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Martinez-Ara M, Comoglio F, van Steensel B. Large-scale analysis of the integration of enhancer-enhancer signals by promoters. eLife 2024; 12:RP91994. [PMID: 39466837 PMCID: PMC11517252 DOI: 10.7554/elife.91994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2024] Open
Abstract
Genes are often regulated by multiple enhancers. It is poorly understood how the individual enhancer activities are combined to control promoter activity. Anecdotal evidence has shown that enhancers can combine sub-additively, additively, synergistically, or redundantly. However, it is not clear which of these modes are more frequent in mammalian genomes. Here, we systematically tested how pairs of enhancers activate promoters using a three-way combinatorial reporter assay in mouse embryonic stem cells. By assaying about 69,000 enhancer-enhancer-promoter combinations we found that enhancer pairs generally combine near-additively. This behaviour was conserved across seven developmental promoters tested. Surprisingly, these promoters scale the enhancer signals in a non-linear manner that depends on promoter strength. A housekeeping promoter showed an overall different response to enhancer pairs, and a smaller dynamic range. Thus, our data indicate that enhancers mostly act additively, but promoters transform their collective effect non-linearly.
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Affiliation(s)
- Miguel Martinez-Ara
- Division of Gene Regulation, Netherlands Cancer InstituteAmsterdamNetherlands
- Oncode InstituteAmsterdamNetherlands
| | - Federico Comoglio
- Division of Gene Regulation, Netherlands Cancer InstituteAmsterdamNetherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer InstituteAmsterdamNetherlands
- Oncode InstituteAmsterdamNetherlands
- Division of Molecular Genetics, Netherlands Cancer InstituteAmsterdamNetherlands
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2
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Abstract
Enhancers control the establishment of spatiotemporal gene expression patterns throughout development. Over the past decade, the development of new technologies has improved our capacity to link enhancers with their target genes based on their colocalization within the same topological domains. However, the mechanisms that regulate how enhancers specifically activate some genes but not others within a given domain remain unclear. In this Review, we discuss recent insights into the factors controlling enhancer specificity, including the genetic composition of enhancers and promoters, the linear and 3D distance between enhancers and their target genes, and cell-type specific chromatin landscapes. We also discuss how elucidating the molecular principles of enhancer specificity might help us to better understand and predict the pathological consequences of human genetic, epigenetic and structural variants.
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Affiliation(s)
- Tomás Pachano
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Albert Einstein 22, 39011 Santander, Spain
| | - Endika Haro
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Albert Einstein 22, 39011 Santander, Spain
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/Universidad de Cantabria/SODERCAN, Albert Einstein 22, 39011 Santander, Spain
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3
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Martinez-Ara M, Comoglio F, van Arensbergen J, van Steensel B. Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome. Mol Cell 2022; 82:2519-2531.e6. [PMID: 35594855 PMCID: PMC9278412 DOI: 10.1016/j.molcel.2022.04.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/17/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Miguel Martinez-Ara
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Federico Comoglio
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Joris van Arensbergen
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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4
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Galouzis CC, Furlong EEM. Regulating specificity in enhancer-promoter communication. Curr Opin Cell Biol 2022; 75:102065. [PMID: 35240372 DOI: 10.1016/j.ceb.2022.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022]
Abstract
Enhancers are cis-regulatory elements that can activate transcription remotely to regulate a specific pattern of a gene's expression. Genes typically have many enhancers that are often intermingled in the loci of other genes. To regulate expression, enhancers must therefore activate their correct promoter while ignoring others that may be in closer linear proximity. In this review, we discuss mechanisms by which enhancers engage with promoters, including recent findings on the role of cohesin and the Mediator complex, and how this specificity in enhancer-promoter communication is encoded. Genetic dissection of model loci, in addition to more recent findings using genome-wide approaches, highlight the core promoter sequence, its accessibility, cofactor-promoter preference, in addition to the surrounding genomic context, as key components.
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Affiliation(s)
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117, Heidelberg, Germany.
