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Aravind L, Anantharaman V, Venancio TM. Apprehending multicellularity: regulatory networks, genomics, and evolution. ACTA ACUST UNITED AC 2009; 87:143-64. [PMID: 19530132 DOI: 10.1002/bdrc.20153] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The genomic revolution has provided the first glimpses of the architecture of regulatory networks. Combined with evolutionary information, the "network view" of life processes leads to remarkable insights into how biological systems have been shaped by various forces. This understanding is critical because biological systems, including regulatory networks, are not products of engineering but of historical contingencies. In this light, we attempt a synthetic overview of the natural history of regulatory networks operating in the development and differentiation of multicellular organisms. We first introduce regulatory networks and their organizational principles as can be deduced using ideas from the graph theory. We then discuss findings from comparative genomics to illustrate the effects of lineage-specific expansions, gene-loss, and nonprotein-coding DNA on the architecture of networks. We consider the interaction between expansions of transcription factors, and cis regulatory and more general chromatin state stabilizing elements in the emergence of morphological complexity. Finally, we consider a case study of the Notch subnetwork, which is present throughout Metazoa, to examine how such a regulatory system has been pieced together in evolution from new innovations and pre-existing components that were originally functionally distinct.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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Qin H, Chan MWY, Liyanarachchi S, Balch C, Potter D, Souriraj IJ, Cheng ASL, Agosto-Perez FJ, Nikonova EV, Yan PS, Lin HJ, Nephew KP, Saltz JH, Showe LC, Huang THM, Davuluri RV. An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. BMC SYSTEMS BIOLOGY 2009; 3:73. [PMID: 19615063 PMCID: PMC2724489 DOI: 10.1186/1752-0509-3-73] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 07/17/2009] [Indexed: 12/24/2022]
Abstract
Background The TGF-β/SMAD pathway is part of a broader signaling network in which crosstalk between pathways occurs. While the molecular mechanisms of TGF-β/SMAD signaling pathway have been studied in detail, the global networks downstream of SMAD remain largely unknown. The regulatory effect of SMAD complex likely depends on transcriptional modules, in which the SMAD binding elements and partner transcription factor binding sites (SMAD modules) are present in specific context. Results To address this question and develop a computational model for SMAD modules, we simultaneously performed chromatin immunoprecipitation followed by microarray analysis (ChIP-chip) and mRNA expression profiling to identify TGF-β/SMAD regulated and synchronously coexpressed gene sets in ovarian surface epithelium. Intersecting the ChIP-chip and gene expression data yielded 150 direct targets, of which 141 were grouped into 3 co-expressed gene sets (sustained up-regulated, transient up-regulated and down-regulated), based on their temporal changes in expression after TGF-β activation. We developed a data-mining method driven by the Random Forest algorithm to model SMAD transcriptional modules in the target sequences. The predicted SMAD modules contain SMAD binding element and up to 2 of 7 other transcription factor binding sites (E2F, P53, LEF1, ELK1, COUPTF, PAX4 and DR1). Conclusion Together, the computational results further the understanding of the interactions between SMAD and other transcription factors at specific target promoters, and provide the basis for more targeted experimental verification of the co-regulatory modules.
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Affiliation(s)
- Huaxia Qin
- Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA.
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Dathe K, Kjaer KW, Brehm A, Meinecke P, Nürnberg P, Neto JC, Brunoni D, Tommerup N, Ott CE, Klopocki E, Seemann P, Mundlos S. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am J Hum Genet 2009; 84:483-92. [PMID: 19327734 DOI: 10.1016/j.ajhg.2009.03.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/20/2009] [Accepted: 03/04/2009] [Indexed: 01/22/2023] Open
Abstract
Autosomal-dominant brachydactyly type A2 (BDA2), a limb malformation characterized by hypoplastic middle phalanges of the second and fifth fingers, has been shown to be due to mutations in the Bone morphogenetic protein receptor 1B (BMPR1B) or in its ligand Growth and differentiation factor 5 (GDF5). A linkage analysis performed in a mutation-negative family identified a novel locus for BDA2 on chromosome 20p12.3 that incorporates the gene for Bone morphogenetic protein 2 (BMP2). No point mutation was identified in BMP2, so a high-density array CGH analysis covering the critical interval of approximately 1.3 Mb was performed. A microduplication of approximately 5.5 kb in a noncoding sequence approximately 110 kb downstream of BMP2 was detected. Screening of other patients by qPCR revealed a similar duplication in a second family. The duplicated region contains evolutionary highly conserved sequences suggestive of a long-range regulator. By using a transgenic mouse model we can show that this sequence is able to drive expression of a X-Gal reporter construct in the limbs. The almost complete overlap with endogenous Bmp2 expression indicates that a limb-specific enhancer of Bmp2 is located within the identified duplication. Our results reveal an additional functional mechanism for the pathogenesis of BDA2, which is duplication of a regulatory element that affects the expression of BMP2 in the developing limb.
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Johnson LA, Zhao Y, Golden K, Barolo S. Reverse-engineering a transcriptional enhancer: a case study in Drosophila. Tissue Eng Part A 2009; 14:1549-59. [PMID: 18687053 DOI: 10.1089/ten.tea.2008.0074] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Enhancers, or cis-regulatory elements, are the principal determinants of spatiotemporal patterning of gene expression. For reasons of clinical and research utility, it is desirable to build customized enhancers that drive novel gene expression patterns, but currently, we largely rely on "found" genomic elements. Synthetic enhancers, assembled from transcription factor binding sites taken from natural signal-regulated enhancers, generally fail to behave like their wild-type counterparts when placed in transgenic animals, suggesting that important aspects of enhancer function are still unexplored. As a step toward the creation of a truly synthetic regulatory element, we have undertaken an extensive structure-function study of an enhancer of the Drosophila decapentaplegic (dpp) gene that drives expression in the developing visceral mesoderm (VM). Although considerable past efforts have been made to dissect the dppVM enhancer, transgenic experiments presented here indicate that its activity cannot be explained by the known regulators alone. dppVM contains multiple, previously uncharacterized, regulatory sites, some of which exhibit functional redundancy. The results presented here suggest that even the best-studied enhancers must be further dissected before they can be fully understood, and before faithful synthetic elements based on them can be created. Implications for developmental genetics, mathematical modeling, and therapeutic applications are discussed.
