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Ye T, Ma W. ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures. Nucleic Acids Res 2020; 48:e123. [PMID: 33074315 PMCID: PMC7708071 DOI: 10.1093/nar/gkaa872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/15/2020] [Accepted: 09/24/2020] [Indexed: 12/29/2022] Open
Abstract
The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to incorrect modeling of diploid genome architecture. Here we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under the Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that ASHIC methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, in the analyses of diploid Hi-C datasets in mouse and human, our ASHIC-ZIPM method produced fine-resolution diploid chromatin maps and 3D structures and provided insights into the allelic chromatin organizations and functions. To summarize, our work provides a statistically rigorous framework for investigating fine-scale allele-specific chromatin conformations. The ASHIC software is publicly available at https://github.com/wmalab/ASHIC.
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Affiliation(s)
- Tiantian Ye
- Genetics, Genomics and Bioinformatics Program
| | - Wenxiu Ma
- Department of Statistics, University of California Riverside, Riverside, CA 92521, USA
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2
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Llères D, Moindrot B, Pathak R, Piras V, Matelot M, Pignard B, Marchand A, Poncelet M, Perrin A, Tellier V, Feil R, Noordermeer D. CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains. Genome Biol 2019; 20:272. [PMID: 31831055 PMCID: PMC6909504 DOI: 10.1186/s13059-019-1896-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genomic imprinting is essential for mammalian development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. So far, the detailed allele-specific chromatin organization of imprinted gene domains has mostly been lacking. Here, we explored the chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints-the Igf2-H19 and Dlk1-Dio3 domains-and assessed the involvement of the insulator protein CTCF in mouse cells. RESULTS Both imprinted domains are located within overarching topologically associating domains (TADs) that are similar on both parental chromosomes. At each domain, a single differentially methylated region is bound by CTCF on the maternal chromosome only, in addition to multiple instances of bi-allelic CTCF binding. Combinations of allelic 4C-seq and DNA-FISH revealed that bi-allelic CTCF binding alone, on the paternal chromosome, correlates with a first level of sub-TAD structure. On the maternal chromosome, additional CTCF binding at the differentially methylated region adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal-specific sub-TAD organization. Perturbation of maternal-specific CTCF binding site at the Dlk1-Dio3 locus, using genome editing, results in perturbed sub-TAD organization and bi-allelic Dlk1 activation during differentiation. CONCLUSIONS Maternal allele-specific CTCF binding at the imprinted Igf2-H19 and the Dlk1-Dio3 domains adds an additional layer of sub-TAD organization, on top of an existing three-dimensional configuration and prior to imprinted activation of protein-coding genes. We speculate that this allele-specific sub-TAD organization provides an instructive or permissive context for imprinted gene activation during development.
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Affiliation(s)
- David Llères
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Benoît Moindrot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Rakesh Pathak
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Vincent Piras
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Mélody Matelot
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Benoît Pignard
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Alice Marchand
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Mallory Poncelet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélien Perrin
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Virgile Tellier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France.
| | - Daan Noordermeer
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-sud and University Paris-Saclay, Gif-sur-Yvette, France.
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Baral K, Rotwein P. The insulin-like growth factor 2 gene in mammals: Organizational complexity within a conserved locus. PLoS One 2019; 14:e0219155. [PMID: 31251794 PMCID: PMC6599137 DOI: 10.1371/journal.pone.0219155] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/17/2019] [Indexed: 01/10/2023] Open
Abstract
The secreted protein, insulin-like growth factor 2 (IGF2), plays a central role in fetal and prenatal growth and development, and is regulated at the genetic level by parental imprinting, being expressed predominantly from the paternally derived chromosome in mice and humans. Here, IGF2/Igf2 and its locus has been examined in 19 mammals from 13 orders spanning ~166 million years of evolutionary development. By using human or mouse DNA segments as queries in genome analyses, and by assessing gene expression using RNA-sequencing libraries, more complexity was identified within IGF2/Igf2 than was annotated previously. Multiple potential 5’ non-coding exons were mapped in most mammals and are presumably linked to distinct IGF2/Igf2 promoters, as shown for several species by interrogating RNA-sequencing libraries. DNA similarity was highest in IGF2/Igf2 coding exons; yet, even though the mature IGF2 protein was conserved, versions of 67 or 70 residues are produced secondary to species-specific maintenance of alternative RNA splicing at a variable intron-exon junction. Adjacent H19 was more divergent than IGF2/Igf2, as expected in a gene for a noncoding RNA, and was identified in only 10/19 species. These results show that common features, including those defining IGF2/Igf2 coding and several non-coding exons, were likely present at the onset of the mammalian radiation, but that others, such as a putative imprinting control region 5’ to H19 and potential enhancer elements 3’ to H19, diversified with speciation. This study also demonstrates that careful analysis of genomic and gene expression repositories can provide new insights into gene structure and regulation.
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Affiliation(s)
- Kabita Baral
- Graduate School, College of Science, University of Texas at El Paso, El Paso, Texas
| | - Peter Rotwein
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech Health University Health Sciences Center, El Paso, Texas
- * E-mail:
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Wang F, Liang R, Tandon N, Matthews ER, Shrestha S, Yang J, Soibam B, Yang J, Liu Y. H19X-encoded miR-424(322)/-503 cluster: emerging roles in cell differentiation, proliferation, plasticity and metabolism. Cell Mol Life Sci 2019; 76:903-920. [PMID: 30474694 PMCID: PMC6394552 DOI: 10.1007/s00018-018-2971-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 02/07/2023]
Abstract
miR-424(322)/-503 are mammal-specific members of the extended miR-15/107 microRNA family. They form a co-expression network with the imprinted lncRNA H19 in tetrapods. miR-424(322)/-503 regulate fundamental cellular processes including cell cycle, epithelial-to-mesenchymal transition, hypoxia and other stress response. They control tissue differentiation (cardiomyocyte, skeletal muscle, monocyte) and remodeling (mammary gland involution), and paradoxically participate in tumor initiation and progression. Expression of miR-424(322)/-503 is governed by unique mechanisms involving sex hormones. Here, we summarize current literature and provide a primer for future endeavors.
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Affiliation(s)
- Fan Wang
- Department of Oncology, The First Affiliated Hospital of Xian Jiaotong University, Xi'an, 710061, Shaanxi, China
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Rui Liang
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Neha Tandon
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Elizabeth R Matthews
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Shreesti Shrestha
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Jiao Yang
- Department of Oncology, The First Affiliated Hospital of Xian Jiaotong University, Xi'an, 710061, Shaanxi, China
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA
| | - Benjamin Soibam
- Computer Science and Engineering Technology, University of Houston-Downtown, Houston, TX, 77002, USA
| | - Jin Yang
- Department of Oncology, The First Affiliated Hospital of Xian Jiaotong University, Xi'an, 710061, Shaanxi, China.
| | - Yu Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204, USA.
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5
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Marášek P, Dzijak R, Studenyak I, Fišerová J, Uličná L, Novák P, Hozák P. Paxillin-dependent regulation of IGF2 and H19 gene cluster expression. J Cell Sci 2015; 128:3106-16. [PMID: 26116569 PMCID: PMC4541046 DOI: 10.1242/jcs.170985] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/31/2015] [Indexed: 12/15/2022] Open
Abstract
Paxillin (PXN) is a focal adhesion protein that has been implicated in signal transduction from the extracellular matrix. Recently, it has been shown to shuttle between the cytoplasm and the nucleus. When inside the nucleus, paxillin promotes cell proliferation. Here, we introduce paxillin as a transcriptional regulator of IGF2 and H19 genes. It does not affect the allelic expression of the two genes; rather, it regulates long-range chromosomal interactions between the IGF2 or H19 promoter and a shared distal enhancer on an active allele. Specifically, paxillin stimulates the interaction between the enhancer and the IGF2 promoter, thus activating IGF2 gene transcription, whereas it restrains the interaction between the enhancer and the H19 promoter, downregulating the H19 gene. We found that paxillin interacts with cohesin and the mediator complex, which have been shown to mediate long-range chromosomal looping. We propose that these interactions occur at the IGF2 and H19 gene cluster and are involved in the formation of loops between the IGF2 and H19 promoters and the enhancer, and thus the expression of the corresponding genes. These observations contribute to a mechanistic explanation of the role of paxillin in proliferation and fetal development.
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Affiliation(s)
- Pavel Marášek
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic Faculty of Science, Charles University in Prague, Prague 128 43, Czech Republic
| | - Rastislav Dzijak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic Department of Genome Integrity, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Irina Studenyak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Jindřiška Fišerová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Lívia Uličná
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology AS CR, Prague 142 00, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
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6
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Tilghman SM. Twists and turns: a scientific journey. Annu Rev Cell Dev Biol 2014; 30:1-21. [PMID: 25288111 DOI: 10.1146/annurev-cellbio-100913-013512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this perspective I look back on the twists and turns that influenced the direction of my scientific career over the past 40 years. From my early ambition to be a chemist to my training in Philadelphia and Bethesda as a molecular biologist, I benefited enormously from generous and valuable mentoring. In my independent career in Philadelphia and Princeton, I was motivated by a keen interest in the changes in gene expression that direct the development of the mammalian embryo and inspired by the creativity and energy of my students, fellows, and research staff. After twelve years as President of Princeton University, I have happily returned to the faculty of the Department of Molecular Biology.