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5
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González-Ramírez M, Ballaré C, Mugianesi F, Beringer M, Santanach A, Blanco E, Di Croce L. Differential contribution to gene expression prediction of histone modifications at enhancers or promoters. PLoS Comput Biol 2021; 17:e1009368. [PMID: 34473698 PMCID: PMC8443064 DOI: 10.1371/journal.pcbi.1009368] [Citation(s) in RCA: 6] [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: 06/11/2021] [Revised: 09/15/2021] [Accepted: 08/21/2021] [Indexed: 12/31/2022] Open
Abstract
The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. We use embryonic stem cells (ESCs), which contain a full spectrum of active and repressed (poised) enhancers, to train predictive models. As many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can also be trained on poised enhancers throughout differentiation and in development. Remarkably, we determine that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation and development. Importantly, we demonstrate that their contribution to the predictive models varies depending on their location in enhancers or promoters. Moreover, we use a local regression (LOESS) to normalize sequencing data from different sources, which allows us to apply predictive models trained in a specific cellular context to a different one. We conclude that the relationship between gene expression and histone modifications at enhancers is universal and different from promoters. Our study provides new insight into how histone modifications relate to gene expression based on their location in enhancers or promoters. Gene expression can be properly predicted by the ChIP-seq signal of histone modifications at promoters, but whether this is also true at enhancers is unclear. In this study we develop predictive models of gene expression that demonstrate the predictive power of histone modifications at enhancers in the context of mouse embryonic stem cells, during differentiation, and in animal development. Moreover, by assessing the contribution of each histone modification, we found that enhancer predictive models and promoter predictive models have different histone modification requirement. Therefore, different histone modifications relate better to enhancer or promoter function(s). Finally, by applying predictive models trained in a specific cellular context to a different one, we concluded that the relationship between gene expression and histone modifications at enhancers is universal.
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Affiliation(s)
- Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Malte Beringer
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alexandra Santanach
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Barcelona, Spain
- * E-mail:
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6
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Abstract
Developmental enhancers mediate on/off patterns of gene expression in specific cell types at particular stages during metazoan embryogenesis. They typically integrate multiple signals and regulatory determinants to achieve precise spatiotemporal expression. Such enhancers can map quite far-one megabase or more-from the genes they regulate. How remote enhancers relay regulatory information to their target promoters is one of the central mysteries of genome organization and function. A variety of contrasting mechanisms have been proposed over the years, including enhancer tracking, linking, looping, and mobilization to transcription factories. We argue that extreme versions of these mechanisms cannot account for the transcriptional dynamics and precision seen in living cells, tissues, and embryos. We describe emerging evidence for dynamic three-dimensional hubs that combine different elements of the classical models.
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Affiliation(s)
- Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, D-69117, Heidelberg, Germany.
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ 08540, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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7
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Carrió E, Díez-Villanueva A, Lois S, Mallona I, Cases I, Forn M, Peinado MA, Suelves M. Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage. Stem Cells 2015; 33:2025-36. [PMID: 25801824 DOI: 10.1002/stem.1998] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/06/2015] [Indexed: 12/17/2022]
Abstract
The progressive restriction of differentiation potential from pluripotent embryonic stem cells (ESCs) to tissue-specific stem cells involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. Skeletal muscle stem cells are required for the growth, maintenance, and regeneration of skeletal muscle. To investigate the contribution of DNA methylation to the establishment of the myogenic program, we analyzed ESCs, skeletal muscle stem cells in proliferating (myoblasts) and differentiating conditions (myotubes), and mature myofibers. About 1.000 differentially methylated regions were identified during muscle-lineage determination and terminal differentiation, mainly located in gene bodies and intergenic regions. As a whole, myogenic stem cells showed a gain of DNA methylation, while muscle differentiation was accompanied by loss of DNA methylation in CpG-poor regions. Notably, the hypomethylated regions in myogenic stem cells were neighbored by enhancer-type chromatin, suggesting the involvement of DNA methylation in the regulation of cell-type specific enhancers. Interestingly, we demonstrated the hypomethylation of the muscle cell-identity Myf5 super-enhancer only in muscle cells. Furthermore, we observed that upstream stimulatory factor 1 binding to Myf5 super-enhancer occurs upon DNA demethylation in myogenic stem cells. Taken altogether, we characterized the unique DNA methylation signature of skeletal muscle stem cells and highlighted the importance of DNA methylation-mediated regulation of cell identity Myf5 super-enhancer during cellular differentiation.