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Affiliation(s)
- Lisa A Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Kim J, He X, Sinha S. Evolution of regulatory sequences in 12 Drosophila species. PLoS Genet 2009; 5:e1000330. [PMID: 19132088 PMCID: PMC2607023 DOI: 10.1371/journal.pgen.1000330] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2008] [Accepted: 12/05/2008] [Indexed: 01/07/2023] Open
Abstract
Characterization of the evolutionary constraints acting on cis-regulatory sequences is crucial to comparative genomics and provides key insights on the evolution of organismal diversity. We study the relationships among orthologous cis-regulatory modules (CRMs) in 12 Drosophila species, especially with respect to the evolution of transcription factor binding sites, and report statistical evidence in favor of key evolutionary hypotheses. Binding sites are found to have position-specific substitution rates. However, the selective forces at different positions of a site do not act independently, and the evidence suggests that constraints on sites are often based on their exact binding affinities. Binding site loss is seen to conform to a molecular clock hypothesis. The rate of site loss is transcription factor–specific and depends on the strength of binding and, in some cases, the presence of other binding sites in close proximity. Our analysis is based on a novel computational method for aligning orthologous CRMs on a tree, which rigorously accounts for alignment uncertainties and exploits binding site predictions through a unified probabilistic framework. Finally, we report weak purifying selection on short deletions, providing important clues about overall spatial constraints on CRMs. Our results present a complex picture of regulatory sequence evolution, with substantial plasticity that depends on a number of factors. The insights gained in this study will help us to understand the combinatorial control of gene regulation and how it evolves. They will pave the way for theoretical models that are cognizant of the important determinants of regulatory sequence evolution and will be critical in genome-wide identification of non-coding sequences under purifying or positive selection. The spatial–temporal expression pattern of a gene, which is crucial to its function, is controlled by cis-regulatory DNA sequences. Forming the basic units of regulatory sequences are transcription factor binding sites, often organized into larger modules that determine gene expression in response to combinatorial environmental signals. Understanding the conservation and change of regulatory sequences is critical to our knowledge of the unity as well as diversity of animal development and phenotypes. In this paper, we study the evolution of sequences involved in the regulation of body patterning in the Drosophila embryo. We find that mutations of nucleotides within a binding site are constrained by evolutionary forces to preserve the site's binding affinity to the cognate transcription factor. Functional binding sites are frequently destroyed during evolution and the rate of loss across evolutionary spans is roughly constant. We also find that the evolutionary fate of a site strongly depends on its context; a pair of interacting sites are more likely to survive mutational forces than isolated sites. Together, these findings provide new insights and pose new challenges to our understanding of cis-regulatory sequences and their evolution.
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Affiliation(s)
- Jaebum Kim
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Xin He
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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Long-range enhancer differentially regulated by c-Jun and JunD controls peptidylarginine deiminase-3 gene in keratinocytes. J Mol Biol 2008; 384:1048-57. [PMID: 18952102 DOI: 10.1016/j.jmb.2008.10.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 09/26/2008] [Accepted: 10/02/2008] [Indexed: 11/23/2022]
Abstract
Long-range cis elements are critical regulators of transcription, particularly for clustered paralogous genes. Such are the five PADI genes in 1p35-36 encoding peptidylarginine deiminases, which catalyze deimination, a Ca2+-dependent post-translational modification. Deimination has been implicated in the pathophysiology of severe human diseases such as multiple sclerosis and rheumatoid arthritis. The PADI genes present different expression patterns. PADI1-3 are expressed in the epidermis, with increased expression levels in the most differentiated keratinocytes. Previous studies on PADI proximal promoters failed to explain such specificity of expression. We identified a conserved intergenic sequence in the PADI locus (IG1), which may play a role in PADI transcriptional regulation. In this work, we identified two DNase I.hypersensitive sites located in IG1, PAD intergenic enhancer segment 1 (PIE-S1) and PIE-S2, which act in synergy as a bipartite enhancer of the PADI3 and probably PADI1 promoters in normal human epidermal keratinocytes differentiated by a high-calcium-containing medium (1.5 mM). PIE-S1 and PIE-S2 present all the hallmarks of transcriptional enhancers: orientation-independence, copy-number dependence and cell-type specificity. PIE-S1 and PIE-S2 comprise conserved putative binding sites for MIBP1/RFX1 and activator protein 1, respectively. Deletion mutant screening revealed that these sites are crucial for the enhancer activity. Furthermore, chromatin immunoprecipitation assays evidenced differential binding of JunD or c-Jun on the activator protein 1 site depending on the cell differentiation state. Our results reveal the molecular bases of the expression specificity of PADI1 and PADI3 during keratinocyte differentiation through a long-range enhancer and support a model of PADI gene regulation depending on c-Jun-JunD competition.
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Hadzhiev Y, Lang M, Ertzer R, Meyer A, Strähle U, Müller F. Functional diversification of sonic hedgehog paralog enhancers identified by phylogenomic reconstruction. Genome Biol 2008; 8:R106. [PMID: 17559649 PMCID: PMC2394741 DOI: 10.1186/gb-2007-8-6-r106] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 05/09/2007] [Accepted: 06/08/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cis-regulatory modules of developmental genes are targets of evolutionary changes that underlie the morphologic diversity of animals. Little is known about the 'grammar' of interactions between transcription factors and cis-regulatory modules and therefore about the molecular mechanisms that underlie changes in these modules, particularly after gene and genome duplications. We investigated the ar-C midline enhancer of sonic hedgehog (shh) orthologs and paralogs from distantly related vertebrate lineages, from fish to human, including the basal vertebrate Latimeria menadoensis. RESULTS We demonstrate that the sonic hedgehog a (shha) paralogs sonic hedgehog b (tiggy winkle hedgehog; shhb) genes of fishes have a modified ar-C enhancer, which specifies a diverged function at the embryonic midline. We have identified several conserved motifs that are indicative of putative transcription factor binding sites by local alignment of ar-C enhancers of numerous vertebrate sequences. To trace the evolutionary changes among paralog enhancers, phylogenomic reconstruction was carried out and lineage-specific motif changes were identified. The relation between motif composition and observed developmental differences was evaluated through transgenic functional analyses. Altering and exchanging motifs between paralog enhancers resulted in reversal of enhancer specificity in the floor plate and notochord. A model reconstructing enhancer divergence during vertebrate evolution was developed. CONCLUSION Our model suggests that the identified motifs of the ar-C enhancer function as binary switches that are responsible for specific activity between midline tissues, and that these motifs are adjusted during functional diversification of paralogs. The unraveled motif changes can also account for the complex interpretation of activator and repressor input signals within a single enhancer.
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Affiliation(s)
- Yavor Hadzhiev
- Laboratory of Developmental Transcription Regulation, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
- Laboratory of Developmental Neurobiology and Genetics, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
| | - Michael Lang
- Department of Zoology and Evolution biology, Faculty of Biology, University of Konstanz, Konstanz D-78457, Germany
- Departament de Genètica, Universitat de Barcelona, Av. Diagonal 645, 08028 Barcelona, Spain
| | - Raymond Ertzer
- Laboratory of Developmental Neurobiology and Genetics, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
| | - Axel Meyer
- Department of Zoology and Evolution biology, Faculty of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Uwe Strähle
- Laboratory of Developmental Neurobiology and Genetics, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
| | - Ferenc Müller
- Laboratory of Developmental Transcription Regulation, Institute of Toxicology and Genetics, Forschungszentrum Karlsruhe, Karlsruhe D-76021, Germany
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Werner T. Bioinformatics applications for pathway analysis of microarray data. Curr Opin Biotechnol 2008; 19:50-4. [PMID: 18207385 DOI: 10.1016/j.copbio.2007.11.005] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 11/12/2007] [Indexed: 12/11/2022]
Abstract
Changes in transcript levels are assessed by microarray analysis on an individual basis, essentially resulting in long lists of genes that were found to have significantly changed transcript levels. However, in biology these changes do not occur as independent events as such lists suggest, but in a highly coordinated and interdependent manner. Understanding the biological meaning of the observed changes requires elucidating such biological interdependencies. The most common way to achieve this is to project the gene lists onto distinct biological processes often represented in the form of gene-ontology (GO) categories or metabolic and regulatory pathways as derived from literature analysis. This review focuses on different approaches and tools employed for this task, starting form GO-ranking methods, covering pathway mappings, finally converging on biological network analysis. A brief outlook of the application of such approaches to the newest microarray-based technologies (Chromatin-ImmunoPrecipitation, ChIP-on-chip) concludes the review.
