions. Our results thus indicate that the LCR increased the stability of the on state by at least 500-fold.
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Affiliation(s)
- D Ronai
- Departments of Immunology and Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada.
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16
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Forsberg EC, Zaboikina TN, Versaw WK, Ahn NG, Bresnick EH. Enhancement of beta-globin locus control region-mediated transactivation by mitogen-activated protein kinases through stochastic and graded mechanisms. Mol Cell Biol 1999; 19:5565-75. [PMID: 10409746 PMCID: PMC84409 DOI: 10.1128/mcb.19.8.5565] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Activation of the mitogen-activated protein kinase (MAPK) pathway enhances long-range transactivation by the beta-globin locus control region (LCR) (W. K. Versaw, V. Blank, N. M. Andrews, and E. H. Bresnick, Proc. Natl. Acad. Sci. USA 95:8756-8760, 1998). The enhancement requires tandem recognition sites for the hematopoietic transcription factor NF-E2 within the hypersensitive site 2 (HS2) subregion of the LCR. To distinguish between mechanisms of induction involving the activation of silent promoters or the increased efficacy of active promoters, we analyzed basal and MAPK-stimulated HS2 enhancer activity in single, living cells. K562 erythroleukemia cells stably transfected with constructs containing the human Agamma-globin promoter linked to an enhanced green fluorescent protein (EGFP) reporter, with or without HS2, were analyzed for EGFP expression by flow cytometry. When most cells in a population expressed EGFP, MAPK augmented the activity of active promoters. However, under conditions of silencing, in which cells reverted to a state with no measurable EGFP expression, MAPK activated silent promoters. Furthermore, studies of populations of EGFP-expressing and non-EGFP-expressing cells isolated by flow cytometry showed that MAPK activation converted nonexpressing cells into expressing cells and increased expression in expressing cells. These results support a model in which MAPK elicits both graded and stochastic responses to increase HS2-mediated transactivation from single chromatin templates.
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Affiliation(s)
- E C Forsberg
- Department of Pharmacology, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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17
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Bahramian MB, Zarbl H. Transcriptional and posttranscriptional silencing of rodent alpha1(I) collagen by a homologous transcriptionally self-silenced transgene. Mol Cell Biol 1999; 19:274-83. [PMID: 9858551 PMCID: PMC83885 DOI: 10.1128/mcb.19.1.274] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/1998] [Accepted: 10/12/1998] [Indexed: 02/05/2023] Open
Abstract
Transient transfection of rodent fibroblasts with plasmids carrying a full-size pro-alpha1(I) collagen gene (pWTC1) results in rapid reduction of the endogenous transcripts by >90%, while the transgene mRNA is undetectable. Using deletion constructs, two adjacent 5' noncoding regions of the gene are identified as causing transcriptional silencing of the endogene in normal and v-fos-transformed cells but not in nontumorigenic revertants, which show partial relief from v-fos transformation-induced alpha1(I) gene suppression. The 3' end of the transgene carries an additional element(s), causing posttranscriptional silencing of the endogene in all cells including the revertant. Data indicate that the transgenes are transcriptionally self-silenced. Genome-integrated transgenes that are transcriptionally active also allow expression of the endogene, suggesting gene activation by chromosomal factors missing in pWTC1. Silencing is not regulated by antisense RNA. Silencing of the endogenous pro-alpha1(I) collagen gene is not linked to the level of transgene expression.
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Affiliation(s)
- M B Bahramian
- Division of Toxicology and Center for Environmental Health Sciences, Whitaker College of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Kringstein AM, Rossi FM, Hofmann A, Blau HM. Graded transcriptional response to different concentrations of a single transactivator. Proc Natl Acad Sci U S A 1998; 95:13670-5. [PMID: 9811858 PMCID: PMC24877 DOI: 10.1073/pnas.95.23.13670] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/1998] [Indexed: 11/18/2022] Open
Abstract
Threshold mechanisms of transcriptional activation are thought to be critical for translating continuous gradients of extracellular signals into discrete all-or-none cellular responses, such as mitogenesis and differentiation. Indeed, unequivocal evidence for a graded transcriptional response in which the concentration of inducer directly correlates with the level of gene expression in individual eukaryotic cells is lacking. By using a novel binary tetracycline regulatable retroviral vector system, we observed a graded rather than a threshold mechanism of transcriptional activation in two different model systems. When polyclonal populations of cells were analyzed at the single cell level, a dose-dependent, stepwise increase in expression of the reporter gene, green fluorescent protein (GFP), was observed by fluorescence-activated cell sorting. These data provide evidence that, in addition to the generally observed all-or-none switch, the basal transcription machinery also can respond proportionally to changes in concentration of extracellular inducers and trancriptional activators.