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Affiliation(s)
- Elvira Carrió
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Anna Díez-Villanueva
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Sergi Lois
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Izaskun Mallona
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Ildefonso Cases
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Marta Forn
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Miguel A Peinado
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Mònica Suelves
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
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8
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Vincent SD, Mayeuf-Louchart A, Watanabe Y, Brzezinski JA, Miyagawa-Tomita S, Kelly RG, Buckingham M. Prdm1 functions in the mesoderm of the second heart field, where it interacts genetically with Tbx1, during outflow tract morphogenesis in the mouse embryo. Hum Mol Genet 2014; 23:5087-101. [PMID: 24821700 DOI: 10.1093/hmg/ddu232] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Congenital heart defects affect at least 0.8% of newborn children and are a major cause of lethality prior to birth. Malformations of the arterial pole are particularly frequent. The myocardium at the base of the pulmonary trunk and aorta and the arterial tree associated with these great arteries are derived from splanchnic mesoderm of the second heart field (SHF), an important source of cardiac progenitor cells. These cells are controlled by a gene regulatory network that includes Fgf8, Fgf10 and Tbx1. Prdm1 encodes a transcriptional repressor that we show is also expressed in the SHF. In mouse embryos, mutation of Prdm1 affects branchial arch development and leads to persistent truncus arteriosus (PTA), indicative of neural crest dysfunction. Using conditional mutants, we show that this is not due to a direct function of Prdm1 in neural crest cells. Mutation of Prdm1 in the SHF does not result in PTA, but leads to arterial pole defects, characterized by mis-alignment or reduction of the aorta and pulmonary trunk, and abnormalities in the arterial tree, defects that are preceded by a reduction in outflow tract size and loss of caudal pharyngeal arch arteries. These defects are associated with a reduction in proliferation of progenitor cells in the SHF. We have investigated genetic interactions with Fgf8 and Tbx1, and show that on a Tbx1 heterozygote background, conditional Prdm1 mutants have more pronounced arterial pole defects, now including PTA. Our results identify PRDM1 as a potential modifier of phenotypic severity in TBX1 haploinsufficient DiGeorge syndrome patients.
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Affiliation(s)
- Stéphane D Vincent
- Department of Developmental & Stem Cell Biology, Institut Pasteur, CNRS URA 2578, Paris, France,
| | - Alicia Mayeuf-Louchart
- Department of Developmental & Stem Cell Biology, Institut Pasteur, CNRS URA 2578, Paris, France
| | - Yusuke Watanabe
- Department of Developmental & Stem Cell Biology, Institut Pasteur, CNRS URA 2578, Paris, France
| | - Joseph A Brzezinski
- Department of Structural Biology, University of Washington, Seattle, WA, USA
| | - Sachiko Miyagawa-Tomita
- Division of Cardiovascular Development and Differentiation, Department of Pediatric Cardiology, Tokyo Women's Medical University, Tokyo, Japan and
| | - Robert G Kelly
- Aix-Marseille Université, Developmental Biology Institute of Marseille, CNRS UMR 7288, Campus de Luminy, Marseille, France
| | - Margaret Buckingham
- Department of Developmental & Stem Cell Biology, Institut Pasteur, CNRS URA 2578, Paris, France
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9
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Blum R, Dynlacht BD. The role of MyoD1 and histone modifications in the activation of muscle enhancers. Epigenetics 2013; 8:778-84. [PMID: 23880568 PMCID: PMC3883780 DOI: 10.4161/epi.25441] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
MyoD1 is a key regulator that orchestrates skeletal muscle differentiation through the regulation of gene expression. Although many studies have focused on its role in transcriptional control at gene promoters, less is known regarding the role of MyoD1 in the assembly of active enhancers. Here, we discuss novel data that point to the ability of MyoD1 to mediate the assembly of active enhancers that augment the transcription of genes essential for muscle development and lineage specification. Based on genome-wide studies of epigenetic marks that typify active enhancers, we recently identified the compendium of distal regulatory elements that dictate transcriptional programs during myogenesis. Superimposition of MyoD1 binding sites upon the locations of muscle enhancers revealed its unequivocal binding to a core region of nearly a third of condition-specific muscle enhancers. Further studies exploring deposition of enhancer-related epigenetic marks in myoblasts lacking MyoD1 demonstrate the dependence of muscle enhancer assembly on the presence of MyoD1. We propose a model wherein MyoD1 mediates recruitment of Set7, H3K4me1, H3K27ac, p300, and RNAP II to MyoD1-bound enhancers to establish condition-specific activation of muscle genes. Moreover, muscle enhancers are modulated through coordinated binding of transcription factors, including c-Jun, Jdp2, Meis, and Runx1, which are recruited to muscle enhancers in a MyoD1-dependent manner. Thus, MyoD1 and enhancer-associated transcription factors function coordinately to assemble and regulate enhancers, thereby augmenting expression of muscle-related genes.