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Affiliation(s)
- Shirley M Tilghman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544;
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Ideraabdullah FY, Thorvaldsen JL, Myers JA, Bartolomei MS. Tissue-specific insulator function at H19/Igf2 revealed by deletions at the imprinting control region. Hum Mol Genet 2014; 23:6246-59. [PMID: 24990148 DOI: 10.1093/hmg/ddu344] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Parent-of-origin-specific expression at imprinted genes is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). This mechanism of gene regulation, where one element controls allelic expression of multiple genes, is not fully understood. Furthermore, the mechanism of gene dysregulation through ICR epimutations, such as loss or gain of DNA methylation, remains a mystery. We have used genetic mouse models to dissect ICR-mediated genetic and epigenetic regulation of imprinted gene expression. The H19/insulin-like growth factor 2 (Igf2) ICR has a multifunctional role including insulation, activation and repression. Microdeletions at the human H19/IGF2 ICR (IC1) are proposed to be responsible for IC1 epimutations associated with imprinting disorders such as Beckwith-Wiedemann syndrome (BWS). Here, we have generated and characterized a mouse model that mimics BWS microdeletions to define the role of the deleted sequence in establishing and maintaining epigenetic marks and imprinted expression at the H19/IGF2 locus. These mice carry a 1.3 kb deletion at the H19/Igf2 ICR [Δ2,3] removing two of four CCCTC-binding factor (CTCF) sites and the intervening sequence, ∼75% of the ICR. Surprisingly, the Δ2,3 deletion does not perturb DNA methylation at the ICR; however, it does disrupt imprinted expression. While repressive functions of the ICR are compromised by the deletion regardless of tissue type, insulator function is only disrupted in tissues of mesodermal origin where a significant amount of CTCF is poly(ADP-ribosyl)ated. These findings suggest that insulator activity of the H19/Igf2 ICR varies by cell type and may depend on cell-specific enhancers as well as posttranslational modifications of the insulator protein CTCF.
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Affiliation(s)
- Folami Y Ideraabdullah
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | - Joanne L Thorvaldsen
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
| | - Jennifer A Myers
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, 9-123 SCTR, 3400 Civic Center Boulevard, Philadelphia PA 19104, USA and
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8
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Eun B, Sampley ML, Van Winkle MT, Good AL, Kachman MM, Pfeifer K. The Igf2/H19 muscle enhancer is an active transcriptional complex. Nucleic Acids Res 2013; 41:8126-34. [PMID: 23842673 PMCID: PMC3783178 DOI: 10.1093/nar/gkt597] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/13/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023] Open
Abstract
In eukaryotic cells, gene expression is mediated by enhancer activation of RNA polymerase at distant promoters. Recently, distinctions between enhancers and promoters have been blurred by the discovery that enhancers are associated with RNA polymerase and are sites of RNA synthesis. Here, we present an analysis of the insulin-like growth factor 2/H19 muscle enhancer. This enhancer includes a short conserved core element that is organized into chromatin typical of mammalian enhancers, binds tissue-specific transcription factors and functions on its own in vitro to activate promoter transcription. However, in a chromosomal context, this element is not sufficient to activate distant promoters. Instead, enhancer function also requires transcription in cis of a long non-coding RNA, Nctc1. Thus, the insulin-like growth factor 2/H19 enhancer is an active transcriptional complex whose own transcription is essential to its function.
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Affiliation(s)
- Bokkee Eun
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA and Core-Laboratory, College of Medicine, Korea University, Seoul 136-701, Republic of Korea
| | - Megan L. Sampley
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA and Core-Laboratory, College of Medicine, Korea University, Seoul 136-701, Republic of Korea
| | - Matthew T. Van Winkle
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA and Core-Laboratory, College of Medicine, Korea University, Seoul 136-701, Republic of Korea
| | - Austin L. Good
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA and Core-Laboratory, College of Medicine, Korea University, Seoul 136-701, Republic of Korea
| | - Marika M. Kachman
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA and Core-Laboratory, College of Medicine, Korea University, Seoul 136-701, Republic of Korea
| | - Karl Pfeifer
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA and Core-Laboratory, College of Medicine, Korea University, Seoul 136-701, Republic of Korea
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Eun B, Sampley ML, Good AL, Gebert CM, Pfeifer K. Promoter cross-talk via a shared enhancer explains paternally biased expression of Nctc1 at the Igf2/H19/Nctc1 imprinted locus. Nucleic Acids Res 2012; 41:817-26. [PMID: 23221643 PMCID: PMC3553941 DOI: 10.1093/nar/gks1182] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Developmentally regulated transcription often depends on physical interactions between distal enhancers and their cognate promoters. Recent genomic analyses suggest that promoter–promoter interactions might play a similarly critical role in organizing the genome and establishing cell-type-specific gene expression. The Igf2/H19 locus has been a valuable model for clarifying the role of long-range interactions between cis-regulatory elements. Imprinted expression of the linked, reciprocally imprinted genes is explained by parent-of-origin-specific chromosomal loop structures between the paternal Igf2 or maternal H19 promoters and their shared tissue-specific enhancer elements. Here, we further analyze these loop structures for their composition and their impact on expression of the linked long non-coding RNA, Nctc1. We show that Nctc1 is co-regulated with Igf2 and H19 and physically interacts with the shared muscle enhancer. In fact, all three co-regulated genes have the potential to interact not only with the shared enhancer but also with each other via their enhancer interactions. Furthermore, developmental and genetic analyses indicate functional significance for these promoter–promoter interactions. Altogether, we present a novel mechanism to explain developmental specific imprinting of Nctc1 and provide new information about enhancer mechanisms and about the role of chromatin domains in establishing gene expression patterns.
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Affiliation(s)
- Bokkee Eun
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, National Institutes of Health, Bethesda, MD 20892, USA
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Girgis HZ, Ovcharenko I. Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. BMC Bioinformatics 2012; 13:25. [PMID: 22313678 PMCID: PMC3359238 DOI: 10.1186/1471-2105-13-25] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 02/07/2012] [Indexed: 12/26/2022] Open
Abstract
Background Researchers seeking to unlock the genetic basis of human physiology and diseases have been studying gene transcription regulation. The temporal and spatial patterns of gene expression are controlled by mainly non-coding elements known as cis-regulatory modules (CRMs) and epigenetic factors. CRMs modulating related genes share the regulatory signature which consists of transcription factor (TF) binding sites (TFBSs). Identifying such CRMs is a challenging problem due to the prohibitive number of sequence sets that need to be analyzed. Results We formulated the challenge as a supervised classification problem even though experimentally validated CRMs were not required. Our efforts resulted in a software system named CrmMiner. The system mines for CRMs in the vicinity of related genes. CrmMiner requires two sets of sequences: a mixed set and a control set. Sequences in the vicinity of the related genes comprise the mixed set, whereas the control set includes random genomic sequences. CrmMiner assumes that a large percentage of the mixed set is made of background sequences that do not include CRMs. The system identifies pairs of closely located motifs representing vertebrate TFBSs that are enriched in the training mixed set consisting of 50% of the gene loci. In addition, CrmMiner selects a group of the enriched pairs to represent the tissue-specific regulatory signature. The mixed and the control sets are searched for candidate sequences that include any of the selected pairs. Next, an optimal Bayesian classifier is used to distinguish candidates found in the mixed set from their control counterparts. Our study proposes 62 tissue-specific regulatory signatures and putative CRMs for different human tissues and cell types. These signatures consist of assortments of ubiquitously expressed TFs and tissue-specific TFs. Under controlled settings, CrmMiner identified known CRMs in noisy sets up to 1:25 signal-to-noise ratio. CrmMiner was 21-75% more precise than a related CRM predictor. The sensitivity of the system to locate known human heart enhancers reached up to 83%. CrmMiner precision reached 82% while mining for CRMs specific to the human CD4+ T cells. On several data sets, the system achieved 99% specificity. Conclusion These results suggest that CrmMiner predictions are accurate and likely to be tissue-specific CRMs. We expect that the predicted tissue-specific CRMs and the regulatory signatures broaden our knowledge of gene transcription regulation.