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Affiliation(s)
- Thomas Werner
- Genomatix Software GmbH, Bayerstr. 85A, D-80335 München, Germany.
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Abstract
The Linnean tercentenary is a most welcome opportunity to celebrate the complimentary contributions of the molecular taxonomists and the morphologists in establishing a "natural order" of living organisms depending on degree of relatedness and the 70th anniversary of birth of our friend and colleague, M. Michael Cohen Jr. These events lead one to reflect on the relationship between evolution and normal, respectively abnormal development. In part due to Mike Cohen's efforts, such reflections will at last also creep into the clinic given that more and more malformations are understood ontogenetically and phylogenetically on the basis of homology in structure, development and genetic basis in more or less closely related organisms. It is inconceivable how such an understanding can allow anyone to deny the reality of evolution and its implications for the antiquity of the earth, and its biosphere and the vulnerability of all species, humans included, for extinction.
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Affiliation(s)
- John M Opitz
- Department of Pediatrics (Division of Medical Genetics), University of Utah Health Sciences Center, Salt Lake City, Utah, USA.
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Bellora N, Farré D, Albà MM. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters. BMC Genomics 2007; 8:459. [PMID: 18078513 PMCID: PMC2249607 DOI: 10.1186/1471-2164-8-459] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 12/13/2007] [Indexed: 01/20/2023] Open
Abstract
Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.
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Affiliation(s)
- Nicolás Bellora
- Research Unit on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain.
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Woolfe A, Elgar G. Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. Genome Biol 2007; 8:R53. [PMID: 17428329 PMCID: PMC1896008 DOI: 10.1186/gb-2007-8-4-r53] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 03/06/2007] [Accepted: 04/11/2007] [Indexed: 02/04/2023] Open
Abstract
Fish-mammal genomic alignments were used to compare over 800 conserved non-coding elements that associate with genes that have undergone fish-specific duplication and retention, revealing a pattern of element retention and loss between paralogs indicative of subfunctionalization. Background A major mechanism for the preservation of gene duplicates in the genome is thought to be mediated via loss or modification of cis-regulatory subfunctions between paralogs following duplication (a process known as regulatory subfunctionalization). Despite a number of gene expression studies that support this mechanism, no comprehensive analysis of regulatory subfunctionalization has been undertaken at the level of the distal cis-regulatory modules involved. We have exploited fish-mammal genomic alignments to identify and compare more than 800 conserved non-coding elements (CNEs) that associate with genes that have undergone fish-specific duplication and retention. Results Using the abundance of duplicated genes within the Fugu genome, we selected seven pairs of teleost-specific paralogs involved in early vertebrate development, each containing clusters of CNEs in their vicinity. CNEs present around each Fugu duplicated gene were identified using multiple alignments of orthologous regions between single-copy mammalian orthologs (representing the ancestral locus) and each fish duplicated region in turn. Comparative analysis reveals a pattern of element retention and loss between paralogs indicative of subfunctionalization, the extent of which differs between duplicate pairs. In addition to complete loss of specific regulatory elements, a number of CNEs have been retained in both regions but may be responsible for more subtle levels of subfunctionalization through sequence divergence. Conclusion Comparative analysis of conserved elements between duplicated genes provides a powerful approach for studying regulatory subfunctionalization at the level of the regulatory elements involved.
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Affiliation(s)
- Adam Woolfe
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20870, USA
| | - Greg Elgar
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
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Keller DM, McWeeney S, Arsenlis A, Drouin J, Wright CVE, Wang H, Wollheim CB, White P, Kaestner KH, Goodman RH. Characterization of pancreatic transcription factor Pdx-1 binding sites using promoter microarray and serial analysis of chromatin occupancy. J Biol Chem 2007; 282:32084-92. [PMID: 17761679 DOI: 10.1074/jbc.m700899200] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The homeobox transcription factor Pdx-1 is necessary for pancreas organogenesis and beta cell function, however, most Pdx-1-regulated genes are unknown. To further the understanding of Pdx-1 in beta cell biology, we have characterized its genomic targets in NIT-1 cells, a mouse insulinoma cell line. To identify novel targets, we developed a microarray that includes traditional promoters as well as non-coding conserved elements, micro-RNAs, and elements identified through an unbiased approach termed serial analysis of chromatin occupancy. In total, 583 new Pdx-1 target genes were identified, many of which contribute to energy sensing and insulin release in pancreatic beta cells. By analyzing 31 of the protein-coding Pdx-1 target genes, we show that 29 are expressed in beta cells and, of these, 68% are down- or up-regulated in cells expressing a dominant negative mutant of Pdx-1. We additionally show that many Pdx-1 targets also interact with NeuroD1/BETA2, including the micro-RNA miR-375, a known regulator of insulin secretion.
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Affiliation(s)
- David M Keller
- Vollum Institute, and Division of Biostatistics, Department of Public Health and Preventative Medicine, Oregon Health & Science University, Portland, Oregon 97239, USA.
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Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS One 2007; 2:e807. [PMID: 17726537 PMCID: PMC1950076 DOI: 10.1371/journal.pone.0000807] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Accepted: 07/24/2007] [Indexed: 01/07/2023] Open
Abstract
Background Transcription factors (TF) regulate expression by binding to specific DNA sequences. A binding event is functional when it affects gene expression. Functionality of a binding site is reflected in conservation of the binding sequence during evolution and in over represented binding in gene groups with coherent biological functions. Functionality is governed by several parameters such as the TF-DNA binding strength, distance of the binding site from the transcription start site (TSS), DNA packing, and more. Understanding how these parameters control functionality of different TFs in different biological contexts is a must for identifying functional TF binding sites and for understanding regulation of transcription. Methodology/Principal Findings We introduce a novel method to screen the promoters of a set of genes with shared biological function (obtained from the functional Gene Ontology (GO) classification) against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. More than 8000 human (and 23,000 mouse) genes, were assigned to one of 134 GO sets. Their promoters were searched (from 200 bp downstream to 1000 bp upstream the TSS) for 414 known DNA motifs. We optimized the sequence similarity score threshold, independently for every location window, taking into account nucleotide heterogeneity along the promoters of the target genes. The method, combined with binding sequence and location conservation between human and mouse, identifies with high probability functional binding sites for groups of functionally-related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were tested experimentally. Conclusions/Significance We identified reliably functional TF binding sites. This is an essential step towards constructing regulatory networks. The promoter region proximal to the TSS is of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.
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Affiliation(s)
- Yuval Tabach
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Ran Brosh
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yossi Buganim
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Anat Reiner
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Or Zuk
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Mark Koudritsky
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Eytan Domany
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail:
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Tsang J, Zhu J, van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 2007; 26:753-67. [PMID: 17560377 PMCID: PMC2072999 DOI: 10.1016/j.molcel.2007.05.018] [Citation(s) in RCA: 537] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 04/03/2007] [Accepted: 05/18/2007] [Indexed: 01/19/2023]
Abstract
MicroRNAs (miRNAs) are regulatory molecules that participate in diverse biological processes in animals and plants. While thousands of mammalian genes are potentially targeted by miRNAs, the functions of miRNAs in the context of gene networks are not well understood. Specifically, it is unknown whether miRNA-containing networks have recurrent circuit motifs, as has been observed in regulatory networks of bacteria and yeast. Here we develop a computational method that utilizes gene expression data to show that two classes of circuits-corresponding to positive and negative transcriptional coregulation of a miRNA and its targets-are prevalent in the human and mouse genomes. Additionally, we find that neuronal-enriched miRNAs tend to be coexpressed with their target genes, suggesting that these miRNAs could be involved in neuronal homeostasis. Our results strongly suggest that coordinated transcriptional and miRNA-mediated regulation is a recurrent motif to enhance the robustness of gene regulation in mammalian genomes.
