101
|
Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, Walhout AJM. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol 2010; 6:367. [PMID: 20461074 PMCID: PMC2890327 DOI: 10.1038/msb.2010.23] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 03/26/2010] [Indexed: 12/15/2022] Open
Abstract
We present the first gene regulatory network (GRN) that pertains to post-developmental gene expression. Specifically, we mapped a transcription regulatory network of Caenorhabditis elegans metabolic gene promoters using gene-centered yeast one-hybrid assays. We found that the metabolic GRN is enriched for nuclear hormone receptors (NHRs) compared with other gene-centered regulatory networks, and that these NHRs organize into functional network modules. The NHR family has greatly expanded in nematodes; C. elegans has 284 NHRs, whereas humans have only 48. We show that the NHRs in the metabolic GRN have metabolic phenotypes, suggesting that they do not simply function redundantly. The mediator subunit MDT-15 preferentially interacts with NHRs that occur in the metabolic GRN. We describe an NHR circuit that responds to nutrient availability and propose a model for the evolution and organization of NHRs in C. elegans metabolic regulatory networks.
Physical and/or regulatory interactions between transcription factors (TFs) and their target genes are essential to establish body plans of multicellular organisms during development, and these interactions have been studied extensively in the context of GRNs. The precise control of differential gene expression is also of critical importance to maintain physiological homeostasis, and many metabolic disorders such as obesity and diabetes coincide with substantial changes in gene expression. Much work has focused on the GRNs that control metazoan development; however, the design principles and organization of the GRNs that control systems physiology remain largely unexplored. In this study, we present the first gene-centered GRN that includes ∼70 genes involved in C. elegans metabolism and physiology, 100 TFs and more than 500 protein–DNA interactions between them. The resulting metabolic GRN is enriched for NHRs, compared with other gene-centered regulatory networks. NHRs are well-known regulators of lipid meta-qj;bolism in mammals. The transcriptional activity of NHRs can be modified by diffusible ligands, which allows these TFs to function as molecular sensors and rapidly alter the expression of their target genes. Interestingly, NHRs comprise the largest family of TFs in nematodes; the C. elegans genome encodes 284 NHRs, most of which are uncharacterized. Furthermore, their organization in GRNs has not yet been investigated. In our study, we show that the C. elegans NHRs that we retrieved in the metabolic GRN organize into network modules, and that most of these NHRs function to maintain lipid homeostasis in the nematode. Interestingly, network modularity has been proposed to facilitate rapid and robust changes in gene expression. Our results suggest that the C. elegans metabolic GRN may have evolved by combining NHR family expansion with the specific modular wiring of NHRs to enable the rapid adaptation of the animal to different environmental cues. NHRs can interact with transcriptional cofactors such as chromatin remodeling complexes and Mediator components. For instance, the C. elegans Mediator subunit, MDT-15, can interact with NHR-49 to regulate the expression of its target genes. To find all the TFs that MDT-15 can interact with, we performed systematic yeast two-hybrid assays with MDT-15 versus 755 full-length TFs. We found that MDT-15 preferentially associates with NHRs, and specifically with those NHRs that confer a metabolic phenotype and that occur in the metabolic GRN. This illustrates the central role of MDT-15 in the regulation of metabolic gene expression. Using a variety of genetic and biochemical approaches, we characterized NHR-86 in more detail. NHR-86 participates in one of the two NHR modules, and has a high-flux capacity; that is it has both a high incoming and a high outgoing degree. We obtained an nhr-86 mutant and generated an NHR-86 antibody, and showed that NHR-86 functions as an auto-repressor in vivo and that nhr-86 mutant animals store abnormally high levels of body fat. Finally, we discovered a novel NHR circuit that responds to nutrient availability. In this circuit NHR-45 regulates the activity of nhr-178 promoter in two distinct physiologically important tissues: the intestine and the hypodermis. Both of these NHRs are required to maintain lipid homeostasis in C. elegans. The expression of nhr-178 is responsive to the nutritional status of the animal, which switches between ON and OFF states in the hypodermis. We found that NHR-45 activity is necessary to control this switch in the hypodermis. Interestingly, NHR-45 has opposite effects on the activity of the nhr-178 promoter in these tissues: NHR-45 activates this promoter in the intestine, but represses it in the hypodermis. Altogether our study leads to a model in which the expansion of the NHR family, TFs that have the capacity to act as fast molecular sensors, is combined with a modular network organization to enable rapid and robust responses to various environmental cues. Gene regulatory networks (GRNs) provide insights into the mechanisms of differential gene expression at a systems level. GRNs that relate to metazoan development have been studied extensively. However, little is still known about the design principles, organization and functionality of GRNs that control physiological processes such as metabolism, homeostasis and responses to environmental cues. In this study, we report the first experimentally mapped metazoan GRN of Caenorhabditis elegans metabolic genes. This network is enriched for nuclear hormone receptors (NHRs). The NHR family has greatly expanded in nematodes: humans have 48 NHRs, but C. elegans has 284, most of which are uncharacterized. We find that the C. elegans metabolic GRN is highly modular and that two GRN modules predominantly consist of NHRs. Network modularity has been proposed to facilitate a rapid response to different cues. As NHRs are metabolic sensors that are poised to respond to ligands, this suggests that C. elegans GRNs evolved to enable rapid and adaptive responses to different cues by a concurrence of NHR family expansion and modular GRN wiring.
