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Summers KM, Bush SJ, Davis MR, Hume DA, Keshvari S, West JA. Fibrillin-1 and asprosin, novel players in metabolic syndrome. Mol Genet Metab 2023; 138:106979. [PMID: 36630758 DOI: 10.1016/j.ymgme.2022.106979] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Fibrillin-1 is a major component of the extracellular microfibrils, where it interacts with other extracellular matrix proteins to provide elasticity to connective tissues, and regulates the bioavailability of TGFβ family members. A peptide consisting of the C-terminal 140 amino acids of fibrillin-1 has recently been identified as a glucogenic hormone, secreted from adipose tissue during fasting and targeting the liver to release glucose. This fragment, called asprosin, also signals in the hypothalamus to stimulate appetite. Asprosin levels are correlated with many of the pathologies indicative of metabolic syndrome, including insulin resistance and obesity. Previous studies and reviews have addressed the therapeutic potential of asprosin as a target in obesity, diabetes and related conditions without considering mechanisms underlying the relationship between generation of asprosin and expression of the much larger fibrillin-1 protein. Profibrillin-1 undergoes obligatory cleavage at the cell surface as part of its assembly into microfibrils, producing the asprosin peptide as well as mature fibrillin-1. Patterns of FBN1 mRNA expression are inconsistent with the necessity for regulated release of asprosin. The asprosin peptide may be protected from degradation in adipose tissue. We present evidence for an alternative possibility, that asprosin mRNA is generated independently from an internal promoter within the 3' end of the FBN1 gene, which would allow for regulation independent of fibrillin-synthesis and is more economical of cellular resources. The discovery of asprosin opened exciting possibilities for treatment of metabolic syndrome related conditions, but there is much to be understood before such therapies could be introduced into the clinic.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, United Kingdom.
| | - Margaret R Davis
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Jennifer A West
- Faculty of Medicine, The University of Queensland, Mayne Medical Building, 288 Herston Road, Herston, Queensland 4006, Australia.
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2
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Benarroch L, Aubart M, Gross MS, Arnaud P, Hanna N, Jondeau G, Boileau C. Reference Expression Profile of Three FBN1 Transcript Isoforms and Their Association with Clinical Variability in Marfan Syndrome. Genes (Basel) 2019; 10:genes10020128. [PMID: 30754709 PMCID: PMC6409622 DOI: 10.3390/genes10020128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/30/2019] [Accepted: 02/06/2019] [Indexed: 11/29/2022] Open
Abstract
Marfan syndrome (MFS) is a rare connective tissue disorder mainly due to mutations in the FBN1 gene. Great phenotypic variability is notable for age of onset, the presence and absence, and the number and the severity of the symptoms. Our team showed that FBN1 gene expression level was a good surrogate endpoint for severity of some MFS clinical features. Eight alternative transcripts are referenced for the FBN1 gene. We hypothesized that MFS clinical variability could be related to specific FBN1 isoforms. Isoform expression profiles were investigated in skin and adventitial fibroblasts from controls and MFS patients. The results of the study showed that, in skin and adventitial fibroblasts, only three isoforms were found: FBN1_001, FBN1_004, and FBN1_009. The main isoform was FBN1_001 and it was significantly reduced in skin and adventitial fibroblasts of MFS patients. The expressions of FBN1_004 and FBN1_009 isoforms were similar between controls and MFS patients. However, the expression of the three isoforms was correlated only in patients. Furthermore, their expression levels were associated with the presence of ectopia lentis in MFS patients. Therefore, our results highlight that the two minor alternatively spliced FBN1 isoforms play a possible role in the pathogenesis of the disease.
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Affiliation(s)
- Louise Benarroch
- Laboratory for Vascular Translational Science, INSERM U1148, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri Huchard, 75018 Paris, France.
| | - Mélodie Aubart
- Laboratory for Vascular Translational Science, INSERM U1148, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri Huchard, 75018 Paris, France.