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Affiliation(s)
- John Tsang
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - Jun Zhu
- Institute for Genome Sciences & Policy and Department of Cell Biology, Duke University, Durham, NC, USA
- Co-corresponding authors: (A.v.O.) or (J.Z.)
| | - Alexander van Oudenaarden
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Co-corresponding authors: (A.v.O.) or (J.Z.)
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Wang Z, Wei GH, Liu DP, Liang CC. Unravelling the world of cis-regulatory elements. Med Biol Eng Comput 2007; 45:709-18. [PMID: 17541666 DOI: 10.1007/s11517-007-0195-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2006] [Accepted: 05/03/2007] [Indexed: 12/16/2022]
Abstract
Genome-wide comparisons indicate that only studying the coding regions will not be enough for explaining the biological complexity of an organism, while the genetic variants and the epigenetic differences of cis-regulatory elements are crucial to elucidate many complicated biological phenomena. Their various regulatory functions also play indispensable roles in forming organismal polymorphism. Recent studies showed that the cis-regulatory elements can regulate gene expression as nuclear organizers, and involve in functional noncoding transcription and produce regulatory noncoding RNA molecules. Novel high-throughput strategies and in silico analysis make a great amount data of cis-regulatory elements available. Particularly, the computational methods could help to combine reductionist studies with network biomedical investigations, and begin the era to understand organismal regulatory events at systems biology level.
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Affiliation(s)
- Zhao Wang
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Dong Dan San Tiao 5, 100005 Beijing, China
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66
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Chandler RL, Chandler KJ, McFarland KA, Mortlock DP. Bmp2 transcription in osteoblast progenitors is regulated by a distant 3' enhancer located 156.3 kilobases from the promoter. Mol Cell Biol 2007; 27:2934-51. [PMID: 17283059 PMCID: PMC1899916 DOI: 10.1128/mcb.01609-06] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 10/16/2006] [Accepted: 01/22/2007] [Indexed: 11/20/2022] Open
Abstract
Bone morphogenetic protein 2 (encoded by Bmp2) has been implicated as an important signaling ligand for osteoblast differentiation and bone formation and as a genetic risk factor for osteoporosis. To initially survey a large genomic region flanking the mouse Bmp2 gene for cis-regulatory function, two bacterial artificial chromosome (BAC) clones that extend far upstream and downstream of the gene were engineered to contain a lacZ reporter cassette and tested in transgenic mice. Each BAC clone directs a distinct subset of normal Bmp2 expression patterns, suggesting a modular arrangement of distant Bmp2 regulatory elements. Strikingly, regulatory sequences required for Bmp2 expression in differentiating osteoblasts, as well as tooth buds, hair placodes, kidney, and other tissues, are located more than 53 kilobases 3' to the promoter. By testing BACs with engineered deletions across this distant 3' region, we parsed these regulatory elements into separate locations and more closely refined the location of the osteoblast progenitor element. Finally, a conserved osteoblast progenitor enhancer was identified within a 656-bp sequence located 156.3 kilobases 3' from the promoter. The identification of this enhancer should permit further investigation of upstream regulatory mechanisms that control Bmp2 transcription during osteoblast differentiation and are relevant to further studies of Bmp2 as a candidate risk factor gene for osteoporosis.
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Affiliation(s)
- Ronald L Chandler
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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67
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Viswanathan P, Murphy K, Julien B, Garza AG, Kroos L. Regulation of dev, an operon that includes genes essential for Myxococcus xanthus development and CRISPR-associated genes and repeats. J Bacteriol 2007; 189:3738-50. [PMID: 17369305 PMCID: PMC1913320 DOI: 10.1128/jb.00187-07] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression of dev genes is important for triggering spore differentiation inside Myxococcus xanthus fruiting bodies. DNA sequence analysis suggested that dev and cas (CRISPR-associated) genes are cotranscribed at the dev locus, which is adjacent to CRISPR (clustered regularly interspaced short palindromic repeats). Analysis of RNA from developing M. xanthus confirmed that dev and cas genes are cotranscribed with a short upstream gene and at least two repeats of the downstream CRISPR, forming the dev operon. The operon is subject to strong, negative autoregulation during development by DevS. The dev promoter was identified. Its -35 and -10 regions resemble those recognized by M. xanthus sigma(A) RNA polymerase, the homolog of Escherichia coli sigma(70), but the spacer may be too long (20 bp); there is very little expression during growth. Induction during development relies on at least two positive regulatory elements located in the coding region of the next gene upstream. At least two positive regulatory elements and one negative element lie downstream of the dev promoter, such that the region controlling dev expression spans more than 1 kb. The results of testing different fragments for dev promoter activity in wild-type and devS mutant backgrounds strongly suggest that upstream and downstream regulatory elements interact functionally. Strikingly, the 37-bp sequence between the two CRISPR repeats that, minimally, are cotranscribed with dev and cas genes exactly matches a sequence in the bacteriophage Mx8 intP gene, which encodes a form of the integrase needed for lysogenization of M. xanthus.
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Affiliation(s)
- Poorna Viswanathan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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68
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Takada S, Jürgens G. Transcriptional regulation of epidermal cell fate in the Arabidopsis embryo. Development 2007; 134:1141-50. [PMID: 17301085 DOI: 10.1242/dev.02803] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
How distinct cell fates are specified at correct positions within the plant embryo is unknown. In Arabidopsis, different cell fates are generated early on, starting with the two daughter cells of the zygote. To address mechanisms of position-dependent gene activation and cell fate specification,we analyzed the regulatory region of the Arabidopsis thaliana MERISTEM LAYER 1 (ATML1) gene, which is already expressed at the one-cell stage and whose expression is later restricted to the outermost, epidermal cell layer from its inception. A sensitive, multiple GFP reporter revealed a modular organization to the ATML1 promoter. Each region contributes positively to specific spatial and temporal aspects of the overall expression pattern, including position-dependent but auxin-independent regulation along the apical-basal axis of the embryo. A 101 bp fragment that conferred all aspects of ATML1 expression contained known binding sites for homeodomain transcription factors and other regulatory sequences. Our results suggest that expression patterns associated with cell fate determination in the plant embryo result from positional signals targeting different regulatory sequences in complex promoters.