Collapse
Affiliation(s)
- H Efsun Arda
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
102
|
Naumova N, Dekker J. Integrating one-dimensional and three-dimensional maps of genomes. J Cell Sci 2010; 123:1979-88. [PMID: 20519580 DOI: 10.1242/jcs.051631] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Genomes exist in vivo as complex physical structures, and their functional output (i.e. the gene expression profile of a cell) is related to their spatial organization inside the nucleus as well as to local chromatin status. Chromatin modifications and chromosome conformation are distinct in different tissues and cell types, which corresponds closely with the diversity in gene-expression patterns found in different tissues of the body. The biological processes and mechanisms driving these general correlations are currently the topic of intense study. An emerging theme is that genome compartmentalization - both along the linear length of chromosomes, and in three dimensions by the spatial colocalization of chromatin domains and genomic loci from across the genome - is a crucial parameter in regulating genome expression. In this Commentary, we propose that a full understanding of genome regulation requires integrating three different types of data: first, one-dimensional data regarding the state of local chromatin - such as patterns of protein binding along chromosomes; second, three-dimensional data that describe the population-averaged folding of chromatin inside cells and; third, single-cell observations of three-dimensional spatial colocalization of genetic loci and trans factors that reveal information about their dynamics and frequency of colocalization.
Collapse
Affiliation(s)
- Natalia Naumova
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605-0103, USA
| | | |
Collapse
|
103
|
Abstract
Cell specification requires that particular subsets of cells adopt unique expression patterns that ultimately define the fates of their descendants. In C. elegans, cell fate specification involves the combinatorial action of multiple signals that produce activation of a small number of "blastomere specification" factors. These initiate expression of gene regulatory networks that drive development forward, leading to activation of "tissue specification" factors. In this review, the C. elegans embryo is considered as a model system for studies of cell specification. The techniques used to study cell fate in this species, and the themes that have emerged, are described.
Collapse
Affiliation(s)
- Morris F Maduro
- Department of Biology, University of California, Riverside, Riverside, California 92521, USA.
| |
Collapse
|
104
|
Gaudet J, McGhee JD. Recent advances in understanding the molecular mechanisms regulating C. elegans transcription. Dev Dyn 2010; 239:1388-404. [PMID: 20175193 DOI: 10.1002/dvdy.22246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We review recent studies that have advanced our understanding of the molecular mechanisms regulating transcription in the nematode C. elegans. Topics covered include: (i) general properties of C. elegans promoters; (ii) transcription factors and transcription factor combinations involved in cell fate specification and cell differentiation; (iii) new roles for general transcription factors; (iv) nucleosome positioning in C. elegans "chromatin"; and (v) some characteristics of histone variants and histone modifications and their possible roles in controlling C. elegans transcription.