- Service de Neuropédiatrie, Hôpital Necker-Enfants-Malades, 149 rue de Sèvres, 75015 Paris, France.
| | - Marie-Sylvie Gross
- Laboratory for Vascular Translational Science, INSERM U1148, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri Huchard, 75018 Paris, France.
| | - Pauline Arnaud
- Laboratory for Vascular Translational Science, INSERM U1148, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri Huchard, 75018 Paris, France.
- Département de Génétique, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri 17 Huchard, 75018 Paris, France.
| | - Nadine Hanna
- Département de Génétique, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri 17 Huchard, 75018 Paris, France.
| | - Guillaume Jondeau
- Laboratory for Vascular Translational Science, INSERM U1148, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri Huchard, 75018 Paris, France.
- Centre de Référence pour le Syndrome de Marfan et syndromes apparentés, Service de Cardiologie, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri Huchard, 75018 Paris, France.
- UFR de Médecine, Université Paris Diderot, 16 rue Henri Huchard, 75018 Paris, France.
| | - Catherine Boileau
- Laboratory for Vascular Translational Science, INSERM U1148, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri Huchard, 75018 Paris, France.
- Département de Génétique, Centre Hospitalo-Universitaire Xavier Bichat, 46 rue Henri 17 Huchard, 75018 Paris, France.
- UFR de Médecine, Université Paris Diderot, 16 rue Henri Huchard, 75018 Paris, France.
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3
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Davis MR, Andersson R, Severin J, de Hoon M, Bertin N, Baillie JK, Kawaji H, Sandelin A, Forrest ARR, Summers KM. Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions. Mol Genet Metab 2014; 112:73-83. [PMID: 24703491 PMCID: PMC4019825 DOI: 10.1016/j.ymgme.2013.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/06/2013] [Accepted: 12/06/2013] [Indexed: 01/23/2023]
Abstract
The fibrillins and latent transforming growth factor binding proteins (LTBPs) form a superfamily of extracellular matrix (ECM) proteins characterized by the presence of a unique domain, the 8-cysteine transforming growth factor beta (TGFβ) binding domain. These proteins are involved in the structure of the extracellular matrix and controlling the bioavailability of TGFβ family members. Genes encoding these proteins show differential expression in mesenchymal cell types which synthesize the extracellular matrix. We have investigated the promoter regions of the seven gene family members using the FANTOM5 CAGE database for human. While the protein and nucleotide sequences show considerable sequence similarity, the promoter regions were quite diverse. Most genes had a single predominant transcription start site region but LTBP1 and LTBP4 had two regions initiating different transcripts. Most of the family members were expressed in a range of mesenchymal and other cell types, often associated with use of alternative promoters or transcription start sites within a promoter in different cell types. FBN3 was the lowest expressed gene, and was found only in embryonic and fetal tissues. The different promoters for one gene were more similar to each other in expression than to promoters of the other family members. Notably expression of all 22 LTBP2 promoters was tightly correlated and quite distinct from all other family members. We located candidate enhancer regions likely to be involved in expression of the genes. Each gene was associated with a unique subset of transcription factors across multiple promoters although several motifs including MAZ, SP1, GTF2I and KLF4 showed overrepresentation across the gene family. FBN1 and FBN2, which had similar expression patterns, were regulated by different transcription factors. This study highlights the role of alternative transcription start sites in regulating the tissue specificity of closely related genes and suggests that this important class of extracellular matrix proteins is subject to subtle regulatory variations that explain the differential roles of members of this gene family.
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Affiliation(s)
- Margaret R Davis
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK.
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark.
| | - Jessica Severin
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan(1); RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan.
| | - Michiel de Hoon
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan(1); RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan.
| | - Nicolas Bertin
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan(1); RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan.
| | - J Kenneth Baillie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK.
| | - Hideya Kawaji
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan(1); RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan; RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan.
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark.
| | - Alistair R R Forrest
- RIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan(1); RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan.
| | - Kim M Summers
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK; The University of Queensland Northside Clinical School, Prince Charles Hospital, Chermside 4032, Australia.