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Affiliation(s)
- Roy Blum
- Department of Pathology and Cancer Institute; Smilow Research Center; New York University School of Medicine; New York, NY USA
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10
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Itm2a is a Pax3 target gene, expressed at sites of skeletal muscle formation in vivo. PLoS One 2013; 8:e63143. [PMID: 23650549 PMCID: PMC3641095 DOI: 10.1371/journal.pone.0063143] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 03/30/2013] [Indexed: 11/19/2022] Open
Abstract
The paired-box homeodomain transcription factor Pax3 is a key regulator of the nervous system, neural crest and skeletal muscle development. Despite the important role of this transcription factor, very few direct target genes have been characterized. We show that Itm2a, which encodes a type 2 transmembrane protein, is a direct Pax3 target in vivo, by combining genetic approaches and in vivo chromatin immunoprecipitation assays. We have generated a conditional mutant allele for Itm2a, which is an imprinted gene, by flanking exons 2–4 with loxP sites and inserting an IRESnLacZ reporter in the 3′ UTR of the gene. The LacZ reporter reproduces the expression profile of Itm2a, and allowed us to further characterize its expression at sites of myogenesis, in the dermomyotome and myotome of somites, and in limb buds, in the mouse embryo. We further show that Itm2a is not only expressed in adult muscle fibres but also in the satellite cells responsible for regeneration. Itm2a mutant mice are viable and fertile with no overt phenotype during skeletal muscle formation or regeneration. Potential compensatory mechanisms are discussed.
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11
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Wu X, Daniels G, Shapiro E, Xu K, Huang H, Li Y, Logan S, Greco MA, Peng Y, Monaco ME, Melamed J, Lepor H, Grishina I, Lee P. LEF1 identifies androgen-independent epithelium in the developing prostate. Mol Endocrinol 2011; 25:1018-26. [PMID: 21527502 DOI: 10.1210/me.2010-0513] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Lymphoid enhancer-binding factor (LEF)1 is a major mediator and a target in canonical Wnt/β-catenin pathway. Interactions between the androgen receptor (AR) and canonical Wnt pathways have been implicated in the development of the genitourinary organs. Here, we investigated the localization and role of LEF1-positive cells during development of the prostate gland in human and in the murine model. We show that during human prostate development, LEF1 is restricted to the basal epithelial layer of the urogenital sinus. During mouse development, Lef1 is also present in the urogenital mesenchyme in addition to the basal epithelial layer of the urogenital sinus. In the course of elongation and branching of the prostatic ducts, Lef1 is localized to the proliferating epithelium at the distal tips of the buds. Notably, during branching morphogenesis, domains of Lef1 and AR are mutually exclusive. We further employed the TOPGAL reporter strain to examine the dynamics of Wnt signaling in the context of prostate regression upon a 7-d treatment with a competitive AR inhibitor, bicalutamide. We found that Wnt/Lef1-positive basal cells are not dependent upon androgen for survival. Furthermore, upon bicalutamide treatment, Wnt/Lef1-positive basal progenitors repopulated the luminal compartment. We conclude that Wnt/Lef1 activity identifies an androgen-independent population of prostate progenitors, which is important for embryonic development and organ maintenance and regeneration in the adult.