Collapse
Affiliation(s)
- Jeb Gaudet
- Department of Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | | |
Collapse
|
105
|
Haynes CM, Yang Y, Blais SP, Neubert TA, Ron D. The matrix peptide exporter HAF-1 signals a mitochondrial UPR by activating the transcription factor ZC376.7 in C. elegans. Mol Cell 2010; 37:529-40. [PMID: 20188671 PMCID: PMC2846537 DOI: 10.1016/j.molcel.2010.01.015] [Citation(s) in RCA: 386] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 06/15/2009] [Accepted: 11/17/2009] [Indexed: 01/02/2023]
Abstract
Genetic analyses previously implicated the matrix-localized protease ClpP in signaling the stress of protein misfolding in the mitochondrial matrix to activate nuclear-encoded mitochondrial chaperone genes in C. elegans (UPR(mt)). Here, we report that haf-1, a gene encoding a mitochondria-localized ATP-binding cassette protein, is required for signaling within the UPR(mt) and for coping with misfolded protein stress. Peptide efflux from isolated mitochondria was ATP dependent and required HAF-1 and the protease ClpP. Defective UPR(mt) signaling in the haf-1-deleted worms was associated with failure of the bZIP protein, ZC376.7, to localize to nuclei in worms with perturbed mitochondrial protein folding, whereas zc376.7(RNAi) strongly inhibited the UPR(mt). These observations suggest a simple model whereby perturbation of the protein-folding environment in the mitochondrial matrix promotes ClpP-mediated generation of peptides whose haf-1-dependent export from the matrix contributes to UPR(mt) signaling across the mitochondrial inner membrane.
Collapse
Affiliation(s)
- Cole M. Haynes
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Yun Yang
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Steven P. Blais
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Thomas A. Neubert
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Department of Pharmacology, New York University School of Medicine, New York, New York 10016
| | - David Ron
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016
- Department of Cell Biology, New York University School of Medicine, New York, New York 10016
- Department of Medicine, New York University School of Medicine, New York, New York 10016
| |
Collapse
|
106
|
bZIP transcription factor zip-2 mediates an early response to Pseudomonas aeruginosa infection in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2010; 107:2153-8. [PMID: 20133860 DOI: 10.1073/pnas.0914643107] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Very little is known about how animals discriminate pathogens from innocuous microbes. To address this question, we examined infection-response gene induction in the nematode Caenorhabditis elegans. We focused on genes that are induced in C. elegans by infection with the bacterial pathogen Pseudomonas aeruginosa, but are not induced by an isogenic attenuated gacA mutant. Most of these genes are induced independently of known immunity pathways. We generated a GFP reporter for one of these genes, infection response gene 1 (irg-1), which is induced strongly by wild-type P. aeruginosa strain PA14, but not by other C. elegans pathogens or by other wild-type P. aeruginosa strains that are weakly pathogenic to C. elegans. To identify components of the pathway that induces irg-1 in response to infection, we performed an RNA interference screen of C. elegans transcription factors. This screen identified zip-2, a bZIP transcription factor that is required for inducing irg-1, as well as several other genes, and is important for defense against infection by P. aeruginosa. These data indicate that zip-2 is part of a specialized pathogen response pathway that is induced by virulent strains of P. aeruginosa and provides defense against this pathogen.
Collapse
|
107
|
Abstract
Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a 'systems level' (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions between genes and their regulators. In the past years, significant progress has been made toward the mapping of GRNs using a variety of experimental and computational approaches. Here, we will discuss gene-centered approaches that we employed to characterize GRNs and describe insights that we have obtained into the global design principles of gene regulation in complex metazoan systems.
Collapse
Affiliation(s)
- H Efsun Arda
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | | |
Collapse
|
108
|
Simicevic J, Deplancke B. DNA-centered approaches to characterize regulatory protein-DNA interaction complexes. MOLECULAR BIOSYSTEMS 2009; 6:462-8. [PMID: 20174675 DOI: 10.1039/b916137f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene regulation is mediated by site-specific DNA-binding proteins or transcription factors (TFs), which form protein complexes at regulatory loci either to activate or repress the expression of a target gene. The study of the dynamic properties of these regulatory DNA-binding complexes has so far been dominated by protein-centered methodologies, aiming to characterize the DNA-binding behavior of one specific protein at a time. With the emerging evidence for a role of DNA in allosterically influencing DNA-binding protein complex formation, there is renewed interest in DNA-centered approaches to capture protein complexes on defined regulatory loci and to correlate changes in their composition with alterations in target gene expression. In this review, we present the current state-of-the-art in such DNA-centered approaches and evaluate recent technological improvements in the purification as well as in the identification of regulatory DNA-binding protein complexes within or outside their biological context. Finally, we suggest possible areas of improvement and assess the putative impact of DNA-centered methodologies on the gene regulation field for the forthcoming years.