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Affiliation(s)
- Shinobu Takada
- Developmental Genetics, Center for Molecular Biology of Plants, University of Tübingen, D-72076 Tübingen, Germany
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69
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Howard-Ashby M, Materna SC, Brown CT, Tu Q, Oliveri P, Cameron RA, Davidson EH. High regulatory gene use in sea urchin embryogenesis: Implications for bilaterian development and evolution. Dev Biol 2006; 300:27-34. [PMID: 17101125 PMCID: PMC1790870 DOI: 10.1016/j.ydbio.2006.10.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Revised: 10/13/2006] [Accepted: 10/13/2006] [Indexed: 01/13/2023]
Abstract
A global scan of transcription factor usage in the sea urchin embryo was carried out in the context of the Strongylocentrotus purpuratus genome sequencing project, and results from six individual studies are here considered. Transcript prevalence data were obtained for over 280 regulatory genes encoding sequence-specific transcription factors of every known family, but excluding genes encoding zinc finger proteins. This is a statistically inclusive proxy for the total "regulome" of the sea urchin genome. Close to 80% of the regulome is expressed at significant levels by the late gastrula stage. Most regulatory genes must be used repeatedly for different functions as development progresses. An evolutionary implication is that animal complexity at the stage when the regulome first evolved was far simpler than even the last common bilaterian ancestor, and is thus of deep antiquity.
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70
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Lanier J, Quina LA, Eng SR, Cox E, Turner EE. Brn3a target gene recognition in embryonic sensory neurons. Dev Biol 2006; 302:703-16. [PMID: 17196582 PMCID: PMC1852532 DOI: 10.1016/j.ydbio.2006.10.050] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 10/05/2006] [Indexed: 11/24/2022]
Abstract
Numerous transcription factors have been identified which have profound effects on developing neurons. A fundamental problem is to identify genes downstream of these factors and order them in developmental pathways. We have previously identified 85 genes with changed expression in the trigeminal ganglia of mice lacking Brn3a, a transcription factor encoded by the Pou4f1 gene. Here we use locus-wide chromatin immunoprecipitation in embryonic trigeminal neurons to show that Brn3a is a direct repressor of two of these downstream genes, NeuroD1 and NeuroD4, and also directly modulates its own expression. Comparison of Brn3a binding to the Pou4f1 locus in vitro and in vivo reveals that not all high affinity sites are occupied, and several Brn3a binding sites identified in the promoters of genes that are silent in sensory ganglia are also not occupied in vivo. Site occupancy by Brn3a can be correlated with evolutionary conservation of the genomic regions containing the recognition sites and also with histone modifications found in regions of chromatin active in transcription and gene regulation, suggesting that Brn3a binding is highly context dependent.
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Affiliation(s)
- Jason Lanier
- Department of Psychiatry, University of California, San Diego and VA San Diego Healthcare System
| | - Lely A. Quina
- Department of Psychiatry, University of California, San Diego and VA San Diego Healthcare System
| | - S. Raisa Eng
- Department of Psychiatry, University of California, San Diego and VA San Diego Healthcare System
| | - Eric Cox
- Department of Psychiatry, University of California, San Diego and VA San Diego Healthcare System
| | - Eric E. Turner
- Department of Psychiatry, University of California, San Diego and VA San Diego Healthcare System
- To whom correspondence should be addressed at: Department of Psychiatry, 0603, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0603. Telephone: 858-534-1568, fax: 858-534-7653, electronic mail:
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71
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Abstract
In this essay I have attempted to provide clues relating to novel research avenues that are likely to have a broad impact on the field of stem cell biology. The specific examples, drawn from other areas, are meant to be instructive and are representative of many more similar efforts. I have suggested that the new areas of systems and synthetic biology may provide a truly deep level of understanding for many aspects of how stem cells make fate choices. Successful application of new avenues will require an integrative approach that combines experimental and computational techniques.
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Affiliation(s)
- Ihor R Lemischka
- Department of Molecular Biology, Washington Road, Princeton University, Princeton, NJ 08544, USA.
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72
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Abstract
The endomesoderm gene regulatory network (GRN) of C. elegans is a rich resource for studying the properties of cell-fate-specification pathways. This GRN contains both cell-autonomous and cell non-autonomous mechanisms, includes network motifs found in other GRNs, and ties maternal factors to terminal differentiation genes through a regulatory cascade. In most cases, upstream regulators and their direct downstream targets are known. With the availability of resources to study close and distant relatives of C. elegans, the molecular evolution of this network can now be examined. Within Caenorhabditis, components of the endomesoderm GRN are well conserved. A cursory examination of the preliminary genome sequences of two parasitic nematodes, Haemonchus contortus and Brugia malayi, suggests that evolution in this GRN is occurring most rapidly for the zygotic genes that specify blastomere identity.
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Affiliation(s)
- Morris F Maduro
- Department of Biology, University of California, Riverside, Riverside, CA 92521, USA.
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73
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Patterson LJ, Gering M, Eckfeldt CE, Green AR, Verfaillie CM, Ekker SC, Patient R. The transcription factors Scl and Lmo2 act together during development of the hemangioblast in zebrafish. Blood 2006; 109:2389-98. [PMID: 17090656 DOI: 10.1182/blood-2006-02-003087] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe transcription factors Scl and Lmo2 are crucial for development of all blood. An important early requirement for Scl in endothelial development has also been revealed recently in zebrafish embryos, supporting previous findings in scl−/− embryoid bodies. Scl depletion culminates most notably in failure of dorsal aorta formation, potentially revealing a role in the formation of hemogenic endothelium. We now present evidence that the requirements for Lmo2 in zebrafish embryos are essentially the same as for Scl. The expression of important hematopoietic regulators is lost, reduced, or delayed, panendothelial gene expression is down-regulated, and aorta-specific marker expression is lost. The close similarity of the phenotypes for Scl and Lmo2 suggest that they perform these early functions in hemangioblast development within a multiprotein complex, as shown for erythropoiesis. Consistent with this, we find that scl morphants cannot be rescued by a non-Lmo2–binding form of Scl but can be rescued by non-DNA–binding forms, suggesting tethering to target genes through DNA-binding partners linked via Lmo2. Interestingly, unlike other hematopoietic regulators, the Scl/Lmo2 complex does not appear to autoregulate, as neither gene's expression is affected by depletion of the other. Thus, expression of these critical regulators is dependent on continued expression of upstream regulators, which may include cell-extrinsic signals.
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Affiliation(s)
- Lucy J Patterson
- Weatherall Institute of Molecular Medicine, Oxford University, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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74
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Suzuki T, Kashiwagi A, Urabe I, Yomo T. Inherent characteristics of gene expression for buffering environmental changes without the corresponding transcriptional regulations. Biophysics (Nagoya-shi) 2006; 2:63-70. [PMID: 27857561 PMCID: PMC5036647 DOI: 10.2142/biophysics.2.63] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 08/30/2006] [Indexed: 12/01/2022] Open
Abstract
Gene expression patterning is crucial for environmental nutritional responses such as the nitrogen response in Escherichia coli. The nitrogen response is primarily regulated by the expression of glutamine synthetase (GS), which catalyzes the sole reaction of glutamine formation, by cis-logic regulatory circuits. Here, by removing the entire corresponding operator and promoter regions required for the control of GS, we constructed an E. coli strain that enables the detection of the basal GS gene expression, which is expressed from a plain promoter unrelated to the nitrogen response, and measured by co-transcribed GFP expression, an indicator of GS expression. Using strain cultures, we found that the GS expression level was able to shift inversely against the change of the environmental glutamine concentration. As a control experiment, we repeated similar experiments with another strain in which the GS regulatory region remained intact and the GFP gene following the plain promoter was introduced into a different chromosomal site. For this strain, we found that the GFP expression level did not shift in accordance with the environmental glutamine concentration. These results showed that GS expression from the plain promoter exhibited a responsive ability to buffer environmental changes, whereas the GS expression shift did not correlate with the specific characteristics of the plain promoter and GFP expression. This study identifies the inherent characteristics of basal gene expression in response to environmental changes, facilitating a deeper understanding of cellular design principles.