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Affiliation(s)
- Xinyu Wu
- Department of Urology, New York University School of Medicine, 423 East 23rd Street, New York, New York 10010, USA
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12
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Dib S, Denarier E, Dionne N, Beaudoin M, Friedman HH, Peterson AC. Regulatory modules function in a non-autonomous manner to control transcription of the mbp gene. Nucleic Acids Res 2010; 39:2548-58. [PMID: 21131280 PMCID: PMC3074125 DOI: 10.1093/nar/gkq1160] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Multiple regulatory modules contribute to the complex expression programs realized by many loci. Although long thought of as isolated components, recent studies demonstrate that such regulatory sequences can physically associate with promoters and with each other and may localize to specific sub-nuclear transcription factories. These associations provide a substrate for putative interactions and have led to the suggested existence of a transcriptional interactome. Here, using a controlled strategy of transgenesis, we analyzed the functional consequences of regulatory sequence interaction within the myelin basic protein (mbp) locus. Interactions were revealed through comparisons of the qualitative and quantitative expression programs conferred by an allelic series of 11 different enhancer/inter-enhancer combinations ligated to a common promoter/reporter gene. In a developmentally contextual manner, the regulatory output of all modules changed markedly in the presence of other sequences. Predicted by transgene expression programs, deletion of one such module from the endogenous locus reduced oligodendrocyte expression levels but unexpectedly, also attenuated expression of the overlapping golli transcriptional unit. These observations support a regulatory architecture that extends beyond a combinatorial model to include frequent interactions capable of significantly modulating the functions conferred through regulatory modules in isolation.
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Affiliation(s)
- Samar Dib
- Department of Human Genetics, Laboratory of Developmental Biology, Royal Victoria Hospital, H-5, McGill University Health Centre, Montreal, Quebec, Canada
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13
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Ferri P, Barbieri E, Burattini S, Guescini M, D'Emilio A, Biagiotti L, Del Grande P, De Luca A, Stocchi V, Falcieri E. Expression and subcellular localization of myogenic regulatory factors during the differentiation of skeletal muscle C2C12 myoblasts. J Cell Biochem 2010; 108:1302-17. [PMID: 19830700 DOI: 10.1002/jcb.22360] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
It is known that the MyoD family members (MyoD, Myf5, myogenin, and MRF4) play a pivotal role in the complex mechanism of skeletal muscle cell differentiation. However, fragmentary information on transcription factor-specific regulation is available and data on their post-transcriptional and post-translational behavior are still missing. In this work, we combined mRNA and protein expression analysis with their subcellular localization. Each myogenic regulator factor (MRF) revealed a specific mRNA trend and a protein quantitative analysis not overlapping, suggesting the presence of post-transcriptional mechanisms. In addition, each MRF showed a specific behavior in situ, characterized by a differentiation stage-dependent localization suggestive of a post-translational regulation also. Consistently with their transcriptional activity, immunogold electron microscopy data revealed MRFs distribution in interchromatin domains. Our results showed a MyoD and Myf5 contrasting expression profile in proliferating myoblasts, as well as myogenin and MRF4 opposite distribution in the terminally differentiated myotubes. Interestingly, MRFs expression and subcellular localization analysis during C2C12 cell differentiation stages showed two main MRFs regulation mechanisms: (i) the protein half-life regulation to modulate the differentiation stage-dependent transcriptional activity and (ii) the cytoplasmic retention, as a translocation process, to inhibit the transcriptional activity. Therefore, our results exhibit that MRFs nucleo-cytoplasmic trafficking is involved in muscle differentiation and suggest that, besides the MRFs expression level, also MRFs subcellular localization, related to their functional activity, plays a key role as a regulatory step in transcriptional control mechanisms.