Collapse
Affiliation(s)
- Jovan Simicevic
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Station 15, 1015 Lausanne, Switzerland.
| | | |
Collapse
|
109
|
Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LSP. In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean. DNA Res 2009; 16:353-69. [PMID: 19884168 PMCID: PMC2780956 DOI: 10.1093/dnares/dsp023] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 10/05/2009] [Indexed: 12/29/2022] Open
Abstract
Sequence-specific DNA-binding transcription factors (TFs) are often termed as 'master regulators' which bind to DNA and either activate or repress gene transcription. We have computationally analysed the soybean genome sequence data and constructed a proper set of TFs based on the Hidden Markov Model profiles of DNA-binding domain families. Within the soybean genome, we identified 4342 loci encoding 5035 TF models which grouped into 61 families. We constructed a database named SoybeanTFDB (http://soybeantfdb.psc.riken.jp) containing the full compilation of soybean TFs and significant information such as: functional motifs, full-length cDNAs, domain alignments, promoter regions, genomic organization and putative regulatory functions based on annotations of gene ontology (GO) inferred by comparative analysis with Arabidopsis. With particular interest in abiotic stress signalling, we analysed the promoter regions for all of the TF encoding genes as a means to identify abiotic stress responsive cis-elements as well as all types of cis-motifs provided by the PLACE database. SoybeanTFDB enables scientists to easily access cis-element and GO annotations to aid in the prediction of TF function and selection of TFs with functions of interest. This study provides a basic framework and an important user-friendly public information resource which enables analyses of transcriptional regulation in soybean.
Collapse
Affiliation(s)
- Keiichi Mochida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takuhiro Yoshida
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Sakurai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Kazuo Shinozaki
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Lam-Son Phan Tran
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
110
|
Yanai I, Hunter CP. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Res 2009; 19:2214-20. [PMID: 19745112 DOI: 10.1101/gr.093815.109] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomic analyses have shown that adjacent genes are often coexpressed. However, it remains unclear whether the observed coexpression is a result of functional organization or a consequence of adjacent active chromatin or transcriptional read-through, which may be free of selective biases. Here, we compare temporal expression profiles of one-to-one orthologs in conserved or divergent genomic positions in two genetically distant nematode species-Caenorhabditis elegans and C. briggsae-that share a near-identical developmental program. We find, for all major patterns of temporal expression, a substantive amount of gene expression divergence. However, this divergence is not random: Genes that function in essential developmental processes show less divergence than genes whose functions are not required for viability. Coexpression of gene neighbors in either species is highly divergent in the other, in particular when the neighborhood is not conserved. Interestingly, essential genes appear to maintain their expression profiles despite changes in neighborhoods suggesting exposure to stronger selection. Our results suggest that a significant fraction of the coexpression observed among gene neighbors may be accounted for by neutral processes, and further that these may be distinguished by comparative gene expression analyses.
Collapse
Affiliation(s)
- Itai Yanai
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | | |
Collapse
|
111
|
Long F, Peng H, Liu X, Kim SK, Myers E. A 3D digital atlas of C. elegans and its application to single-cell analyses. Nat Methods 2009; 6:667-72. [PMID: 19684595 PMCID: PMC2882208 DOI: 10.1038/nmeth.1366] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 07/22/2009] [Indexed: 11/09/2022]
Abstract
We built a digital nuclear atlas of the newly hatched, first larval stage (L1) of the wild-type hermaphrodite of Caenorhabditis elegans at single-cell resolution from confocal image stacks of 15 individual worms. The atlas quantifies the stereotypy of nuclear locations and provides other statistics on the spatial patterns of the 357 nuclei that could be faithfully segmented and annotated out of the 558 present at this developmental stage. We then developed an automated approach to assign cell names to each nucleus in a three-dimensional image of an L1 worm. We achieved 86% accuracy in identifying the 357 nuclei automatically. This computational method will allow high-throughput single-cell analyses of the post-embryonic worm, such as gene expression analysis, or ablation or stimulation of cells under computer control in a high-throughput functional screen.
Collapse
Affiliation(s)
- Fuhui Long
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | | | | | | | | |
Collapse
|
112
|
Abstract
Despite the successes of genomics, little is known about how genetic information produces complex organisms. A look at the crucial functional elements of fly and worm genomes could change that. The National Human Genome Research Institute's modENCODE project (the model organism ENCyclopedia Of DNA Elements) was set up in 2007 with the goal of identifying all the sequence-based functional elements in the genomes of two important experimental organisms, Caenorhabditis elegans and Drosophila melanogaster. Armed with modENCODE data, geneticists will be able to undertake the comprehensive molecular studies of regulatory networks that hold the key to how complex multicellular organisms arise from the list of instructions coded in the genome. In this issue, modENCODE team members outline their plan of campaign. Data from the project are to be made available on http://www.modencode.org and elsewhere as the work progresses.