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Harmston N, Baresic A, Lenhard B. The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci 2013; 368:20130021. [PMID: 24218634 PMCID: PMC3826495 DOI: 10.1098/rstb.2013.0021] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Regions of several dozen to several hundred base pairs of extreme conservation have been found in non-coding regions in all metazoan genomes. The distribution of these elements within and across genomes has suggested that many have roles as transcriptional regulatory elements in multi-cellular organization, differentiation and development. Currently, there is no known mechanism or function that would account for this level of conservation at the observed evolutionary distances. Previous studies have found that, while these regions are under strong purifying selection, and not mutational coldspots, deletion of entire regions in mice does not necessarily lead to identifiable changes in phenotype during development. These opposing findings lead to several questions regarding their functional importance and why they are under strong selection in the first place. In this perspective, we discuss the methods and techniques used in identifying and dissecting these regions, their observed patterns of conservation, and review the current hypotheses on their functional significance.
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Affiliation(s)
- Nathan Harmston
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London and MRC Clinical Sciences Centre, , Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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Guo G, Rödelsperger C, Digweed M, Robinson PN. Regulation of fibrillin-1 gene expression by Sp1. Gene 2013; 527:448-55. [PMID: 23860323 DOI: 10.1016/j.gene.2013.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 07/01/2013] [Accepted: 07/05/2013] [Indexed: 11/28/2022]
Abstract
Mutations in the fibrillin-1 gene (FBN1) cause Marfan Syndrome (MFS), a hereditary disorder of connective tissue. The transcription of FBN1 has been reported to be driven by a short ultraconserved region (SUPR) in the 5' untranslated exon A of FBN1, but the nature of other factors involved in FBN1 gene regulation has not been clarified. In this study, we characterized the transcription factors involved in FBN1 gene regulation. The results show that Sp1 protein binds to two putative binding sites in the promoter of FBN1. Overexpression of Sp1 resulted in a significant increase in both promoter activity and FBN1 mRNA level in HEK 293 cells, whereas inhibition or knockdown of Sp1 decreased FBN1 gene expression. In addition, we found that Poly [ADP-ribose] polymerase 1 (PARP1) binds to the palindromic sequence TCTCGCGAGA in the ultraconserved region of the FBN1 promoter and that the regulation of FBN1 expression by PARP1 is dependent on Sp1. These results indicate that both Sp1 and PARP1 contribute to FBN1 gene expression. These observations add to our understanding of the transcriptional regulation of FBN1 gene expression.
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Affiliation(s)
- Gao Guo
- Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
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6
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Davis MR, Summers KM. Structure and function of the mammalian fibrillin gene family: implications for human connective tissue diseases. Mol Genet Metab 2012; 107:635-47. [PMID: 22921888 DOI: 10.1016/j.ymgme.2012.07.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 07/30/2012] [Accepted: 07/30/2012] [Indexed: 12/31/2022]
Abstract
Fibrillins and latent transforming growth factor β binding proteins (LTBPs) are components of the extracellular matrix of connective tissue. While fibrillins are integral to the 10nm microfibrils, and often associated with elastin, all family members are likely to have an additional role in regulating the bioavailability of transforming growth factor β (TGBβ). Both fibrillins and LTBPs are large glycoproteins, containing a series of calcium binding epidermal growth factor domains as well as a number of copies of a unique 8 cysteine domain found only in this protein superfamily. There are three mammalian fibrillins and four LTBPs. Fibrillin monomers link head to tail in microfibrils which can then form two and three dimensional structures. In some tissues elastin is recruited to the fibrillin microfibrils to provide elasticity to the tissue. LTBPs are part of the TGBβ large latent complex which sequesters TGBβ in the extracellular matrix. Fibrillin-1 appears to bind to LTBPs to assist in this process and is thus involved in regulating the bioavailability of TGBβ. Mutation of fibrillin genes results in connective tissue phenotypes which reflect both the increased level of active TGBβ and the structural failure of the extracellular matrix due to the absence or abnormality of fibrillin protein. Fibrillinopathies include Marfan syndrome, familial ectopia lentis, familial thoracic aneurysm (mutations of FBN1) and congenital contractural arachnodactyly (mutation of FBN2). There are no diseases currently associated with mutation of FBN3 in humans, and this gene is no longer active in rodents. Expression patterns of fibrillin genes are consistent with their role in extracellular matrix structure of connective tissue. FBN1 expression is high in most cell types of mesenchymal origin, particularly bone. Human and mouse FBN2 expression is high in fetal cells and has more restricted expression in mesenchymal cell types postnatally. FBN3 is expressed early in development (embryonic and fetal tissues) in humans. The fibrillins are thus important in maintaining the structure and integrity of the extracellular matrix and, in combination with their sequence family members the LTBPs, also contribute to the regulation of the TGFβ family of major growth factors.