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Affiliation(s)
- A M Kringstein
- Department of Molecular Pharmacology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5332, USA
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19
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Abstract
In eukaryotes, transcription of genes by RNA polymerase II yields messenger RNA intermediates from which protein products are synthesized. Transcriptional enhancers are discrete DNA elements that contain specific sequence motifs with which DNA-binding proteins interact and transmit molecular signals to genes. Here, current models regarding the role of enhancers in the regulation of transcription by RNA polymerase II are presented.
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Affiliation(s)
- E M Blackwood
- Department of Biology and Center for Molecular Genetics, University of California, San Diego, La Jolla, CA 92093-347, USA
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Affiliation(s)
- J R Gorman
- Howard Hughes Medical Institute, Children's Hospital, Boston, Massachusetts 02115, USA
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21
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Graubert TA, Hug BA, Wesselschmidt R, Hsieh CL, Ryan TM, Townes TM, Ley TJ. Stochastic, stage-specific mechanisms account for the variegation of a human globin transgene. Nucleic Acids Res 1998; 26:2849-58. [PMID: 9611227 PMCID: PMC147660 DOI: 10.1093/nar/26.12.2849] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The random insertion of transgenes into the genomic DNA of mice usually leads to widely variable levels of expression in individual founder lines. To study the mechanisms that cause variegation, we designed a transgene that we expected to variegate, which consisted of a beta-globin locus control region 5' HS-2 linked in tandem to a tagged human beta-globin gene (into which a Lac-Z cassette had been inserted). All tested founder lines exhibited red blood cell-specific expression, but levels of expression varied >1000-fold from the lowest to the highest expressing line. Most of the variation in levels of expression appeared to reflect differences in the percentage of cells in the peripheral blood that expressed the transgene, which ranged from 0.3% in the lowest expressing line to 88% in the highest; the level of transgene expression per cell varied no more than 10-fold from the lowest to the highest expressing line. These differences in expression levels could not be explained by the location of transgene integration, by an effect of beta-galactosidase on red blood cell survival, by the half life of the beta-galactosidase enzyme or by the age of the animals. The progeny of all early erythroid progenitors (BFU-E colony-forming cells) exhibited the same propensity to variegate in methylcellulose-based cultures, suggesting that the decision to variegate occurs after the BFU-E stage of erythroid differentiation. Collectively, these data suggest that variegation in levels of transgene expression are due to local, integration site-dependent phenomena that alter the probability that a transgene will be expressed in an appropriate cell; however, these local effects have a minimal impact on the transgene's activity in the cells that initiate transcription.
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Affiliation(s)
- T A Graubert
- Division of Bone Marrow Transplantation and Stem Cell Biology, Departments of Medicine and Genetics, Washington University School of Medicine, Campus Box 8007, 660 South Euclid Avenue, St Louis, MO 63110-1093, USA.
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22
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Transcriptional Behavior of LCR Enhancer Elements Integrated at the Same Chromosomal Locus by Recombinase-Mediated Cassette Exchange. Blood 1997. [DOI: 10.1182/blood.v90.9.3332] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Efficient integration of transgenes at preselected chromosomal locations was achieved in mammalian cells by recombinase-mediated-cassette-exchange (RMCE), a novel procedure that makes use of the CRE recombinase together with Lox sites bearing different spacer regions. We have applied RMCE to the study of the human β-globin gene Locus Control Region by integrating at the same genetic locus in MEL cells, a LacZ gene driven by the human β-globin promoter linked to HS2 and HS3 alone or in combination with HS4. Expression studies at the cell population level and in individual cells before and after induction of differentiation with hemin or DMSO show that the presence of these enhancers is associated with variegated patterns of expression. We were able to show that the LCR fragments tested act by controlling both the probability of expression and the rate of transcription of the linked β-globin promoter. Both of these factors were also dependent on the state of differentiation of the MELc and on the presence of a second transcription unit located in cis. The ability to manipulate by RMCE constructs integrated into chromosomes should help in the creation of complex, rationally designed, artificial genetic loci.
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