Collapse
|
113
|
Grove CA, de Masi F, Barrasa MI, Newburger DE, Alkema MJ, Bulyk ML, Walhout AJ. A multiparameter network reveals extensive divergence between C. elegans bHLH transcription factors. Cell 2009; 138:314-27. [PMID: 19632181 PMCID: PMC2774807 DOI: 10.1016/j.cell.2009.04.058] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 03/06/2009] [Accepted: 04/23/2009] [Indexed: 01/20/2023]
Abstract
Differences in expression, protein interactions, and DNA binding of paralogous transcription factors ("TF parameters") are thought to be important determinants of regulatory and biological specificity. However, both the extent of TF divergence and the relative contribution of individual TF parameters remain undetermined. We comprehensively identify dimerization partners, spatiotemporal expression patterns, and DNA-binding specificities for the C. elegans bHLH family of TFs, and model these data into an integrated network. This network displays both specificity and promiscuity, as some bHLH proteins, DNA sequences, and tissues are highly connected, whereas others are not. By comparing all bHLH TFs, we find extensive divergence and that all three parameters contribute equally to bHLH divergence. Our approach provides a framework for examining divergence for other protein families in C. elegans and in other complex multicellular organisms, including humans. Cross-species comparisons of integrated networks may provide further insights into molecular features underlying protein family evolution. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.
Collapse
Affiliation(s)
- Christian A. Grove
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Federico de Masi
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - M. Inmaculada Barrasa
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel E. Newburger
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mark J. Alkema
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences & Technology, Harvard Medical School, Boston, MA 02115, USA
| | - Albertha J.M. Walhout
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
114
|
Deplancke B. Experimental advances in the characterization of metazoan gene regulatory networks. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:12-27. [PMID: 19324929 DOI: 10.1093/bfgp/elp001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gene regulatory networks (GRNs) play a vital role in metazoan development and function, and deregulation of these networks is often implicated in disease. GRNs depict the dynamic interactions between genomic and regulatory state components. The genomic components comprise genes and their associated cis-regulatory elements. The regulatory state components consist primarily of transcriptional complexes that bind the latter elements. With the availability of complete genome sequences, several approaches have recently been developed which promise to significantly enhance our ability to identify either the genomic or regulatory state components, or the interactions between these two. In this review, I provide an in-depth overview of these approaches and detail how each contributes to a more comprehensive understanding of GRN composition and function.
Collapse
Affiliation(s)
- Bart Deplancke
- Ecole Polytechnique Fédérale de Lausanne, School of Life Sciences, Institute of Bioengineering, Lausanne, Switzerland.
| |
Collapse
|
115
|
Jovelin R. Rapid sequence evolution of transcription factors controlling neuron differentiation in Caenorhabditis. Mol Biol Evol 2009; 26:2373-86. [PMID: 19589887 DOI: 10.1093/molbev/msp142] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Whether phenotypic evolution proceeds predominantly through changes in regulatory sequences is a controversial issue in evolutionary genetics. Ample evidence indicates that the evolution of gene regulatory networks via changes in cis-regulatory sequences is an important determinant of phenotypic diversity. However, recent experimental work suggests that the role of transcription factor (TF) divergence in developmental evolution may be underestimated. In order to help understand what levels of constraints are acting on the coding sequence of developmental regulatory genes, evolutionary rates were investigated among 48 TFs required for neuronal development in Caenorhabditis elegans. Allelic variation was then sampled for 28 of these genes within a population of the related species Caenorhabditis remanei. Neuronal TFs are more divergent, both within and between species, than structural genes. TFs affecting different neuronal classes are under different levels of selective constraints. The regulatory genes controlling the differentiation of chemosensory neurons evolve particularly fast and exhibit higher levels of within- and between-species nucleotide variation than TFs required for the development of several neuronal classes and TFs required for motorneuron differentiation. The TFs affecting chemosensory neuron development are also more divergent than chemosensory genes expressed in the neurons they differentiate. These results illustrate that TFs are not as highly constrained as commonly thought and suggest that the role of divergence in developmental regulatory genes during the evolution of gene regulatory networks requires further attention.