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Affiliation(s)
- Hani Z Girgis
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 9600 Rockville Pike, Bethesda, MD 20896, USA
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11
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Gabory A, Ripoche MA, Le Digarcher A, Watrin F, Ziyyat A, Forné T, Jammes H, Ainscough JFX, Surani MA, Journot L, Dandolo L. H19 acts as a trans regulator of the imprinted gene network controlling growth in mice. Development 2009; 136:3413-21. [PMID: 19762426 DOI: 10.1242/dev.036061] [Citation(s) in RCA: 270] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The imprinted H19 gene produces a non-coding RNA of unknown function. Mice lacking H19 show an overgrowth phenotype, due to a cis effect of the H19 locus on the adjacent Igf2 gene. To explore the function of the RNA itself, we produced transgenic mice overexpressing H19. We observed postnatal growth reduction in two independent transgenic lines and detected a decrease of Igf2 expression in embryos. An extensive analysis of several other genes from the newly described imprinted gene network (IGN) was performed in both loss- and gain-of-function animals. We found that H19 deletion leads to the upregulation of several genes of the IGN. This overexpression is restored to the wild-type level by transgenic expression of H19. We therefore propose that the H19 gene participates as a trans regulator in the fine-tuning of this IGN in the mouse embryo. This is the first in vivo evidence of a functional role for the H19 RNA. Our results also bring further experimental evidence for the existence of the IGN and open new perspectives in the comprehension of the role of genomic imprinting in embryonic growth and in human imprinting pathologies.
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Affiliation(s)
- Anne Gabory
- Genetics and Development Department, Inserm U567, CNRS UMR 8104, University of Paris Descartes, Institut Cochin, Paris, France
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12
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Mishra A, Ormerod AK, Cibull ML, Spear BT, Kraner SD, Kaetzel DM. PDGF-A promoter and enhancer elements provide efficient and selective antineoplastic gene therapy in multiple cancer types. Cancer Gene Ther 2009; 16:298-309. [PMID: 18989353 PMCID: PMC2730454 DOI: 10.1038/cgt.2008.92] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 08/13/2008] [Accepted: 09/27/2008] [Indexed: 11/08/2022]
Abstract
Development of antineoplastic gene therapies is impaired by a paucity of transcription control elements with efficient, cancer cell-specific activity. We investigated the utility of promoter (AChP) and 5'-distal enhancer (ACE66) elements from the platelet-derived growth factor-A (PDGF-A) gene, which are hyperactive in many human cancers. Efficacy of these elements was tested in multiple tumor cell lines, both in cell culture and as tumor explants in athymic nude mice. Plasmid and viral vectors were constructed with the AChP promoter alone or in fusion with three copies of the ACE66 enhancer for expression of the prototype suicide gene, thymidine kinase (TK). ACE/AChP and AChP cassettes elicited ganciclovir (GCV)-induced cytotoxicity in multiple tumor cell lines. The ACE enhancer element also exhibited synergism with placental and liver-specific promoter elements. An adenovirus containing the AChP-TK cassette produced striking increases in GCV sensitivity in cultured tumor cell lines, as well as GCV-induced regression of U87 MG glioblastoma explants in vivo. TK expression was distributed throughout tumors receiving the therapeutic virus, whereas TdT-mediated dUTP nick end labeling (TUNEL) analysis revealed numerous regions undergoing apoptosis. Vascularization and reticulin fiber networks were less pronounced in virus-GCV-treated tumors, suggesting that both primary and stromal cell types may have been targeted. These studies provide proof-of-principle for utility of the PDGF-A promoter and ACE66 enhancer in antineoplastic gene therapy for a diverse group of human cancers.
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Affiliation(s)
- A Mishra
- Department of Molecular and Biomedical Pharmacology, College of Medicine, University of Kentucky, Lexington, KY, USA
| | | | - ML Cibull
- Department of Pathology, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - BT Spear
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - SD Kraner
- Department of Molecular and Biomedical Pharmacology, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - DM Kaetzel
- Department of Molecular and Biomedical Pharmacology, College of Medicine, University of Kentucky, Lexington, KY, USA
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13
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Wan LB, Bartolomei MS. Regulation of imprinting in clusters: noncoding RNAs versus insulators. ADVANCES IN GENETICS 2008; 61:207-23. [PMID: 18282507 DOI: 10.1016/s0065-2660(07)00007-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genomic imprinting is an epigenetic mechanism of transcriptional regulation through which expression of a subset of mammalian genes is restricted to one parental allele. An intriguing characteristic of imprinted genes is that they often cluster in megabase-sized chromosomal domains, indicating that domain-specific mechanisms regulate imprinting. Detailed study of the known imprinted domains has revealed a number of common characteristics. First, all clusters have an imprinting control region (ICR) that is typically 1-5 kb in size and differentially methylated, and that regulates imprinting across the entire domain. Second, the clusters have at least one noncoding RNA (ncRNA) that is usually expressed from the maternal allele and multiple paternally expressed protein-coding genes. Finally, the clusters are likely regulated by one of two mechanisms, transcription of a long ncRNA that silences expression of protein-coding genes bidirectionally in cis and blocking of shared enhancer elements by CCCTC binding factor (CTCF) binding insulators. More recent experiments may even suggest that both mechanisms operate at some clusters. In this chapter, we will describe what is known about imprinting at five well-studied imprinted loci and highlight some of the critical experiments that are required before a full understanding of imprinting mechanisms is achieved.
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Affiliation(s)
- Le-Ben Wan
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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14
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Simões PD, Ramos T. Human pluripotent embryonal carcinoma NTERA2 cl.D1 cells maintain their typical morphology in an angiomyogenic medium. J Negat Results Biomed 2007; 6:5. [PMID: 17442106 PMCID: PMC1863432 DOI: 10.1186/1477-5751-6-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Accepted: 04/18/2007] [Indexed: 01/28/2023] Open
Abstract
Background Pluripotent embryonal carcinomas are good potential models, to study, "in vitro," the mechanisms that control differentiation during embryogenesis. The NTERA2cl.D1 (NT2/D1) cell line is a well known system of ectodermal differentiation. Retinoic acid (RA) induces a dorsal pattern of differentiation (essentially neurons) and bone morphogenetic protein (BMP) or hexamethylenebisacetamide (HMBA) induces a more ventral (epidermal) pattern of differentiation. However, whether these human cells could give rise to mesoderm derivatives as their counterpart in mouse remained elusive. We analyzed the morphological characteristics and transcriptional activation of genes pertinent in cardiac muscle and endothelium differentiation, during the growth of NT2/D1 cells in an inductive angiomyogenic medium with or without Bone Morphogenetic Protein 2 (BMP2). Results Our experiments showed that NT2/D1 maintains their typical actin organization in angiomyogenic medium. Although the beta myosin heavy chain gene was never detected, all the other 15 genes analyzed maintained their expression throughout the time course of the experiment. Among them were early and late cardiac, endothelial, neuronal and teratocarcinoma genes. Conclusion Our results suggest that despite the NT2/D1 cells natural tendency to differentiate into neuroectodermal lineages, they can activate genes of mesodermal lineages. Therefore, we believe that these pluripotent cells might still be a good model to study biological development of mesodermal derivatives, provided the right culture conditions are met.
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Affiliation(s)
- Pedro D Simões
- Instituto de Tecnologia Biomédica, Laboratório de Biomateriais, Faculdade de Medicina Dentária da Universidade de Lisboa, Cidade Universitária, 1649-003 Lisbon, Portugal
| | - Teresa Ramos
- Instituto de Tecnologia Biomédica, Laboratório de Biomateriais, Faculdade de Medicina Dentária da Universidade de Lisboa, Cidade Universitária, 1649-003 Lisbon, Portugal
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15
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Varrault A, Gueydan C, Delalbre A, Bellmann A, Houssami S, Aknin C, Severac D, Chotard L, Kahli M, Le Digarcher A, Pavlidis P, Journot L. Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth. Dev Cell 2007; 11:711-22. [PMID: 17084362 DOI: 10.1016/j.devcel.2006.09.003] [Citation(s) in RCA: 347] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 06/13/2006] [Accepted: 09/05/2006] [Indexed: 12/21/2022]
Abstract
Genomic imprinting is an epigenetic mechanism of regulation that restrains the expression of a small subset of mammalian genes to one parental allele. The reason for the targeting of these approximately 80 genes by imprinting remains uncertain. We show that inactivation of the maternally repressed Zac1 transcription factor results in intrauterine growth restriction, altered bone formation, and neonatal lethality. A meta-analysis of microarray data reveals that Zac1 is a member of a network of coregulated genes comprising other imprinted genes involved in the control of embryonic growth. Zac1 alters the expression of several of these imprinted genes, including Igf2, H19, Cdkn1c, and Dlk1, and it directly regulates the Igf2/H19 locus through binding to a shared enhancer. Accordingly, these data identify a network of imprinted genes, including Zac1, which controls embryonic growth and which may be the basis for the implementation of a common mechanism of gene regulation during mammalian evolution.
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Affiliation(s)
- Annie Varrault
- Institut de Génomique Fonctionnelle, CNRS-UMR5203, INSERM-U661, Université Montpellier 1, Université Montpellier 2, Montpellier, F-34094, France
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16
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Reese KJ, Bartolomei MS. Establishment and maintenance of H19 imprinting in the germline and preimplantation embryo. Cytogenet Genome Res 2006; 113:153-8. [PMID: 16575175 DOI: 10.1159/000090827] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2005] [Accepted: 09/12/2005] [Indexed: 12/20/2022] Open
Abstract
The mouse H19 and Igf2 genes are oppositely imprinted and share enhancers that reside 3' to the genes. The imprinted expression of these genes is coordinated by a 2-kb regulatory element, the differentially methylated domain (DMD), positioned between the two genes. The methylation status of this region determines the ability of the insulator factor CTCF to bind to its sites in the DMD. Deletions and mutations of the DMD that affect imprinting in the soma have little effect on the methylation pattern of H19 in the germline, suggesting that additional sequences and factors contribute to the earliest stages of imprinting regulation at this locus. Less is known about these initial steps, which include the marking of the parental alleles, the onset of allele-specific expression patterns and maintenance of the imprints in the preimplantation embryo. Here, we will focus on these early steps, summarizing what is known and what questions remain to be addressed.