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Affiliation(s)
- Paola Ferri
- Dipartimento di Scienze dell'Uomo, dell'Ambiente e della Natura, University of Urbino Carlo Bo, I-61029 Urbino, Italy
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14
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Hinterberger TJ. A conserved MRF4 promoter drives transgenic expression in Xenopus embryonic somites and adult muscle. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2010; 54:617-25. [PMID: 20209434 DOI: 10.1387/ijdb.082715th] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The muscle regulatory factor MRF4 is expressed in both embryonic and adult vertebrate skeletal muscle cells. In mammals the MRF4 gene has a complex cis-regulatory structure, with many kilobases (kb) of upstream sequence required for embryonic expression in transgenic mice. Here, initial functional comparison between Xenopus and mammalian MRF4 genes revealed that 610 base pairs (bp) of the XMRF4a proximal promoter drove substantial transgenic expression in X. laevis myogenic cells, from somites of neurula embryos through adult myofibers, and as little as 180 bp gave detectable expression. Over 300 bp of XMRF4a proximal promoter sequence is highly conserved among three X. laevis and X. tropicalis MRF4 genes, but only about 150 bp shows significant identity to mammalian MRF4 genes. This most-conserved XMRF4a region contains a putative MEF2 binding site essential for expression both in transgenic embryos and in transfected mouse muscle cells. A rat MRF4 minimal promoter including the conserved region also was active in transgenic X. laevis embryos, demonstrating a striking difference between the mouse and Xenopus transgenic systems. The longest XMRF4a promoter construct tested, with 9.5 kb of 5'-flanking sequence, produced significantly greater expression in transfected mouse cells than did promoters 4.3-kb or shorter, suggesting that the intervening region contains an enhancer, although no increased expression was evident when this region was included in transgenic X. laevis embryos. Further identification and analysis of Xenopus MRF4 transcriptional control elements will offer insights into the evolution of this gene and of the myogenic gene regulatory network.
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15
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Sun WH, Zhu Q, Jiang XS, Du HR. [Genetic diversity and genetic effects of Myf6 gene in chickens]. YI CHUAN = HEREDITAS 2008; 30:71-6. [PMID: 18244905 DOI: 10.3724/sp.j.1005.2008.00071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The population genetic information about genetic distribution, variation and heterozygosity of Myf6 gene in five purelines and three crossbreds of chicken was analyzed using PCR-SSCP. And the genetic effects of Myf6 gene on fiber density and partial carcass traits were investigated. Only one mutation G/A at base position 47 of the whole CDS was found among individuals in each line. The distribution of Myf6 genotype strayed off the Hardy-Weinberg equilibrium and the heterozygosity was low in two purelines but not in three crossbreds. The wild-type allele A had significant positive effects on live-weight, carcass-weight, breast-muscle-weight and leg-muscle-weight (P<0.05), but had negative effects on most of meat quality traits. The A allele had additive effects of increasing 45.54 g of the live-weight, 41.03 g of the carcass-weight, 6 g of the breast-muscle-weight, 9.775 g of the leg-muscle-weight. The A allele had dominant effects of increasing 1.025 mm of the diameter of muscle fiber, -29.99 mm2 of the density of muscle fiber.
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Affiliation(s)
- Wen-Hao Sun
- College of Animal Science, Sichuan Agricultural University, Ya'an 625014, China.
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Bajolle F, Zaffran S, Meilhac SM, Dandonneau M, Chang T, Kelly RG, Buckingham ME. Myocardium at the base of the aorta and pulmonary trunk is prefigured in the outflow tract of the heart and in subdomains of the second heart field. Dev Biol 2008; 313:25-34. [DOI: 10.1016/j.ydbio.2007.09.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Revised: 09/12/2007] [Accepted: 09/14/2007] [Indexed: 10/22/2022]
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17
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Chang THT, Vincent SD, Buckingham ME, Zammit PS. TheA17 enhancer directs expression ofMyf5 to muscle satellite cells butMrf4 to myonuclei. Dev Dyn 2007; 236:3419-26. [DOI: 10.1002/dvdy.21356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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18
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Bajard L, Relaix F, Lagha M, Rocancourt D, Daubas P, Buckingham ME. A novel genetic hierarchy functions during hypaxial myogenesis: Pax3 directly activates Myf5 in muscle progenitor cells in the limb. Genes Dev 2006; 20:2450-64. [PMID: 16951257 PMCID: PMC1560418 DOI: 10.1101/gad.382806] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We address the molecular control of myogenesis in progenitor cells derived from the hypaxial somite. Null mutations in Pax3, a key regulator of skeletal muscle formation, lead to cell death in this domain. We have developed a novel allele of Pax3 encoding a Pax3-engrailed fusion protein that acts as a transcriptional repressor. Heterozygote mouse embryos have an attenuated mutant phenotype, with partial conservation of the hypaxial somite and its myogenic derivatives, including some hindlimb muscles. At these sites, expression of Myf5 is compromised, showing that Pax3 acts genetically upstream of this myogenic determination gene. We have characterized a 145-base-pair (bp) regulatory element, at -57.5 kb from Myf5, that directs transgene expression to the mature somite, notably to myogenic cells of the hypaxial domain that form ventral trunk and limb muscles. A Pax3 consensus site in this sequence binds Pax3 in vitro and in vivo. Multimers of the 145-bp sequence direct transgene expression to sites of Pax3 function, and an assay of its activity in the chick embryo shows Pax3 dependence. Mutation of the Pax3 site abolishes all expression controlled by the 145-bp sequence in transgenic mouse embryos. We conclude that Pax3 directly regulates Myf5 in the hypaxial somite and its derivatives.