Collapse
Affiliation(s)
- Richard Jovelin
- Center for Ecology and Evolutionary Biology, University of Oregon, Oregon, USA.
| |
Collapse
|
116
|
Berger MF, Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 2009; 4:393-411. [PMID: 19265799 DOI: 10.1038/nprot.2008.195] [Citation(s) in RCA: 268] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein-binding microarray (PBM) technology provides a rapid, high-throughput means of characterizing the in vitro DNA-binding specificities of transcription factors (TFs). Using high-density, custom-designed microarrays containing all 10-mer sequence variants, one can obtain comprehensive binding-site measurements for any TF, regardless of its structural class or species of origin. Here, we present a protocol for the examination and analysis of TF-binding specificities at high resolution using such 'all 10-mer' universal PBMs. This procedure involves double-stranding a commercially synthesized DNA oligonucleotide array, binding a TF directly to the double-stranded DNA microarray and labeling the protein-bound microarray with a fluorophore-conjugated antibody. We describe how to computationally extract the relative binding preferences of the examined TF for all possible contiguous and gapped 8-mers over the full range of affinities, from highest affinity sites to nonspecific sites. Multiple proteins can be tested in parallel in separate chambers on a single microarray, enabling the processing of a dozen or more TFs in a single day.
Collapse
Affiliation(s)
- Michael F Berger
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
117
|
A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009; 10:252-63. [PMID: 19274049 DOI: 10.1038/nrg2538] [Citation(s) in RCA: 1095] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Transcription factors are key cellular components that control gene expression: their activities determine how cells function and respond to the environment. Currently, there is great interest in research into human transcriptional regulation. However, surprisingly little is known about these regulators themselves. For example, how many transcription factors does the human genome contain? How are they expressed in different tissues? Are they evolutionarily conserved? Here, we present an analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and evolutionary conservation. Much remains to be explored, but this study provides a solid foundation for future investigations to elucidate regulatory mechanisms underlying diverse mammalian biological processes.
Collapse
|
118
|
Martinez NJ, Walhout AJM. The interplay between transcription factors and microRNAs in genome-scale regulatory networks. Bioessays 2009; 31:435-45. [PMID: 19274664 PMCID: PMC3118512 DOI: 10.1002/bies.200800212] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Metazoan genomes contain thousands of protein-coding and non-coding RNA genes, most of which are differentially expressed, i.e., at different locations, at different times during development, or in response to environmental signals. Differential gene expression is achieved through complex regulatory networks that are controlled in part by two types of trans-regulators: transcription factors (TFs) and microRNAs (miRNAs). TFs bind to cis-regulatory DNA elements that are often located in or near their target genes, while miRNAs hybridize to cis-regulatory RNA elements mostly located in the 3' untranslated region of their target mRNAs. Here, we describe how these trans-regulators interact with each other in the context of gene regulatory networks to coordinate gene expression at the genome-scale level, and discuss future challenges of integrating these networks with other types of functional networks.
Collapse
Affiliation(s)
- Natalia J. Martinez
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albertha J. M. Walhout
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| |
Collapse
|
119
|
Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R. TFCat: the curated catalog of mouse and human transcription factors. Genome Biol 2009; 10:R29. [PMID: 19284633 PMCID: PMC2691000 DOI: 10.1186/gb-2009-10-3-r29] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 02/26/2009] [Accepted: 03/12/2009] [Indexed: 11/20/2022] Open
Abstract
TFCat is a catalog of mouse and human transcription factors based on a reliable core collection of annotations obtained by expert review of the scientific literature Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. The collection, including proven and homology-based candidate TFs, is annotated within a function-based taxonomy and DNA-binding proteins are organized within a classification system. All data and user-feedback mechanisms are available at the TFCat portal .
Collapse
Affiliation(s)
- Debra L Fulton
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada.
| | | | | | | | | | | | | |
Collapse
|
120
|
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes Dev 2008; 22:2535-49. [PMID: 18794350 DOI: 10.1101/gad.1678608] [Citation(s) in RCA: 188] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
MicroRNAs (miRNAs) and transcription factors (TFs) are primary metazoan gene regulators. Whereas much attention has focused on finding the targets of both miRNAs and TFs, the transcriptional networks that regulate miRNA expression remain largely unexplored. Here, we present the first genome-scale Caenorhabditis elegans miRNA regulatory network that contains experimentally mapped transcriptional TF --> miRNA interactions, as well as computationally predicted post-transcriptional miRNA --> TF interactions. We find that this integrated miRNA network contains 23 miRNA <--> TF composite feedback loops in which a TF that controls a miRNA is itself regulated by that same miRNA. By rigorous network randomizations, we show that such loops occur more frequently than expected by chance and, hence, constitute a genuine network motif. Interestingly, miRNAs and TFs in such loops are heavily regulated and regulate many targets. This "high flux capacity" suggests that loops provide a mechanism of high information flow for the coordinate and adaptable control of miRNA and TF target regulons.