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Affiliation(s)
- K J Reese
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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17
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Gabory A, Ripoche MA, Yoshimizu T, Dandolo L. The H19 gene: regulation and function of a non-coding RNA. Cytogenet Genome Res 2006; 113:188-93. [PMID: 16575179 DOI: 10.1159/000090831] [Citation(s) in RCA: 187] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2005] [Accepted: 11/14/2005] [Indexed: 12/18/2022] Open
Abstract
The H19 gene encodes a 2.3-kb non-coding mRNA which is strongly expressed during embryogenesis. This gene belongs to an imprinted cluster, conserved on mouse chromosome 7 and human chromosome 11p15. H19 is maternally expressed and the neighbouring Igf2 gene is transcribed from the paternal allele. These two genes are co-expressed in endoderm- and mesoderm-derived tissues during embryonic development, which suggests a common mechanism of regulation. The regulatory elements (imprinted control region, CTCF insulation, different enhancer sequences, promoters of the two genes, matrix attachment regions) confer a differential chromatin architecture to the two parental alleles leading to reciprocal expression. The role of the H19 gene is unclear but different aspects have been proposed. H19 influences growth by way of a cis control on Igf2 expression. Although H19(-/-) mice are viable, a role for this gene during development has been suggested by viable H19(-/-) parthenogenetic mice. Finally it has been described as a putative tumour suppressor gene. H19 has been studied by numerous laboratories over the last fifteen years, nevertheless the function of this non-coding RNA remains to be elucidated.
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Affiliation(s)
- A Gabory
- Department of Genetics and Development, Institut Cochin, INSERM U567, CNRS UMR 8104, University Paris V Descartes, Paris, France
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18
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Verona RI, Bartolomei MS. Role of H19 3' sequences in controlling H19 and Igf2 imprinting and expression. Genomics 2005; 84:59-68. [PMID: 15203204 DOI: 10.1016/j.ygeno.2003.12.001] [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] [Received: 10/02/2003] [Accepted: 12/02/2003] [Indexed: 01/19/2023]
Abstract
The regulation of H19 and Igf2 imprinting and expression depends on common elements. Using comparative analysis between human and mouse, we identified conserved regions 3' of the H19 transcription unit, including the H19/Igf2 endodermal enhancers and elements within a 4.2-kb domain between the H19 transcription unit and the enhancers. Transgene experiments implicate these elements in imprinting regulation. To establish whether they are required at the endogenous locus, first we replaced the endodermal enhancers with the alpha-fetoprotein endodermal enhancers (H19Afp). Second, we deleted the 4.2-kb region (H19delta4.2). Our analysis revealed that H19 and Igf2 imprinting and tissue-specific expression were maintained for both mutations, except for a slight reduction in paternal Igf2 expression from the H19Afp allele in liver. These results demonstrate that the H19 insulator can interact with heterologous enhancers to imprint Igf2. Furthermore, for H19, chromatin context or additional sequences possibly compensate for loss of conserved 3' elements.
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Affiliation(s)
- Raluca I Verona
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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19
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Bartolomei MS. Epigenetics: role of germ cell imprinting. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2004; 518:239-45. [PMID: 12817692 DOI: 10.1007/978-1-4419-9190-4_21] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Affiliation(s)
- Marisa S Bartolomei
- Howard Hughes Medical Institute, Department of Cell & Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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20
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Engel N, Bartolomei MS. Mechanisms of Insulator Function in Gene Regulation and Genomic Imprinting. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 232:89-127. [PMID: 14711117 DOI: 10.1016/s0074-7696(03)32003-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Correct temporal and spatial patterns of gene expression are required to establish unique cell types. Several levels of genome organization are involved in achieving this intricate regulatory feat. Insulators are elements that modulate interactions between other cis-acting sequences and separate chromatin domains with distinct condensation states. Thus, they are proposed to play an important role in the partitioning of the genome into discrete realms of expression. This review focuses on the roles that insulators have in vivo and reviews models of insulator mechanisms in the light of current understanding of gene regulation.
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Affiliation(s)
- Nora Engel
- Howard Hughes Medical Institute and Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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21
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Zhu WG, Dai Z, Ding H, Srinivasan K, Hall J, Duan W, Villalona-Calero MA, Plass C, Otterson GA. Increased expression of unmethylated CDKN2D by 5-aza-2'-deoxycytidine in human lung cancer cells. Oncogene 2001; 20:7787-96. [PMID: 11753657 DOI: 10.1038/sj.onc.1204970] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2001] [Revised: 09/05/2001] [Accepted: 09/13/2001] [Indexed: 11/09/2022]
Abstract
DNA hypermethylation of CpG islands in the promoter region of genes is associated with transcriptional silencing. Treatment with hypo-methylating agents can lead to expression of these silenced genes. However, whether inhibition of DNA methylation influences the expression of unmethylated genes has not been extensively studied. We analysed the methylation status of CDKN2A and CDKN2D in human lung cancer cell lines and demonstrated that the CDKN2A CpG island is methylated, whereas CDKN2D is unmethylated. Treatment of cells with 5-aza-2'-deoxycytidine (5-Aza-CdR), an inhibitor of DNA methyltransferase 1, induced a dose and duration dependent increased expression of both p16(INK4a) and p19(INK4d), the products of CDKN2A and CDKN2D, respectively. These data indicate that global DNA demethylation not only influences the expression of methylated genes but also of unmethylated genes. Histone acetylation is linked to methylation induced transcriptional silencing. Depsipeptide, an inhibitor of histone deacetylase, acts synergistically with 5-Aza-CdR in inducing expression of p16(INK4a) and p19(INK4d). However, when cells were treated with higher concentrations of 5-Aza-CdR and depsipeptide, p16(INK4a) expression was decreased together with significant suppression of cell growth. Interestingly, p19(INK4d) expression was enhanced even more by the higher concentrations of 5-Aza-CdR and depsipeptide. Our data suggest that p19(INK4d) plays a distinct role from other INK4 family members in response to the cytotoxicity induced by inhibition of DNA methylation and histone deacetylation.
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Affiliation(s)
- W G Zhu
- Division of Hematology/Oncology, Department of Internal Medicine, The Ohio State University-Comprehensive Cancer Center, Columbus, OH 43210, USA
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22
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23
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Holmgren C, Kanduri C, Dell G, Ward A, Mukhopadhya R, Kanduri M, Lobanenkov V, Ohlsson R. CpG methylation regulates the Igf2/H19 insulator. Curr Biol 2001; 11:1128-30. [PMID: 11509237 DOI: 10.1016/s0960-9822(01)00314-1] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The differentially methylated 5'-flank of the mouse H19 gene unidirectionally regulates the communication between enhancer elements and gene promoters and presumably represses maternal Igf2 expression in vivo [1-6]. The specific activation of the paternally inherited Igf2 allele has been proposed to involve methylation-mediated inactivation of the H19 insulator function during male germline development [1-4, 6]. Here, we addressed the role of methylation by inserting a methylated fragment of the H19-imprinting control region (ICR) into a nonmethylated episomal H19 minigene construct, followed by the transfection of ligation mixture into Hep3B cells. Individual clones were expanded and analyzed for genotype, methylation status, chromatin conformation, and insulator function. The results show that the methylated status of the H19 ICR could be propagated for several passages without spreading into the episomal vector. Moreover, the nuclease hypersensitive sites, which are typical for the maternally inherited H19 ICR allele [1], were absent on the methylated ICR, underscoring the suggestion that the methylation mark dictates parent of origin-specific chromatin conformations [1] that involve CTCF [2]. Finally, the insulator function was strongly attenuated in stably maintained episomes. Collectively, these results provide the first experimental support that the H19 insulator function is regulated by CpG methylation.
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Affiliation(s)
- C Holmgren
- Department of Development and Genetics, Uppsala University, Norbyvägen 18A, S-752 36, Uppsala, Sweden
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24
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Cranston MJ, Spinka TL, Elson DA, Bartolomei MS. Elucidation of the Minimal Sequence Required to Imprint H19 Transgenes. Genomics 2001; 73:98-107. [PMID: 11352570 DOI: 10.1006/geno.2001.6514] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The imprinted mouse H19 gene exhibits maternal allele-specific expression and paternal allele-specific hypermethylation. We previously demonstrated that a 14-kb H19 minitransgene possessing 5' differentially methylated sequence recapitulates the endogenous H19 imprinting pattern when present as high-copy arrays. To investigate the minimal sequences that are sufficient for H19 transgene imprinting, we have tested new transgenes in mice. While transgenes harboring limited or no 3' H19 sequence indicate that multiple elements within the 8-kb 3' fragment are required for appropriate imprinting, transgenes incorporating 1.7 kb of additional 5' sequence mimic the endogenous H19 pattern, including proper imprinting of low-copy arrays. One of these imprinted lines had a single 15.7-kb transgene integrant. This is the smallest H19 transgene identified thus far to display imprinting properties characteristic of the endogenous gene, suggesting that all cis-acting elements required for H19 imprinting in endodermal tissues reside within the 15.7-kb transgenic sequence.