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Affiliation(s)
- Margaret R Davis
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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7
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Zou S, Gu Z, Ni P, Liu X, Wang J, Fan Q. SP1 plays a pivotal role for basal activity of TIGAR promoter in liver cancer cell lines. Mol Cell Biochem 2011; 359:17-23. [PMID: 21761199 DOI: 10.1007/s11010-011-0993-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 07/06/2011] [Indexed: 12/21/2022]
Abstract
TIGAR expression resulted in down-regulation of glycolysis, reduction of intracellular levels of reactive oxygen species, and protection from apoptosis. Despite biological importance, its promoter has not yet been characterized. In this study, we characterized that transcription factor SP1 plays a pivotal role for basal activity of TIGAR promoter. By 5'RACE, the transcription start site was identified locating at 134 bp upstream of the translation initiation site. Different portions of 5'-flanking and 5'-untranslated regions were fused to a luciferase reporter gene to create reporter plasmids, and constructs were transiently transfected into HepG2, Bel-7402, and Smmc-7721 cell lines for luciferase analysis. A minimal region -56/-4 bearing a SP1-binding site was characterized and plays a vital role. Data from electrophoretic mobility shift assay and chromatin immunoprecipitation showed that SP1 can interact with the SP1-binding site within TIGAR promoter in vitro and in vivo. Conclusively, SPl is indispensable for basal activity of TIGAR promoter.
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Affiliation(s)
- Shubiao Zou
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China
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8
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Mahony S, Mazzoni EO, McCuine S, Young RA, Wichterle H, Gifford DK. Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis. Genome Biol 2011; 12:R2. [PMID: 21232103 PMCID: PMC3091300 DOI: 10.1186/gb-2011-12-1-r2] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 12/10/2010] [Accepted: 01/13/2011] [Indexed: 01/31/2023] Open
Abstract
Background Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating retinoic acid receptor (RAR)-mediated transcription. RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the retinoid ligand. However, little is known about where RAR binds to the genome or how it selects target sites. Results We tested the constitutive RAR binding model using the retinoic acid-driven differentiation of mouse embryonic stem cells into differentiated motor neurons. We find that retinoic acid treatment results in widespread changes in RAR genomic binding, including novel binding to genes directly responsible for anterior-posterior specification, as well as the subsequent recruitment of the basal polymerase machinery. Finally, we discovered that the binding of transcription factors at the embryonic stem cell stage can accurately predict where in the genome RAR binds after initial differentiation. Conclusions We have characterized a ligand-dependent shift in RAR genomic occupancy at the initiation of neurogenesis. Our data also suggest that enhancers active in pluripotent embryonic stem cells may be preselecting regions that will be activated by RAR during neuronal differentiation.