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Affiliation(s)
- Lola Bajard
- Centre National de la Recherche Scientifique URA 2578, Department of Developmental Biology, Pasteur Institute, 75015 Paris, France
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Tan X, Zhang Y, Zhang PJ, Xu P, Xu Y. Molecular structure and expression patterns of flounder (Paralichthys olivaceus) Myf-5, a myogenic regulatory factor. Comp Biochem Physiol B Biochem Mol Biol 2006; 145:204-13. [PMID: 16963299 DOI: 10.1016/j.cbpb.2006.07.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 06/29/2006] [Accepted: 07/15/2006] [Indexed: 12/01/2022]
Abstract
Myf-5, a member of the myogenic regulatory factors (MRF), has been shown to be expressed in muscle precursors in early stage zebrafish embryos. The MRFs, including MyoD, Myf-5, Myogenin and MRF4, belong to the basic Helix-Loop-Helix transcription factors that contain a conserved basic Helix-Loop-Helix (bHLH) domain. To better understand the role of Myf-5 in the development of fish muscles, we have isolated the Myf-5 genomic sequence and cDNA from Flounder (Paralichthys olivaceus), and analyzed its structures and patterns of expression. Promoter analysis identified several putative transcription factor binding sites such as an E-box, NF-Y sites that might confer muscle-specific expression. Myf-5 transcripts were first detected in the paraxial mesoderm that gives rise to slow muscles. During somitogenesis, Myf-5 expression was found in developing somites. Myf-5 expression decreased gradually in somites in the anterior region, but remained strong in the newly formed somites. In the hatching stage, the expression was also detected in other muscle cells such as head muscle and fin muscle. In the growing fish, RT-PCR results showed that Myf-5 was expressed in the skeletal muscle and intestine.
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Affiliation(s)
- Xungang Tan
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, P.R. China
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20
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Maak S, Neumann K, Swalve HH. Identification and analysis of putative regulatory sequences for the MYF5/MYF6 locus in different vertebrate species. Gene 2006; 379:141-7. [PMID: 16820272 DOI: 10.1016/j.gene.2006.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2006] [Revised: 05/02/2006] [Accepted: 05/04/2006] [Indexed: 02/07/2023]
Abstract
The myogenic factors (MYF) 5 and 6 are integral to the initiation and development of skeletal muscle and to the maintenance of its phenotype. Thus, they are candidate genes for growth- and meat quality-related traits. We performed a comparative sequence analysis of the MYF5/MYF6 locus in swine, cattle, dog, chicken and zebrafish on the basis of structural and functional information from human and mouse. Beside the characterization of upstream regulatory elements recently identified in mice, we demonstrate the existence of further highly conserved elements (E1 to E4) which may play a role in the regulation of MYF5 and MYF6 expression. Comparative sequence analysis of putative regulatory sequences in swine revealed a total of 21 single nucleotide polymorphisms (SNP) including 1 and 6 SNPs new for the promoters of MYF5 and MYF6, respectively. The conserved organization of the locus in vertebrates indicates a common basic mechanism of muscle development. However, the existence of numerous regulatory elements at large distances to MYF5 and MYF6 points to a very complex pattern of the gene regulation with significant differences between species.