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Affiliation(s)
- Takao Suzuki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Akiko Kashiwagi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Itaru Urabe
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Complex Systems Biology Project, ERATO, JST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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75
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Pipes GCT, Creemers EE, Olson EN. The myocardin family of transcriptional coactivators: versatile regulators of cell growth, migration, and myogenesis. Genes Dev 2006; 20:1545-56. [PMID: 16778073 DOI: 10.1101/gad.1428006] [Citation(s) in RCA: 377] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The association of transcriptional coactivators with sequence-specific DNA-binding proteins provides versatility and specificity to gene regulation and expands the regulatory potential of individual cis-regulatory DNA sequences. Members of the myocardin family of coactivators activate genes involved in cell proliferation, migration, and myogenesis by associating with serum response factor (SRF). The partnership of myocardin family members and SRF also controls genes encoding components of the actin cytoskeleton and confers responsiveness to extracellular growth signals and intracellular changes in the cytoskeleton, thereby creating a transcriptional-cytoskeletal regulatory circuit. These functions are reflected in defects in smooth muscle differentiation and function in mice with mutations in myocardin family members. This article reviews the functions and mechanisms of action of the myocardin family of coactivators and the physiological significance of transcriptional coactivation in the context of signal-dependent and cell-type-specific gene regulation.
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Affiliation(s)
- G C Teg Pipes
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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76
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Muratoglu S, Garratt B, Hyman K, Gajewski K, Schulz RA, Fossett N. Regulation of Drosophila friend of GATA gene, u-shaped, during hematopoiesis: a direct role for serpent and lozenge. Dev Biol 2006; 296:561-79. [PMID: 16730345 DOI: 10.1016/j.ydbio.2006.04.455] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 04/12/2006] [Accepted: 04/19/2006] [Indexed: 10/24/2022]
Abstract
Friend of GATA proteins interact with GATA factors to regulate development in a variety of tissues. We analyzed cis- and trans-regulation of the Drosophila gene, u-shaped, to better understand the transcriptional control of this important gene family during hematopoiesis. Using overlapping genomic fragments driving tissue-specific reporter-gene (lacZ) expression, we identified two minimal hematopoietic enhancers within the 7.4 kb region upstream of the transcription start site. One enhancer was active in all classes of hemocytes, whereas the other was active in hemocyte precursors and plasmatocytes only. The GATA factor, Serpent, directly regulated the activity of both enhancers. However, activity in the crystal cell lineage not only required Serpent but also the RUNX homologue, Lozenge. This is the first demonstration of GATA and RUNX direct regulation of Friend of GATA gene expression and provides additional evidence for the combinatorial control of crystal cell lineage commitment by Serpent, Lozenge, and U-shaped. In addition, we analyzed cis-regulation of ush expression in the lymph gland and identified similarities and differences between regulatory strategies used during embryonic and lymph gland hematopoiesis. The results of these studies provide information to analyze further the regulation of this conserved gene family and its role during hematopoietic lineage commitment.
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Affiliation(s)
- Selen Muratoglu
- Center for Vascular and Inflammatory Diseases and the Department of Pathology, University of Maryland School of Medicine, 800 W. Baltimore Street, Baltimore, MD 21201, USA
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77
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Swiers G, Patient R, Loose M. Genetic regulatory networks programming hematopoietic stem cells and erythroid lineage specification. Dev Biol 2006; 294:525-40. [PMID: 16626682 DOI: 10.1016/j.ydbio.2006.02.051] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 02/24/2006] [Accepted: 02/28/2006] [Indexed: 10/24/2022]
Abstract
Erythroid cell production results from passage through cellular hierarchies dependent on differential gene expression under the control of transcription factors responsive to changing niches. We have constructed Genetic Regulatory Networks (GRNs) describing this process, based predominantly on mouse data. Regulatory network motifs identified in E. coli and yeast GRNs are found in combination in these GRNs. Feed-forward motifs with autoregulation generate forward momentum and also control its rate, which is at its lowest in hematopoietic stem cells (HSCs). The simultaneous requirement for multiple regulators in multi-input motifs (MIMs) provides tight control over expression of target genes. Combinations of MIMs, exemplified by the SCL/LMO2 complexes, which have variable content and binding sites, explain how individual regulators can have different targets in HSCs and erythroid cells and possibly also how HSCs maintain stem cell functions while expressing lineage-affiliated genes at low level, so-called multi-lineage priming. MIMs combined with cross-antagonism describe the relationship between PU.1 and GATA-1 and between two of their target genes, Fli-1 and EKLF, with victory for GATA-1 and EKLF leading to erythroid lineage specification. These GRNs are useful repositories for current regulatory information, are accessible in interactive form via the internet, enable the consequences of perturbation to be predicted, and can act as seed networks to organize the rapidly accumulating microarray data.
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Affiliation(s)
- Gemma Swiers
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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78
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Abstract
Rett syndrome (RTT) is an X-linked dominant disabling neurodevelopmental disorder caused by loss of function mutations in the MECP2 gene, located at Xq28, which encodes a multifunctional protein. MECP2 expression is regulated in a developmental stage and cell-type-specific manner. The need for tightly controlled MeCP2 levels in brain is strongly suggested by neurologically abnormal phenotypes of mouse models with mild overexpression and by mental retardation in human males with MECP2 duplication. We set out to identify long-range cis-regulatory sequences that differentially regulate MECP2 transcription and, when mutated, may contribute to the pathogenesis of RTT, autism or X-linked mental retardation. By inter-species sequence comparisons, we detected 27 highly conserved non-coding DNA sequences within a 210 kb region covering MECP2. We functionally confirmed four enhancer and two silencer elements by performing luciferase reporter assays in four different human cell lines. The transcription factor binding capability of the identified regulatory elements was tested by gel shift assays. To locate the human MECP2 core promoter, we dissected the promoter region by reporter assays with deletion constructs. We then used chromosome conformation capture methods to document long-range interactions of three enhancers and two silencers with the MECP2 promoter. Acting over distances of up to 130 kb, these elements may influence chromatin configurations and regulate MECP2 transcription. Our study has defined the "MECP2 functional expression module" and identified enhancer and silencer elements that are likely to be responsible for the tissue-specific, developmental stage-specific or splice-variant-specific control of MeCP2 protein expression.
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Affiliation(s)
- Jinglan Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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79
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Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefèbvre C, Deblois G, Giguère V, Ferretti V, Bergeron D, Coulombe B, Robert F. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 2006; 16:656-68. [PMID: 16606704 PMCID: PMC1457048 DOI: 10.1101/gr.4866006] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The identification of regulatory regions is one of the most important and challenging problems toward the functional annotation of the human genome. In higher eukaryotes, transcription-factor (TF) binding sites are often organized in clusters called cis-regulatory modules (CRM). While the prediction of individual TF-binding sites is a notoriously difficult problem, CRM prediction has proven to be somewhat more reliable. Starting from a set of predicted binding sites for more than 200 TF families documented in Transfac, we describe an algorithm relying on the principle that CRMs generally contain several phylogenetically conserved binding sites for a few different TFs. The method allows the prediction of more than 118,000 CRMs within the human genome. A subset of these is shown to be bound in vivo by TFs using ChIP-chip. Their analysis reveals, among other things, that CRM density varies widely across the genome, with CRM-rich regions often being located near genes encoding transcription factors involved in development. Predicted CRMs show a surprising enrichment near the 3' end of genes and in regions far from genes. We document the tendency for certain TFs to bind modules located in specific regions with respect to their target genes and identify TFs likely to be involved in tissue-specific regulation. The set of predicted CRMs, which is made available as a public database called PReMod (http://genomequebec.mcgill.ca/PReMod), will help analyze regulatory mechanisms in specific biological systems.