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Affiliation(s)
- Shaun Mahony
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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9
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van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y, Veenstra GJC. Nucleotide composition-linked divergence of vertebrate core promoter architecture. Genome Res 2011; 21:410-21. [PMID: 21284373 DOI: 10.1101/gr.111724.110] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Transcription initiation involves the recruitment of basal transcription factors to the core promoter. A variety of core promoter elements exists; however for most of these motifs, the distribution across species is unknown. Here we report on the comparison of human and amphibian promoter sequences. We have used oligo-capping in combination with deep sequencing to determine transcription start sites in Xenopus tropicalis. To systematically predict regulatory elements, we have developed a de novo motif finding pipeline using an ensemble of computational tools. A comprehensive comparison of human and amphibian promoter sequences revealed both similarities and differences in core promoter architecture. Some of the differences stem from a highly divergent nucleotide composition of Xenopus and human promoters. Whereas the distribution of some core promoter motifs is conserved independently of species-specific nucleotide bias, the frequency of another class of motifs correlates with the single nucleotide frequencies. This class includes the well-known TATA box and SP1 motifs, which are more abundant in Xenopus and human promoters, respectively. While these motifs are enriched above the local nucleotide background in both organisms, their frequency varies in step with this background. These differences are likely adaptive as these motifs can recruit TFIID to either CpG island or sharply initiating promoters. Our results highlight both the conserved and diverged aspects of vertebrate transcription, most notably showing co-opted motif usage to recruit the transcriptional machinery to promoters with diverging nucleotide composition. This shows how sweeping changes in nucleotide composition are compatible with highly conserved mechanisms of transcription initiation.
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Affiliation(s)
- Simon J van Heeringen
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
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When needles look like hay: how to find tissue-specific enhancers in model organism genomes. Dev Biol 2010; 350:239-54. [PMID: 21130761 DOI: 10.1016/j.ydbio.2010.11.026] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 11/11/2010] [Accepted: 11/22/2010] [Indexed: 01/22/2023]
Abstract
A major prerequisite for the investigation of tissue-specific processes is the identification of cis-regulatory elements. No generally applicable technique is available to distinguish them from any other type of genomic non-coding sequence. Therefore, researchers often have to identify these elements by elaborate in vivo screens, testing individual regions until the right one is found. Here, based on many examples from the literature, we summarize how functional enhancers have been isolated from other elements in the genome and how they have been characterized in transgenic animals. Covering computational and experimental studies, we provide an overview of the global properties of cis-regulatory elements, like their specific interactions with promoters and target gene distances. We describe conserved non-coding elements (CNEs) and their internal structure, nucleotide composition, binding site clustering and overlap, with a special focus on developmental enhancers. Conflicting data and unresolved questions on the nature of these elements are highlighted. Our comprehensive overview of the experimental shortcuts that have been found in the different model organism communities and the new field of high-throughput assays should help during the preparation phase of a screen for enhancers. The review is accompanied by a list of general guidelines for such a project.
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11
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Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res 2010; 21:447-55. [PMID: 21106904 DOI: 10.1101/gr.112623.110] [Citation(s) in RCA: 390] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Accurate functional annotation of regulatory elements is essential for understanding global gene regulation. Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblastoid cell lines, which is comprised of sites corresponding to 239 position weight matrices of known transcription factor binding motifs, and 49 novel sequence motifs. To generate this map, we developed a probabilistic framework that integrates cell- or tissue-specific experimental data such as histone modifications and DNase I cleavage patterns with genomic information such as gene annotation and evolutionary conservation. Comparison to empirical ChIP-seq data suggests that our method is highly accurate yet has the advantage of targeting many factors in a single assay. We anticipate that this approach will be a valuable tool for genome-wide studies of gene regulation in a wide variety of cell types or tissues under diverse conditions.
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Affiliation(s)
- Roger Pique-Regi
- Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.