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Affiliation(s)
- M J Cranston
- Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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25
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Weber M, Milligan L, Delalbre A, Antoine E, Brunel C, Cathala G, Forné T. Extensive tissue-specific variation of allelic methylation in the Igf2 gene during mouse fetal development: relation to expression and imprinting. Mech Dev 2001; 101:133-41. [PMID: 11231066 DOI: 10.1016/s0925-4773(00)00573-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The imprinted Igf2 gene is active only on the paternal allele in most tissues. Its imprinting involves a cis-acting imprinting-control region (ICR) located upstream of the neighboring and maternally expressed H19 gene. It is thought that differential methylation of the parental alleles at the ICR is crucial for parental imprinting of both genes. Differentially methylated regions (DMRs) have also been identified within the Igf2 gene and their differential methylation is thought to be established during early development. To gain further insight into the function of these DMRs, we performed a quantitative analysis of their allelic methylation levels in different tissues during fetal development and the postnatal period in the mouse. Surprisingly, we found that the methylation levels of Igf2 DMRs vary extensively during fetal development, mostly on the expressed paternal allele. In particular, in skeletal muscle, differential allelic methylation in both DMR 1 and DMR 2 occurs only after birth, whereas correct paternal monoallelic expression is always observed, including in the embryonic stages. This suggests that differential methylation in the DMR 1 and DMR 2 of the Igf2 gene is dispensable for its imprinting in skeletal muscle. Furthermore, progressive methylation of the Igf2 paternal allele appears to be correlated with concomitant postnatal down-regulation and silencing of the gene. We discuss possible relations between Igf2 allelic methylation and expression during fetal development.
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Affiliation(s)
- M Weber
- Institut de Génétique Moléculaire, UMR 5535 CNRS-Université Montpellier II, IFR 24, 1919, Route de Mende, 34293 Cedex 5, Montpellier, France
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26
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Vernucci M, Cerrato F, Besnard N, Casola S, Pedone PV, Bruni CB, Riccio A. The H19 endodermal enhancer is required for Igf2 activation and tumor formation in experimental liver carcinogenesis. Oncogene 2000; 19:6376-85. [PMID: 11175353 DOI: 10.1038/sj.onc.1204024] [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: 12/16/2022]
Abstract
The expression of the linked but reciprocally imprinted Igf2 and H19 genes is activated in adult liver in the course of tumor development. By in situ hybridization analysis we have shown that both the Igf2 and H19 RNAs are expressed in the majority of the neoplastic nodules, and that hepatocellular carcinomas are developed in an experimental model of liver carcinogenesis. H19 is also highly activated in smaller and less distinct hyperplastic regions. The few neoplastic areas showing Igf2 but no H19 RNA display loss of the maternally inherited allele at the Igf2/H19 locus. These data are compatible with the existence of a common activation mechanism of these two genes during liver carcinogenesis and with a stronger H19 induction in the pre-neoplastic lesions. By using mice carrying a deletion of the H19 endodermal enhancer, we show that this regulatory element is necessary for the activation of the Igf2 and H19 genes upon induction of liver carcinogenesis. Furthermore, multiple sites of the H19 endodermal enhancer region become hypersensitive to DNase I when the carcinogenesis process is induced. Lastly, liver tumors developed in mice paternally inheriting the H19 enhancer deletion are found to have marked growth delays, increased frequency of apoptotic nuclei, and lack of Igf2 mRNA expression, thus indicating that this regulatory element plays a major role in the progression of liver carcinogenesis, since it is required for the activation of the anti-apoptotic Igf2 gene.
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MESH Headings
- Animals
- Apoptosis
- Chromatin/metabolism
- Deoxyribonucleases/chemistry
- Endoderm/metabolism
- Enhancer Elements, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Linkage
- Genomic Imprinting
- In Situ Hybridization
- Insulin-Like Growth Factor II/genetics
- Insulin-Like Growth Factor II/metabolism
- Liver/pathology
- Liver Neoplasms, Experimental/genetics
- Liver Neoplasms, Experimental/metabolism
- Liver Neoplasms, Experimental/pathology
- Male
- Mice
- Mice, Transgenic
- RNA, Long Noncoding
- RNA, Messenger/biosynthesis
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Sequence Deletion
- Transcriptional Activation
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Affiliation(s)
- M Vernucci
- Centro di Endocrinologia ed Oncologia Sperimentale 'G Salvatore', CNR; Dipartimento di Biologia e Patologia Cellulare e Molecolare 'L Califano', Università di Napoli 'Federico II', Napoli, Italy
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27
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Milligan L, Antoine E, Bisbal C, Weber M, Brunel C, Forné T, Cathala G. H19 gene expression is up-regulated exclusively by stabilization of the RNA during muscle cell differentiation. Oncogene 2000; 19:5810-6. [PMID: 11126368 DOI: 10.1038/sj.onc.1203965] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
H19 is a paternally imprinted gene whose expression produces a 2.4 kb RNA in most tissues during development and in mammalian myoblastic cell lines upon differentiation. Deletion of the active maternal allele of H19 and its flanking regions in the mouse leads to biallelic methylation and loss of imprinting of the neighbouring Igf2 gene. The function of H19 RNA remains unknown and, although polysome-associated, the absence of a conserved open reading frame suggests that it does not encode a protein product. We describe a novel post-transcriptional regulation of H19 gene expression which, in spite of this lack of coding capacity, is dependent on translational activity. We show that stabilization of the RNA is solely responsible for its accumulation during in vitro muscle cell differentiation. This conclusion is based on the finding that inhibition of protein synthesis results in a dramatic destabilization of H19 RNA in proliferating mouse C2C12 myoblastic cells but not in differentiated cells, and on run-on experiments which showed that the rate of transcription of H19 RNA remains constant during muscle cell differentiation. This mechanism could also be involved in H19 gene expression during mouse development in addition to its transcriptional activation which we have shown to occur.
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Affiliation(s)
- L Milligan
- Institut de Génétique Moléculaire, UMR 5535 CNRS-Université Montpellier II, France
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28
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Grave L, Dreyer D, Dieterle A, Leroy P, Michou AI, Doderer C, Pavirani A, Lusky M, Mehtali M. Differential influence of the E4 adenoviral genes on viral and cellular promoters. J Gene Med 2000; 2:433-43. [PMID: 11199264 DOI: 10.1002/1521-2254(200011/12)2:6<433::aid-jgm143>3.0.co;2-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Strong and stable transgene expression is fundamental to the success of recombinant adenovirus vectors in human gene therapy. However, control of transgene expression is a complex process, involving both viral and cellular factors. In this study, the influence of the E4 adenoviral region on the activity of various promoters was investigated in vitro and in vivo. METHODS Pairs of isogenic E1o and E1oE4o vectors were generated and compared. Levels of transgene expression were determined by Northern blot, ELISA and FACS analysis. Initiation of transcription was studied by nuclear run-on assays. RESULTS Similar to the viral CMV and RSV promoters, the activity of the ubiquitous cellular PGK promoter required the presence of the E4 genes in vitro and in vivo. In contrast, transgene expression from selected liver- and tumor-specific promoters did not require E4 functions. CONCLUSION Together with the reported low liver toxicity of E1oE4o vectors, the independence of E4 of liver-specific promoters renders such vectors interesting alternatives to the use of gutless vectors.
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Affiliation(s)
- L Grave
- Transgène SA, Strasbourg, France.
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29
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Ainscough JF, John RM, Barton SC, Surani MA. A skeletal muscle-specific mouse Igf2 repressor lies 40 kb downstream of the gene. Development 2000; 127:3923-30. [PMID: 10952890 DOI: 10.1242/dev.127.18.3923] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Igf2 and H19 are closely linked and reciprocally expressed genes on distal chromosome 7 in the mouse. We have previously shown that a 130 kb YAC transgene contains multiple tissue-specific enhancers for expression of both genes during embryogenesis. The YAC also contains all the crucial elements responsible for initiating and maintaining appropriate parent-of-origin-specific expression of these genes at ectopic sites, with expression of Igf2 after paternal inheritance and of H19 after maternal inheritance. Located centrally between Igf2 and H19 are two prominent DNaseI hypersensitive sites, and two stretches of sequence that are conserved between mouse and human. In this study, we have deleted, from the transgene, a one kb part of the intergenic region that contains the hypersensitive sites and one of the homologous stretches. We demonstrate that this deletion results in loss of maternal Igf2 repression in skeletal muscle cells, most strikingly in the tongue, late in embryogenesis. We propose that the intergenic region functions as a tissue-specific repressor element, forming an integral part of the complex regulatory mechanism that controls monoallelic gene expression in this domain.