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Affiliation(s)
- Mathieu Blanchette
- McGill Centre for Bioinformatics, Montreal, Quebec, Canada, H3A 2B4
- Corresponding authors.E-mail ; fax (514) 398-3387.E-mail ; fax (514) 987-5743
| | - Alain R. Bataille
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada H2W 1R7
| | - Xiaoyu Chen
- McGill Centre for Bioinformatics, Montreal, Quebec, Canada, H3A 2B4
| | - Christian Poitras
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada H2W 1R7
| | - Josée Laganière
- Molecular Oncology Group Department of Medicine, Oncology and Biochemistry, McGill University, Montreal, Quebec, Canada H3A 1A1
| | - Céline Lefèbvre
- Molecular Oncology Group Department of Medicine, Oncology and Biochemistry, McGill University, Montreal, Quebec, Canada H3A 1A1
| | - Geneviève Deblois
- Molecular Oncology Group Department of Medicine, Oncology and Biochemistry, McGill University, Montreal, Quebec, Canada H3A 1A1
| | - Vincent Giguère
- Molecular Oncology Group Department of Medicine, Oncology and Biochemistry, McGill University, Montreal, Quebec, Canada H3A 1A1
| | - Vincent Ferretti
- McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada H3A 1A4
| | - Dominique Bergeron
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada H2W 1R7
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada H2W 1R7
| | - François Robert
- Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada H2W 1R7
- Corresponding authors.E-mail ; fax (514) 398-3387.E-mail ; fax (514) 987-5743
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80
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Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res 2005; 16:1-10. [PMID: 16344566 PMCID: PMC1356123 DOI: 10.1101/gr.4222606] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Transcriptional promoters comprise one of many classes of eukaryotic transcriptional regulatory elements. Identification and characterization of these elements are vital to understanding the complex network of human gene regulation. Using full-length cDNA sequences to identify transcription start sites (TSS), we predicted more than 900 putative human transcriptional promoters in the ENCODE regions, representing a comprehensive sampling of promoters in 1% of the genome. We identified 387 fragments that function as promoters in at least one of 16 cell lines by measuring promoter activity in high-throughput transient transfection reporter assays. These positive functional results demonstrate widespread use of alternative promoters. We show a strong correlation between promoter activity and the corresponding endogenous RNA transcript levels, providing the first experimental quantitative estimate of promoter contribution to gene regulation. Finally, we identified functional regions within a randomly selected subset of 45 promoters using deletion analyses. These experiments showed that, on average, the sequence -300 to -50 bp of the TSS positively contributes to core promoter activity. Interestingly, putative negative elements were identified -1000 to -500 bp upstream of the TSS for 55% of genes tested. These data provide the largest and most comprehensive view of promoter function in the human genome.
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Affiliation(s)
- Sara J Cooper
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
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81
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Efimenko E, Bubb K, Mak HY, Holzman T, Leroux MR, Ruvkun G, Thomas JH, Swoboda P. Analysis of xbx genes in C. elegans. Development 2005; 132:1923-34. [PMID: 15790967 DOI: 10.1242/dev.01775] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cilia and flagella are widespread eukaryotic subcellular components that are conserved from green algae to mammals. In different organisms they function in cell motility, movement of extracellular fluids and sensory reception. While the function and structural description of cilia and flagella are well established, there are many questions that remain unanswered. In particular, very little is known about the developmental mechanisms by which cilia are generated and shaped and how their components are assembled into functional machineries. To find genes involved in cilia development we used as a search tool a promoter motif, the X-box, which participates in the regulation of certain ciliary genes in the nematode Caenorhabditis elegans. By using a genome search approach for X-box promoter motif-containing genes (xbx genes) we identified a list of about 750 xbx genes (candidates). This list comprises some already known ciliary genes as well as new genes, many of which we hypothesize to be important for cilium structure and function. We derived a C. elegans X-box consensus sequence by in vivo expression analysis. We found that xbx gene expression patterns were dependent on particular X-box nucleotide compositions and the distance from the respective gene start. We propose a model where DAF-19, the RFX-type transcription factor binding to the X-box, is responsible for the development of a ciliary module in C. elegans, which includes genes for cilium structure, transport machinery, receptors and other factors.
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Affiliation(s)
- Evgeni Efimenko
- Karolinska Institute, Department of Biosciences and Södertörn University College, Section of Natural Sciences, S-14189 Huddinge, Sweden
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Kiyama T, Zhang N, Dayal S, Yun Lee P, Liang S, Villinski JT, Klein WH. Strongylocentrotus purpuratus transcription factor GATA-E binds to and represses transcription at an Otx-Goosecoid cis-regulatory element within the aboral ectoderm-specific spec2a enhancer. Dev Biol 2005; 280:436-47. [PMID: 15882584 DOI: 10.1016/j.ydbio.2005.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Revised: 01/03/2005] [Accepted: 01/18/2005] [Indexed: 11/29/2022]
Abstract
During Strongylocentrotus purpuratus embryogenesis, aboral ectoderm-specific expression of spec2a relies on an upstream enhancer that confers its spatial specificity largely through repression. The purpose of this study was to determine how spec2a expression is repressed in endoderm and oral ectoderm territories. A 78-base pair DNA sequence within the enhancer contains five tightly spaced cis-regulatory elements including proximal (TAATCT) and distal (TAATCC) elements that bind to both SpOtx, a broadly distributed transcriptional activator, and SpGoosecoid (SpGsc), an oral ectoderm-restricted transcriptional repressor. We show here that these two seemingly redundant Otx/Gsc elements have distinct functions. The proximal element bound to SpGATA-E, an endomesoderm-specific transcription factor. Treatment with SpGATA-E and SpGsc morpholino antisense oligonucleotides (MASOs) resulted in enhanced transcriptional activity from the proximal element, suggesting that both factors functioned as repressors at this site. SpGATA-E MASO-treated embryos failed to express ectoderm markers, indicating a role for SpGATA-E in ectoderm differentiation. The spec2a proximal element was distinct from the corresponding element in the related spec1 enhancer, and swaps between spec1 and spec2a cis-regulatory elements indicated, that for optimal repression, the proximal element had to interact with a nearby CCAAT-binding factor element. Our results show that the recently evolved proximal element contributes to the repression of spec2a in endomesoderm and oral ectoderm territories.