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Mikula M, Gaj P, Dzwonek K, Rubel T, Karczmarski J, Paziewska A, Dzwonek A, Bragoszewski P, Dadlez M, Ostrowski J. Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter. DNA Res 2010; 17:245-60. [PMID: 20587588 PMCID: PMC2920758 DOI: 10.1093/dnares/dsq016] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Definitive identification of promoters, their cis-regulatory motifs, and their trans-acting proteins requires experimental analysis. To define the HNRNPK promoter and its cognate DNA–protein interactions, we performed a comprehensive study combining experimental approaches, including luciferase reporter gene assays, chromatin immunoprecipitations (ChIP), electrophoretic mobility shift assays (EMSA), and mass spectrometry (MS). We discovered that out of the four potential HNRNPK promoters tested, the one containing the palindromic motif TCTCGCGAGA exhibited the highest activity in a reporter system assay. Although further EMSA and MS analyses, performed to uncover the identity of the palindrome-binding transcription factor, did identify a complex of DNA-binding proteins, neither method unambiguously identified the pertinent direct trans-acting protein(s). ChIP revealed similar chromatin states at the promoters with the palindromic motif and at housekeeping gene promoters. A ChIP survey showed significantly higher recruitment of PARP1, a protein identified by MS as ubiquitously attached to DNA probes, within heterochromatin sites. Computational analyses indicated that this palindrome displays features that mark nucleosome boundaries, causing the surrounding DNA landscape to be constitutively open. Our strategy of diverse approaches facilitated the direct characterization of various molecular properties of HNRNPK promoter bearing the palindromic motif TCTCGCGAGA, despite the obstacles that accompany in vitro methods.
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Affiliation(s)
- Michal Mikula
- Department of Gastroenterology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena, Warsaw, Poland
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13
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Magyar I, Colman D, Arnold E, Baumgartner D, Bottani A, Fokstuen S, Addor MC, Berger W, Carrel T, Steinmann B, Mátyás G. Quantitative sequence analysis of FBN1 premature termination codons provides evidence for incomplete NMD in leukocytes. Hum Mutat 2009; 30:1355-64. [PMID: 19618372 DOI: 10.1002/humu.21058] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We improved, evaluated, and used Sanger sequencing for quantification of single nucleotide polymorphism (SNP) variants in transcripts and gDNA samples. This improved assay resulted in highly reproducible relative allele frequencies (e.g., for a heterozygous gDNA 50.0+/-1.4%, and for a missense mutation-bearing transcript 46.9+/-3.7%) with a lower detection limit of 3-9%. It provided excellent accuracy and linear correlation between expected and observed relative allele frequencies. This sequencing assay, which can also be used for the quantification of copy number variations (CNVs), methylations, mosaicisms, and DNA pools, enabled us to analyze transcripts of the FBN1 gene in fibroblasts and blood samples of patients with suspected Marfan syndrome not only qualitatively but also quantitatively. We report a total of 18 novel and 19 known FBN1 sequence variants leading to a premature termination codon (PTC), 26 of which we analyzed by quantitative sequencing both at gDNA and cDNA levels. The relative amounts of PTC-containing FBN1 transcripts in fresh and PAXgene-stabilized blood samples were significantly higher (33.0+/-3.9% to 80.0+/-7.2%) than those detected in affected fibroblasts with inhibition of nonsense-mediated mRNA decay (NMD) (11.0+/-2.1% to 25.0+/-1.8%), whereas in fibroblasts without NMD inhibition no mutant alleles could be detected. These results provide evidence for incomplete NMD in leukocytes and have particular importance for RNA-based analyses not only in FBN1 but also in other genes.
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Affiliation(s)
- István Magyar
- Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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Rödelsperger C, Köhler S, Schulz MH, Manke T, Bauer S, Robinson PN. Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts. Genomics 2009; 94:308-16. [DOI: 10.1016/j.ygeno.2009.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 07/17/2009] [Accepted: 07/21/2009] [Indexed: 01/03/2023]
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15
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Summers KM, Bokil NJ, Baisden JM, West MJ, Sweet MJ, Raggatt LJ, Hume DA. Experimental and bioinformatic characterisation of the promoter region of the Marfan syndrome gene, FBN1. Genomics 2009; 94:233-40. [DOI: 10.1016/j.ygeno.2009.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/01/2009] [Accepted: 06/19/2009] [Indexed: 01/06/2023]
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