Collapse
|
121
|
Ow MC, Martinez NJ, Olsen PH, Silverman HS, Barrasa MI, Conradt B, Walhout AJ, Ambros V. The FLYWCH transcription factors FLH-1, FLH-2, and FLH-3 repress embryonic expression of microRNA genes in C. elegans. Genes Dev 2008; 22:2520-34. [PMID: 18794349 PMCID: PMC2546698 DOI: 10.1101/gad.1678808] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 07/21/2008] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally via antisense base-pairing. Although miRNAs are involved in a variety of important biological functions, little is known about their transcriptional regulation. Using yeast one-hybrid assays, we identified transcription factors with a FLYWCH Zn-finger DNA-binding domain that bind to the promoters of several Caenorhabditis elegans miRNA genes. The products of the flh-1 and flh-2 genes function redundantly to repress embryonic expression of lin-4, mir-48, and mir-241, miRNA genes that are normally expressed only post-embryonically. Although single mutations in either flh-1 or flh-2 genes result in a viable phenotype, double mutation of flh-1 and flh-2 results in early larval lethality and an enhanced derepression of their target miRNAs in embryos. Double mutations in flh-2 and a third FLYWCH Zn-finger-containing transcription factor, flh-3, also result in enhanced precocious expression of target miRNAs. Mutations of lin-4 or mir-48&mir-241 do not rescue the lethal flh-1; flh-2 double-mutant phenotype, suggesting that the inviability is not solely the result of precocious expression of these miRNAs. Therefore, the FLH-1 and FLH-2 proteins likely play a more general role in regulating gene expression in embryos.
Collapse
Affiliation(s)
- Maria C. Ow
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Natalia J. Martinez
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Philip H. Olsen
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
| | - Howard S. Silverman
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
| | - M. Inmaculada Barrasa
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Barbara Conradt
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
| | - Albertha J.M. Walhout
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| |
Collapse
|
122
|
Haerty W, Artieri C, Khezri N, Singh RS, Gupta BP. Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution. BMC Genomics 2008; 9:399. [PMID: 18752680 PMCID: PMC2533025 DOI: 10.1186/1471-2164-9-399] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 08/27/2008] [Indexed: 11/23/2022] Open
Abstract
Background Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human) we sought to identify orthologous TFs and characterized their patterns of evolution. Results We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set), approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types) and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription factors even across distant evolutionary lineages and form the basis for future experiments to examine TF gene function in nematodes and other divergent phyla.
Collapse
Affiliation(s)
- Wilfried Haerty
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
| | | | | | | | | |
Collapse
|
123
|
Pujol N, Zugasti O, Wong D, Couillault C, Kurz CL, Schulenburg H, Ewbank JJ. Anti-fungal innate immunity in C. elegans is enhanced by evolutionary diversification of antimicrobial peptides. PLoS Pathog 2008; 4:e1000105. [PMID: 18636113 PMCID: PMC2453101 DOI: 10.1371/journal.ppat.1000105] [Citation(s) in RCA: 184] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Accepted: 06/19/2008] [Indexed: 12/24/2022] Open
Abstract
Encounters with pathogens provoke changes in gene transcription that are an integral part of host innate immune responses. In recent years, studies with invertebrate model organisms have given insights into the origin, function, and evolution of innate immunity. Here, we use genome-wide transcriptome analysis to characterize the consequence of natural fungal infection in Caenorhabditis elegans. We identify several families of genes encoding putative antimicrobial peptides (AMPs) and proteins that are transcriptionally up-regulated upon infection. Many are located in small genomic clusters. We focus on the nlp-29 cluster of six AMP genes and show that it enhances pathogen resistance in vivo. The same cluster has a different structure in two other Caenorhabditis species. A phylogenetic analysis indicates that the evolutionary diversification of this cluster, especially in cases of intra-genomic gene duplications, is driven by natural selection. We further show that upon osmotic stress, two genes of the nlp-29 cluster are strongly induced. In contrast to fungus-induced nlp expression, this response is independent of the p38 MAP kinase cascade. At the same time, both involve the epidermal GATA factor ELT-3. Our results suggest that selective pressure from pathogens influences intra-genomic diversification of AMPs and reveal an unexpected complexity in AMP regulation as part of the invertebrate innate immune response. We are interested in how exactly the nematode Caenorhabditi elegans, widely used in biological research, defends itself against fungal infection. Like most animals, this worm responds to infection by switching on defense genes. We used DNA chips to measure the levels of all the worm's 20,000 genes and discovered new inducible defense genes. Many of them encode small proteins or peptides that can probably kill microbes. By looking in other nematode species, we saw that these antimicrobial peptide genes are evolving rapidly. This means that they could be important for the worms' survival in their natural environment. We also looked at how some of these genes are regulated and uncovered a sophisticated control mechanism involving a series of proteins called kinases that relay signals within cells. The genes we looked at are active in the worm's skin. Some of the antimicrobial peptide genes that we looked at are also switched on in the skin by high salt, but in this case, the regulation doesn't involve the same cascade of kinases. The responses to both infection and high salt do, however, require the same transcription factor (the protein that actually switches genes on), in this case called a GATA factor.