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MESH Headings
- Alleles
- Animals
- Attachment Sites, Microbiological/genetics
- Base Sequence
- DNA, Intergenic/genetics
- Deoxyribonuclease I/metabolism
- Female
- Gene Expression Regulation, Developmental
- Gene Silencing
- Genomic Imprinting/genetics
- Insulin-Like Growth Factor II/genetics
- Male
- Mice
- Mice, Inbred Strains
- Mice, Transgenic
- Molecular Sequence Data
- Muscle, Skeletal/embryology
- Muscle, Skeletal/metabolism
- Organ Specificity
- RNA, Long Noncoding
- RNA, Untranslated/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Sequence Deletion/genetics
- Tongue/embryology
- Tongue/metabolism
- Transgenes/genetics
- Yolk Sac/metabolism
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Affiliation(s)
- J F Ainscough
- Wellcome/CRC Institute of Cancer and Developmental Biology, and Physiological Laboratory, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.
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30
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Kaffer CR, Srivastava M, Park KY, Ives E, Hsieh S, Batlle J, Grinberg A, Huang SP, Pfeifer K. A transcriptional insulator at the imprinted H19/Igf2 locus. Genes Dev 2000; 14:1908-19. [PMID: 10921905 PMCID: PMC316810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Igf2 and H19 exhibit parent-of-origin-specific monoallelic expression. H19 is expressed from the maternal chromosome and Igf2 from the paternal. The two genes share enhancer elements and monoallelic expression of both genes is dependent on cis-acting sequences upstream of the H19 promoter. In this work we examine the mechanisms by which this region silences the maternal Igf2 allele and we demonstrate that deletion of this region can result in high levels of activation of both H19 and Igf2 from a single chromosome. Moreover, by inserting this cis element between a promoter and its enhancer at a heterologous position, we demonstrate that the sequences carry both insulator activity and the ability to be stably imprinted. We also characterize the insulator in vitro and show that it is neither enhancer nor promoter specific.
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Affiliation(s)
- C R Kaffer
- Laboratory of Mammalian Genes and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892 USA.
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31
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Bell AC, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 2000; 405:482-5. [PMID: 10839546 DOI: 10.1038/35013100] [Citation(s) in RCA: 1279] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The expression of the insulin-like growth factor 2 (Igf2) and H19 genes is imprinted. Although these neighbouring genes share an enhancer, H19 is expressed only from the maternal allele, and Igf2 only from the paternally inherited allele. A region of paternal-specific methylation upstream of H19 appears to be the site of an epigenetic mark that is required for the imprinting of these genes. A deletion within this region results in loss of imprinting of both H19 and Igf2 (ref. 5). Here we show that this methylated region contains an element that blocks enhancer activity. The activity of this element is dependent upon the vertebrate enhancer-blocking protein CTCF. Methylation of CpGs within the CTCF-binding sites eliminates binding of CTCF in vitro, and deletion of these sites results in loss of enhancer-blocking activity in vivo, thereby allowing gene expression. This CTCF-dependent enhancer-blocking element acts as an insulator. We suggest that it controls imprinting of Igf2. The activity of this insulator is restricted to the maternal allele by specific DNA methylation of the paternal allele. Our results reveal that DNA methylation can control gene expression by modulating enhancer access to the gene promoter through regulation of an enhancer boundary.
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Affiliation(s)
- A C Bell
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0540, USA
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32
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Kanduri C, Holmgren C, Pilartz M, Franklin G, Kanduri M, Liu L, Ginjala V, Ullerås E, Mattsson R, Ohlsson R. The 5' flank of mouse H19 in an unusual chromatin conformation unidirectionally blocks enhancer-promoter communication. Curr Biol 2000; 10:449-57. [PMID: 10801414 DOI: 10.1016/s0960-9822(00)00442-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND During mouse prenatal development, the neighbouring insulin-like growth factor II (Igf2) and H19 loci are expressed monoallelically from the paternal and maternal alleles, respectively. Identical spatiotemporal expression patterns and enhancer deletion experiments show that the Igf2 and H19 genes share a common set of enhancers. Deletion of a differentially methylated region in the 5' flank of the H19 gene partially relieves the repression of the maternal Igf2 and paternal H19 alleles in the soma. The mechanisms underlying the function of the 5' flank of the H19 gene are, however, unknown. RESULTS Chromatin analysis showed that the 5' flank of the mouse H19 gene contains maternal-specific, multiple nuclease hypersensitive sites that map to linker regions between positioned nucleosomes. These features could be recapitulated in an episomal-based H19 minigene, which was propagated in human somatic cells. Although the 5' flank of the H19 promoter has no intrinsic silencer activity under these conditions, it unidirectionally extinguished promoter-enhancer communications in a position-dependent manner, without directly affecting the enhancer function. CONCLUSIONS The unmethylated 5' flank of the H19 gene adopts an unusual and maternal-specific chromatin conformation in somatic cells and regulates enhancer-promoter communications, thereby providing an explanation for its role in manifesting the repressed state of the maternally inherited Igf2 allele.
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Affiliation(s)
- C Kanduri
- Department of Animal Development and Genetics, Uppsala University, Uppsala, S-752 36, Sweden
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33
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Peyton DK, Huang MC, Giglia MA, Hughes NK, Spear BT. The alpha-fetoprotein promoter is the target of Afr1-mediated postnatal repression. Genomics 2000; 63:173-80. [PMID: 10673330 DOI: 10.1006/geno.1999.6073] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The alpha-fetoprotein (AFP) gene is transcribed at high levels in the fetal liver and is repressed at birth, leading to low but detectable levels of AFP mRNA in the adult liver. This repression is regulated, in part, by a locus that is unlinked to AFP called Alpha-fetoprotein regulator 1 (Afr1). Previous studies showed that Afr1 regulation is independent of the AFP enhancers but requires the 1-kb AFP promoter/repressor region. Here, we demonstrate that a transgene with the 250-bp AFP promoter region linked to AFP enhancer element EII is expressed in the fetal liver and is postnatally repressed. In addition, this transgene is regulated by Afr1. These data indicate that the promoter is involved in postnatal AFP repression. Furthermore, we provide a high-resolution map of the Afr1 locus on mouse chromosome 15.
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MESH Headings
- Animals
- Animals, Newborn
- Base Sequence
- Chromosome Mapping
- DNA Primers/genetics
- Enhancer Elements, Genetic
- Female
- Fetus/metabolism
- Gene Expression Regulation, Developmental
- Genes, Regulator
- Humans
- Liver/metabolism
- Mice
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Mice, Transgenic
- Pregnancy
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- alpha-Fetoproteins/genetics
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Affiliation(s)
- D K Peyton
- Department of Microbiology and Immunology, University of Kentucky College of Medicine, 800 Rose Street, Lexington, Kentucky 40536-0298, USA
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34
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Wise TL, Pravtcheva DD. The undermethylated state of a CpG island region in igf2 transgenes is dependent on the H19 enhancers. Genomics 1999; 60:258-71. [PMID: 10493826 DOI: 10.1006/geno.1999.5921] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CpG islands are GC-rich regions located in the promoter regions of housekeeping genes and many tissue-specific genes. While most CpG islands are normally unmethylated, island methylation can occur and is associated with silencing of the corresponding gene. Experiments with transgenic mice and DNA transfection in pluripotential embryonic cells have led to the conclusion that the information required for protecting the islands from methylation is contained within the CpG islands themselves and have identified Sp1 binding sites as an important element in establishing and/or maintaining the methylation-free state of CpG islands. To examine the generality of these observations, we analyzed the methylation of one of the mouse Igf2 CpG islands and its flanks in transgenic mice. We observed that the undermethylated state of this region is dependent on the presence of a separate cis-regulatory element, the H19 enhancers. These tissue-specific enhancers had a ubiquitous, non-tissue-specific effect on island region methylation. Structural alterations outside of the island and these enhancers also affected this region's methylation. These findings indicate that the methylation of some CpG island-containing regions is more sensitive than previously believed to the activity of distant cis-regulatory elements and to structural alterations in nonisland sequences in cis.