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Affiliation(s)
- Takae Kiyama
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, Houston, 77030, USA
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83
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Abstract
Ascidians, or sea squirts, are lower chordates, and share basic gene repertoires and many characteristics, both developmental and physiological, with vertebrates. Therefore, decoding cis-regulatory systems in ascidians will contribute toward elucidating the genetic regulatory systems underlying the developmental and physiological processes of vertebrates. cis-Regulatory DNAs can also be used for tissue-specific genetic manipulation, a powerful tool for studying ascidian development and physiology. Because the ascidian genome is compact compared with vertebrate genomes, both intergenic regions and introns are relatively small in ascidians. Short upstream intergenic regions contain a complete set of cis-regulatory elements for spatially regulated expression of a majority of ascidian genes. These features of the ascidian genome are a great advantage in identifying cis-regulatory sequences and in analyzing their functions. Function of cis-regulatory DNAs has been analyzed for a number of tissue-specific and developmentally regulated genes of ascidians by introducing promoter-reporter fusion constructs into ascidian embryos. The availability of the whole genome sequences of the two Ciona species, Ciona intestinalis and Ciona savignyi, facilitates comparative genomics approaches to identify cis-regulatory DNAs. Recent studies demonstrate that computational methods can help identify cis-regulatory elements in the ascidian genome. This review presents a comprehensive list of ascidian genes whose cis-regulatory regions have been subjected to functional analysis, and highlights the recent advances in bioinformatics and comparative genomics approaches to cis-regulatory systems in ascidians.
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Affiliation(s)
- Takehiro Kusakabe
- Department of Life Science, Graduate School of Life Science, University of Hyogo, Japan.
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84
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Villinski JT, Kiyama T, Dayal S, Zhang N, Liang S, Klein WH. Structure, expression, and transcriptional regulation of the Strongylocentrotus franciscanus spec gene family encoding intracellular calcium-binding proteins. Dev Genes Evol 2005; 215:410-22. [PMID: 15871032 DOI: 10.1007/s00427-005-0489-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Accepted: 04/07/2005] [Indexed: 10/25/2022]
Abstract
The mechanisms by which gene expression patterns emerge during evolution are poorly understood. The sea urchin spec genes offer a useful means to investigate evolutionary mechanisms. Genes of the spec family from Strongylocentrotus purpuratus and Lytechinus pictus have identical patterns of aboral ectoderm-specific expression but exhibit species-specific differences in copy number, genomic structure, temporal expression, and cis-regulatory architecture. Here, we identify spec genes from a phylogenetic intermediate, Strongylocentrotus franciscanus, to gain insight into the evolution of the spec gene family and its transcriptional regulation. We identified two spec genes in the S. franciscanus genome, sfspec1a and sfspec1b, that were orthologous to spec1 from S. purpuratus. sfspec1b transcripts began to accumulate at the blastula stage and became progressively more abundant; this was reminiscent of spec expression in L. pictus but different from that in S. purpuratus. As expected, sfspec1b expression was restricted to aboral ectoderm cells. The six-exon structure of the sfspec1b genomic locus was identical to that of the S. purpuratus spec genes and was bounded by two repeat-spacer-repeat (RSR) repetitive sequence elements, which are conserved features of S. purpuratus spec genes and function as transcriptional enhancers. The enhancer activity of the sfspec1b RSRs was comparable to that of their S. purpuratus counterparts, although the placement and orientation of crucial cis-regulatory elements within the RSRs differed. We discovered a spec gene in S. franciscanus that was only distantly related to other spec genes but was highly conserved in S. purpuratus. Unexpectedly, this gene was expressed exclusively in endoderm lineages. Our results show that the evolution of spec cis-regulatory elements is highly dynamic and that substantial alterations can occur when maintaining or grossly modifying gene expression patterns.
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Affiliation(s)
- Jeffrey T Villinski
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 117, Houston 77030, USA
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85
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Abstract
With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.
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Affiliation(s)
- Mónica Medina
- Department of Evolutionary Genomics, Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
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86
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Jones BW. Transcriptional control of glial cell development in Drosophila. Dev Biol 2005; 278:265-73. [PMID: 15680348 DOI: 10.1016/j.ydbio.2004.11.022] [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: 10/19/2004] [Revised: 11/15/2004] [Accepted: 11/16/2004] [Indexed: 10/26/2022]
Abstract
Neurons and glia are generated from multipotent neural progenitors. In Drosophila, the transcriptional regulation of glial vs. neuronal fates is controlled by the expression of the transcription factor encoded by the glial cells missing gene (gcm) in multiple neural lineages. The cis-regulatory control of gcm transcription serves as a nodal point to translate a complex array of spatially and temporally regulated transcription factors in distinct neural lineages into glial-specific expression. Gcm acts synergistically with several downstream transcription factors to initiate and maintain glial-specific gene expression. The identification of a large set of glial-specific genes through the application of computational and whole genome tools provides the opportunity to analyze the transcriptional regulation of glial cell development at the genomic level in a relatively simple genetic model system.
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Affiliation(s)
- Bradley W Jones
- Department of Biology, The University of Mississippi, 122 Shoemaker Hall, University, MS 38677, USA.
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87
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Xu M, Kirov N, Rushlow C. Peak levels of BMP in theDrosophilaembryo control target genes by a feed-forward mechanism. Development 2005; 132:1637-47. [PMID: 15728670 DOI: 10.1242/dev.01722] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Gradients of morphogens determine cell fates by specifying discrete thresholds of gene activities. In the Drosophila embryo, a BMP gradient subdivides the dorsal ectoderm into amnioserosa and dorsal epidermis,and also inhibits neuroectoderm formation. A number of genes are differentially expressed in response to the gradient, but how their borders of expression are established is not well understood. We present evidence that the BMP gradient, via the Smads, provides a two-fold input in regulating the amnioserosa-specific target genes such as Race. Peak levels of Smads in the presumptive amnioserosa set the expression domain of zen, and then Smads act in combination with Zen to directly activate Race. This situation resembles a feed-forward mechanism of transcriptional regulation. In addition, we demonstrate that ectopically expressed Zen can activate targets like Race in the presence of low level Smads,indicating that the role of the highest activity of the BMP gradient is to activate zen.
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Affiliation(s)
- Mu Xu
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
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88
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Kleinjan DA, van Heyningen V. Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet 2005; 76:8-32. [PMID: 15549674 PMCID: PMC1196435 DOI: 10.1086/426833] [Citation(s) in RCA: 645] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2004] [Accepted: 10/08/2004] [Indexed: 02/04/2023] Open
Abstract
Transcriptional control is a major mechanism for regulating gene expression. The complex machinery required to effect this control is still emerging from functional and evolutionary analysis of genomic architecture. In addition to the promoter, many other regulatory elements are required for spatiotemporally and quantitatively correct gene expression. Enhancer and repressor elements may reside in introns or up- and downstream of the transcription unit. For some genes with highly complex expression patterns--often those that function as key developmental control genes--the cis-regulatory domain can extend long distances outside the transcription unit. Some of the earliest hints of this came from disease-associated chromosomal breaks positioned well outside the relevant gene. With the availability of wide-ranging genome sequence comparisons, strong conservation of many noncoding regions became obvious. Functional studies have shown many of these conserved sites to be transcriptional regulatory elements that sometimes reside inside unrelated neighboring genes. Such sequence-conserved elements generally harbor sites for tissue-specific DNA-binding proteins. Developmentally variable chromatin conformation can control protein access to these sites and can regulate transcription. Disruption of these finely tuned mechanisms can cause disease. Some regulatory element mutations will be associated with phenotypes distinct from any identified for coding-region mutations.
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Affiliation(s)
- Dirk A Kleinjan
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, United Kingdom
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