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Affiliation(s)
- S Maak
- Institute of Animal Breeding and Husbandry with Veterinary Clinic, Martin Luther University Halle Wittenberg, Halle, Germany.
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21
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Urbański P, Flisikowski K, Starzyński RR, Kurył J, Kamyczek M. A new SNP in the promoter region of the porcine MYF5 gene has no effect on its transcript level in m. longissimus dorsi. J Appl Genet 2006; 47:59-61. [PMID: 16424610 DOI: 10.1007/bf03194600] [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: 10/18/2022]
Abstract
Myogenic factor 5 (myf-5) is the product of the MYF5 gene, belonging to the MyoD family. This transcription factor participates in the control of myogenesis. We identified 3 new mutations in the promoter region of the gene: A65C, C580T and C613T. The aim of this study was to evaluate the influence of the A65C transversion on gene expression. The analysis was conducted on 15 Polish Large White gilts. The relative content of MYF5 mRNA in m. longissimus dorsi did not differ significantly across MYF5 genotypes (AA, AC, CC). This result suggests that the A65C transversion may not play an important role in the expression of the MYF5 gene in analysed adult muscle but it abolishes a putative binding site for two transcription factors (CDP and HSF1) and creates such a site for Sp1.
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Affiliation(s)
- Pawel Urbański
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, Postepu 1, 05-552 Wolka Kosowska, Poland.
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22
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Huh MS, Smid JK, Rudnicki MA. Muscle function and dysfunction in health and disease. ACTA ACUST UNITED AC 2005; 75:180-92. [PMID: 16187312 DOI: 10.1002/bdrc.20045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Skeletal muscles of the trunk and limbs developmentally originate from the cells of the dermomyotomal compartment of the somite. A wealth of knowledge has been accumulated with regard to understanding the molecular regulation of embryonic skeletal myogenesis. Myogenic induction is controlled through a complex series of spatiotemporal dependent signaling cascades. Secreted signaling molecules from surrounding structures not only initiate the myogenic program, but also influence proliferation and differentiation decisions. The proper coordination of these molecular events is thus critical for the formation of physiologically functional skeletal muscles. Hereditary congenital skeletal muscle defects arise due to genetics lesions in myogenic specific components. Understanding the mechanistic routes of congenital skeletal muscle disease therefore requires a comprehensive knowledge of the developmental system. Ultimately, the application of this knowledge will improve the diagnostic and therapeutic methodologies for such diseases. The aim of this review is to overview our current understanding of skeletal muscle development and associated human congenital diseases.
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Affiliation(s)
- Michael S Huh
- Ottawa Health Research Institute, Molecular Medicine Program, and the Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Echizenya M, Kondo S, Takahashi R, Oh J, Kawashima S, Kitayama H, Takahashi C, Noda M. The membrane-anchored MMP-regulator RECK is a target of myogenic regulatory factors. Oncogene 2005; 24:5850-7. [PMID: 16007210 DOI: 10.1038/sj.onc.1208733] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The membrane-anchored MMP-regulator RECK is down regulated in many solid tumors; the extent of RECK down regulation correlates with poor prognosis. Forced expression of RECK in tumor cells results in suppression of angiogenesis, invasion, and metastasis. Studies on the roles and the mechanisms of regulation of the RECK gene during normal development may therefore yield important insights into how the malignant behaviors of tumor cells arise and how they can be controlled. Our previous studies indicate that mice lacking RECK die around E10.5 with reduced tissue integrity. In the present study, we have found that in later stage wild-type embryos, RECK is abundantly expressed in skeletal muscles, especially in the areas where the myoblast differentiation factor MRF4 is expressed. Consistent with this finding, the RECK-promoter is activated by MRF4 in cultured cells. In contrast, a myoblast determination factor MyoD suppresses the RECK-promoter. Myoblastic cells lacking RECK expression give rise to myotubes at higher efficiency than the cells expressing RECK, indicating that RECK suppresses myotube formation. These findings suggest that MyoD down regulates RECK to facilitate myotube formation, whereas MRF4 up regulates RECK to promote other aspects of myogenesis that require extracellular matrix integrity.
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Affiliation(s)
- Michiko Echizenya
- Department of Molecular Oncology, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Japan
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