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Affiliation(s)
- T L Wise
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, New York, 10314, USA
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35
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Adriaenssens E, Lottin S, Dugimont T, Fauquette W, Coll J, Dupouy JP, Boilly B, Curgy JJ. Steroid hormones modulate H19 gene expression in both mammary gland and uterus. Oncogene 1999; 18:4460-73. [PMID: 10442637 DOI: 10.1038/sj.onc.1202819] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
H19 is an imprinted and developmentally regulated gene whose product remains apparently untranslated. In a previous study on breast adenocarcinomas, we reported that overexpression of the H19 gene was significantly correlated with the presence of steroid receptors, suggesting the putative role of hormones in H19 transcription. To determine the mode of steroid action, we have detected levels of H19 RNA synthesis during mammary gland development by in situ hybridization (ISH): two peaks of H19 transcription occur during puberty and pregnancy. Furthermore, we demonstrated by ISH that in the uterus H19 RNA synthesis is high during estrus and metestrus phases. To test steroid control of H19 transcription, ovariectomized and adrenalectomized mice were supplemented, 1 week after surgery, with 17-beta-estradiol (E2, 20 microg/kg/day), progesterone (P, 1 mg/kg/day) or corticosterone (B, 0.3 mg/ kg/day) for 2 weeks. According to ISH data, E2 and to a lesser extent B stimulated H19 transcription in the uterus, whereas P inhibited it. To confirm the in vivo results, in vitro experiments were performed using cultures of MCF-7 cells (a hormone-sensitive mammary cell line). E2 stimulated the endogenous H19 gene of this cell line and tamoxifen inhibited this effect. Furthermore, we performed transient cotransfections in MCF-7, in HBL-100 (another hormone-sensitive mammary cell line) and in BT-20 (a hormone-insensitive mammary cell line) with various constructs of ERalpha (WT or mutated) and PR-A, in presence or absence of steroid hormones. We demonstrated that ERalpha up-regulated the H19 promoter in MCF-7 and in HBL-100, whereas PR-A did not have any effect per se. Moreover, in MCF-7, PR-A antagonized clearly the ERalpha-mediated promoter enhancement, but in HBL-100 this counteracting effect on the ERalpha up-regulation was not found. Interestingly, the same experiments performed in BT-20 cell line provided very similar results as those obtained in MCF-7 cells, with a clear down-regulation mediated by PR-A on the H19 promoter. All these in vitro data are in agreement with in vivo results. In addition, data obtained with ERalpha mutants indicate that H19 promoter activation is both ligand-dependent and ligand-independent. We have thus demonstrated that H19 gene expression is controlled by steroid hormones; furthermore, this gene is highly expressed in hormone-sensitive organs when the hormonal stimulation is accompanied with a morphological repair.
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Affiliation(s)
- E Adriaenssens
- Laboratoire de Biologie du Dévelppement, UPRES EA 1033, Lille, France
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36
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Ohana P, Kopf E, Bibi O, Ayesh S, Schneider T, Laster M, Tykocinski M, de Groot N, Hochberg A. The expression of the H19 gene and its function in human bladder carcinoma cell lines. FEBS Lett 1999; 454:81-4. [PMID: 10413100 DOI: 10.1016/s0014-5793(99)00780-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The human H19 gene is a paternally imprinted oncofetal gene, highly expressed in several fetal tissues, down-regulated in nearly all adult tissues but re-expressed in carcinomas of tissues which express the gene in fetal life. It has no known protein product and till today, no function could be designated to H19 RNA. Cells derived from bladder carcinomas and hepatocellular carcinomas were transfected with plasmids carrying a luciferase reporter gene under the control of a 800 nucleotides long promoter region of the H19 gene either alone or together with different parts of a 5 kb downstream region, previously shown to possess enhancer activity. Our results provide evidence that three regions of the 3' downstream sequence can independently stimulate the H19 promoter activity in a tissue and cell specific manner. The growth rate of two cell populations, both derived from the same bladder carcinoma cell line and which differ in their H19 RNA content, were compared. The cells with a high H19 RNA level stopped their proliferation after 48 h when cultivated in a low serum containing media while the cells lacking H19 RNA continued their proliferation for at least an additional 48 h period.
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Affiliation(s)
- P Ohana
- Department of Biological Chemistry, Institute of Life Sciences, Hebrew University, Jerusalem, Israel
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37
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Franklin GC. Mechanisms of transcriptional regulation. Results Probl Cell Differ 1999; 25:171-87. [PMID: 10339746 DOI: 10.1007/978-3-540-69111-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- G C Franklin
- Department of Animal Development & Genetics, Uppsala University, Sweden
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38
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Abstract
Genes are recognized as undergoing genomic imprinting when they are capable of being expressed only from the paternal or only from the maternal chromosome. The process can occur coordinately within large physical domains in mammalian chromosomes. One interesting facet of the study of genomic imprinting is that it offers insight into the regulation of large chromosomal regions. Understanding this regulation involves elucidating the cis-acting regulators of gene expression and defining the elements that maintain chromatin insulation, both required for understanding more practically applicable areas of biological research, such as efficient transgene production. This review is focused on the regulation of the imprinted domain of human chromosome 11p15.5, responsible for Beckwith-Wiedemann syndrome (BWS). Recent findings indicate that the maintenance of imprinting within this domain is critically dependent on the stable maintenance of chromatin insulation.
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Affiliation(s)
- J M Greally
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA.
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39
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Abstract
Genomic imprinting in mammals is an epigenetic process that results in differential expression of the two parental alleles. The tightly linked murine H19 and Igf2 genes are reciprocally imprinted: H19 is expressed from the maternal chromosome while Igf2 is expressed from the paternal chromosome. A single regulatory region in the 5' flank of the H19 gene has been implicated in silencing both genes. On the paternal chromosome, this region is heavily methylated at CpG residues, leading to repression of the H19 gene. The mechanism by which the same region in an unmethylated state on the maternal chromosome silences Igf2 is less well understood. We have probed the chromatin structure of the region by assessing its sensitivity to nuclease digestion. Two regions of nuclease hypersensitivity that are specific to the maternal chromosome were identified. These coincide with the region that is most heavily methylated on the paternal chromosome. As is the case with paternal methylation, hypersensitivity is present in all tissues surveyed, irrespective of H19 expression. We suggest that the chromatin structure of the maternal 5' flank of the H19 gene may represent an epigenetic mark involved in the silencing of Igf2.
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Affiliation(s)
- A T Hark
- Howard Hughes Medical Institute and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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40
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Kopf E, Bibi O, Ayesh S, Tykocinski M, Vitner K, Looijenga LH, de Groot N, Hochberg A. The effect of retinoic acid on the activation of the human H19 promoter by a 3' downstream region. FEBS Lett 1998; 432:123-7. [PMID: 9720909 DOI: 10.1016/s0014-5793(98)00841-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The human H19 is paternally imprinted (maternally expressed). It is transcribed by RNA pol II, but has no protein product. Its function is unknown. We showed that the transcription of the human H19 gene is under the simultaneous control of both a 5' upstream (promoter) region and a 3' downstream region in cell lines derived from human choriocarcinomas. Moreover, the activation of the H19 promoter by retinoic acid in cells derived from human testicular germ cell tumors is dependent upon the 3' downstream region. The possibility that the action of retinoic acid on the H19 promoter is an indirect one and involves a member of the AP2 transcription factor family is discussed.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Chloramphenicol O-Acetyltransferase/drug effects
- Chloramphenicol O-Acetyltransferase/genetics
- DNA, Neoplasm/genetics
- Enhancer Elements, Genetic/drug effects
- Enhancer Elements, Genetic/genetics
- Gene Expression Regulation/drug effects
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Muscle Proteins/drug effects
- Muscle Proteins/genetics
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/genetics
- RNA, Long Noncoding
- RNA, Untranslated
- Recombinant Proteins/drug effects
- Recombinant Proteins/genetics
- Simian virus 40/genetics
- Transcription, Genetic/drug effects
- Transcription, Genetic/genetics
- Transfection
- Tretinoin/pharmacology
- Tumor Cells, Cultured/cytology
- Tumor Cells, Cultured/drug effects
- Tumor Cells, Cultured/metabolism
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Affiliation(s)
- E Kopf
- The Department of Biological Chemistry, the Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
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41
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42
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Obata Y, Kaneko-Ishino T, Koide T, Takai Y, Ueda T, Domeki I, Shiroishi T, Ishino F, Kono T. Disruption of primary imprinting during oocyte growth leads to the modified expression of imprinted genes during embryogenesis. Development 1998; 125:1553-60. [PMID: 9502736 DOI: 10.1242/dev.125.8.1553] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Parthenogenetic embryos, which contained one genome from a neonate-derived non-growing oocyte and the other from a fully grown oocyte, developed to day 13.5 of gestation in mice, 3 days longer than previously recorded for parthenogenetic development. To investigate the hypothesis that disruption of primary imprinting during oocyte growth leads to the modified expression of imprinted genes and this parthenogenetic phenotype, we have examined Peg1/Mest, Igf2, Peg3, Snrpn, H19, Igf2r and excess p57KIP2. We show that paternally expressed genes, Peg1/Mest, Peg3 and Snrpn, are expressed in the parthenotes, presumably due to a lack of maternal epigenetic modifications during oocyte growth. In contrast, the expression of Igf2, which is repressed in a competitive manner by transcription of the H19 gene, was very low. Furthermore, we show that the maternally expressed Igf2r and p57KIP2 genes were repressed in the alleles of the non-growing oocyte indicating maternal modifications during oocyte growth are necessary for its expression. Thus, our results show that primary imprinting during oocyte growth exhibits a crucial effect on both the expression and repression of maternal alleles during embryogenesis.
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Affiliation(s)
- Y Obata
- NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
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43
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Webber AL, Ingram RS, Levorse JM, Tilghman SM. Location of enhancers is essential for the imprinting of H19 and Igf2 genes. Nature 1998; 391:711-5. [PMID: 9490417 DOI: 10.1038/35655] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genomic imprinting is the process in mammals by which gamete-specific epigenetic modifications establish the differential expression of the two alleles of a gene. The tightly linked H19 and Igf2 genes are expressed in tissues of endodermal and mesodermal origin, with H19 expressed from the maternal chromosome and Igf2 expressed from the paternal chromosome. A model has been proposed to explain the reciprocal imprinting of these genes; in this model, expression of the genes is governed by competition between their promoters for a common set of enhancers. An extra set of enhancers might be predicted to relieve the competition, thereby eliminating imprinting. Here we tested this prediction by generating mice with a duplication of the endoderm-specific enhancers. The normally silent Igf2 gene on the maternal chromosome was expressed in liver, consistent with relief from competition. We then generated a maternal chromosome containing a single set of enhancers located equidistant from 1gf2 and H19; the direction of the imprint was reversed. Thus, the location of the enhancers determines the outcome of competition in liver, and the strength of the H19 promoter is not sufficient to silence Igf2.
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Affiliation(s)
- A L Webber
- Howard Hughes Medical Institute and Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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44
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Dell G, Ward A, Engström W. Regulation of a promoter from the mouse insulin like growth factor II gene by glucocorticoids. FEBS Lett 1997; 419:161-5. [PMID: 9428626 DOI: 10.1016/s0014-5793(97)01434-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have microinjected constructs containing the murine IG II P3 promoter linked to different flanking sequences and a luciferase reporter gene into mouse pronuclei to establish transgenic lines of mice. The offspring was used as a source of embryonic fibroblast cultures and the effect of exogenous addition of glucocorticoids on transgene expression was analysed. It was found that both dexamethasone and hydrocortisone gave rise to a functional stimulation of the IGF II P3 promoter when the construct also contained other elements. This study demonstrates for the first time that there is an effect of glucocorticoids on the activation of an embryonic IGF II promoter, thus providing a molecular rationale for previous findings that glucocorticoids can under certain circumstances give rise to an increased transcriptional activity of the IGF II gene.
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Affiliation(s)
- G Dell
- Developmental Biology Programme, School of Biology and Biochemistry, University of Bath, UK
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45
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Zubair M, Hilton K, Saam JR, Surani MA, Tilghman SM, Sasaki H. Structure and expression of the mouse L23mrp gene downstream of the imprinted H19 gene: biallelic expression and lack of interaction with the H19 enhancers. Genomics 1997; 45:290-6. [PMID: 9344651 DOI: 10.1006/geno.1997.4961] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human L23 (mitochondrial)-related protein gene, located 40 kb downstream of the imprinted H19 gene, is biallelically expressed. We have cloned and characterized its mouse homolog, L23mrp, which maps to the conserved syntenic region on mouse chromosome 7. The promoter of L23mrp is a CpG island that is transcribed ubiquitously, but at different levels, in different fetal tissues. Allele-specific expression analysis revealed that both parental alleles are equally active. Since the enhancers located between H19 and L23mrp had been shown to be involved in the imprinted expression of Ins-2, Igf-2, and H19, we asked whether they also influence L23mrp. Analysis of mice with a targeted deletion of the enhancers demonstrated that they were not disrupted in the expression of L23mrp. These findings indicate that L23mrp is functionally insulated from the Ins-2/Igf-2/H19 domain in terms of both imprinting and enhancer action.
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Affiliation(s)
- M Zubair
- Institute of Genetic Information, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-82, Japan
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46
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Abstract
The insulin-like growth factor II (IGFII) is a mitogen for a number of cell types in vitro and is required for normal embryonic growth. It has been hypothesized that overexpression of IGF2 is responsible for the increased growth and tumor predisposition in patients with Beckwith-Wiedemann syndrome. Association of increased levels of IGFII with increased growth is also incorporated in a current model for the evolution of Igf2 imprinting. Different experimental approaches to increasing IGFII levels in the mouse have yielded different results with respect to its effects on growth, viability, and tumor development. To investigate the consequences of IGf2 overexpression in the embryonic period, without alterations in the activity of other genes, we produced transgenic mice that express the Igf2 gene under the control of the H19 enhancers. Transgene expression in the embryonic period had no significant effect on the overall size of the embryos, but was associated with perinatal lethality in homozygous, and some heterozygous, mice. A large fraction of homozygous mice also developed a cleft palate. These findings indicate that overexpression of Igf2 can have an adverse effect on viability in the absence of a pronounced effect on overall body growth. The results are consistent with the view that growth and perinatal viability are affected differently by Igf2 overexpression in endodermal and mesodermal tissues.
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Affiliation(s)
- T L Wise
- Saint Louis University Health Sciences Center, Dept. of Pediatrics, MO 63110, USA
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47
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Ainscough JF, Koide T, Tada M, Barton S, Surani MA. Imprinting of Igf2 and H19 from a 130 kb YAC transgene. Development 1997; 124:3621-32. [PMID: 9342054 DOI: 10.1242/dev.124.18.3621] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A stringent test for imprint control elements is to examine their function at ectopic loci in transgenic experiments. Igf2 and H19 are part of a larger imprinting region and as a first step, we examined these reciprocally imprinted genes in transgenic experiments using a 130 kb YAC clone. After paternal inheritance, H19 was appropriately repressed and Igf2 was expressed, irrespective of copy number or genetic background. After maternal inheritance H19 was consistently expressed, albeit with some variability. The levels of H19 expression per copy of the transgene inversely correlated with Igf2 (-lacZ) expression in cis. The consistent imprinting of H19 from this YAC contrasts with the previously described imprinting of mini-H19 transgenes, which only occurs at multi-copy loci, is inconsistent, and is prone to genetic background effects. We propose a novel model in which silencing of the H19 gene is the default state and its activation after maternal inheritance is the key mechanistic event for imprinting in this region. In addition, in situ analysis of the Igf2-lacZ reporter indicates that additional mesoderm-specific enhancers are present within the YAC clone. No obvious phenotype was detected from the excess gene dosage of H19.
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MESH Headings
- Animals
- Chromosomes, Artificial, Yeast
- DNA Methylation
- Embryo, Mammalian/metabolism
- Enhancer Elements, Genetic
- Female
- Gene Dosage
- Genes, Reporter
- Genomic Imprinting
- Insulin-Like Growth Factor II/genetics
- Male
- Mesoderm/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Inbred CBA
- Mice, Transgenic
- Models, Genetic
- Muscle Proteins/genetics
- Phenotype
- RNA, Long Noncoding
- RNA, Untranslated
- Transgenes
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Affiliation(s)
- J F Ainscough
- Wellcome/CRC Institute of Cancer and Developmental Biology, University of Cambridge, UK.
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48
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Lyko F, Brenton JD, Surani MA, Paro R. An imprinting element from the mouse H19 locus functions as a silencer in Drosophila. Nat Genet 1997; 16:171-3. [PMID: 9171828 DOI: 10.1038/ng0697-171] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genomic imprinting as originally described in Sciara is displayed by many organisms. In mammals, X-inactivation and the parent-of-origin-specific silencing of imprinted genes are examples of this phenomenon. A heritable chromatin structural modification may be the critical mechanism in such instances of chromosome condensation and preferential gene inactivation. H19 is an imprinted gene in which the repressed paternal allele is hypermethylated and the compacted chromatin is relatively resistant to digestion by nucleases. In order to uncover underlying conserved epigenetic mechanisms we have introduced a mouse H19 transgene into Drosophila. We show here that a 1.2-kb H19 upstream sequence functions in cis as a parent-of-origin independent silencing element in Drosophila. Strikingly, this cis-acting element is located within an upstream region that is necessary for H19 imprinting in mice. These results suggest involvement of an evolutionary conserved mechanism in both genes silencing in Drosophila and imprinting in mice.
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Affiliation(s)
- F Lyko
- ZMBH, University of Heidelberg, Germany
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49
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Affiliation(s)
- L H Looijenga
- Dr. Daniel den Hoed Cancer Center, University Hospital Rotterdam, the Netherlands
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50
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Jin DK, Feuerman MH. Sequence requirements for Afr-2 regulation of alpha-fetoprotein gene expression during liver regeneration. SOMATIC CELL AND MOLECULAR GENETICS 1996; 22:211-26. [PMID: 8914606 DOI: 10.1007/bf02369911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Alpha-fetoprotein (AFP) gene expression occurs in the yolk sac, fetal liver and gut, and in the adult liver during regeneration and tumorigenesis. Polymorphism at a single genetic locus, Afr-2 (formerly known as Rif) between inbred mouse strains C3H/He and C57B1/6, results in different levels of AFP expression during liver regeneration. We examined AFP, histone H3, and albumin gene expression during liver regeneration and found that the strain-specific variance in AFP gene expression could not be attributed to a difference in the numbers of dividing cells. Experiments with transgenic mice revealed sequences required for Afr-2 regulation included 172 bp between -1010 and -838 bp and 118 bp immediately upstream of the AFP transcriptional start site-the same regions required for induction during liver regeneration. This suggests that the Afr-2 phenotype may stem from an allelic difference in a gene regulating gene expression during liver regeneration.
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Affiliation(s)
- D K Jin
- Department of Biochemistry, State University of New York, Brooklyn 11203, USA
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