Collapse
Affiliation(s)
- Nathalie Pujol
- Centre d'Immunologie de Marseille-Luminy, Université de la Méditerranée, Case 906, Marseille, France
| | | | | | | | | | | | | |
Collapse
|
124
|
Thomas JH. Genome evolution in Caenorhabditis. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:211-6. [PMID: 18573804 DOI: 10.1093/bfgp/eln022] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Since the completion of the Caenorhabditis elegans genome sequence 10 years ago, efforts of the large community of C. elegans geneticists have resulted in a high-quality annotation of the structures and sequence relatedness of nearly all the protein encoding and RNA genes. Based on increasingly accurate gene counts in other species, it now appears that C. elegans has more functional genes than most insects and approximately the same number as most mammals. In the last few years, draft genome sequences for several other nematodes have been published (C. briggsae and Brugia malayi) or publicly released (C. remanei, C. brenneri, C. japonica, Pristionchus pacificus, Trichinella spiralis and Haemonchus contortus). Comparisons of gene content within the phylum and to other phyla reveal complex patterns of genome evolution. These patterns include substantial numbers of genes conserved across all the major metazoan phyla (core metazoan genes) and many nematode-specific genes and gene families. Nematode-specific genes are located predominantly on autosomal arms, which also have higher recombination rates. It appears that evolutionary innovations occur mostly in these regions, probably facilitated by higher recombination. Few of these genes have gross phenotypes when knocked down by RNAi, suggesting that many of them function in specific aspects of nematode biology that were not tested, including chemosensation, pathogen response and xenobiotic detoxification.
Collapse
Affiliation(s)
- James H Thomas
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| |
Collapse
|
125
|
Moerman DG, Barstead RJ. Towards a mutation in every gene in Caenorhabditis elegans. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:195-204. [PMID: 18417533 DOI: 10.1093/bfgp/eln016] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The combined efforts of the Caenorhabditis elegans Knockout Consortium and individuals within the worm community are moving us closer to the goal of identifying mutations in every gene in the nematode C. elegans. At present, we count about 7000 deletion alleles that fall within 5500 genes. The principal method used to detect deletion mutations in the nematode utilizes polymerase chain reaction (PCR). More recently, the Moerman group has incorporated array comparative genome hybridization (aCGH) to detect deletions across the entire coding genome. Other methods used to detect mutant alleles in C. elegans include targeting induced local lesion in genomes (TILLING), transposon tagging, using either Tc1 or Mos1 and resequencing. These combined strategies have improved the overall throughput of the gene-knockout labs, and have broadened the types of mutations that we, and others, can identify. In this review, we will discuss these different approaches.
Collapse
Affiliation(s)
- Donald G Moerman
- Department of Zoology, University of British Columbia, Life Sciences Centre, 2350 Health Sciences Mall, Vancouver B.C. V6T 1Z3 Canada.
| | | |
Collapse
|
126
|
Grove CA, Walhout AJM. Transcription factor functionality and transcription regulatory networks. MOLECULAR BIOSYSTEMS 2008; 4:309-14. [PMID: 18354784 DOI: 10.1039/b715909a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Now that numerous high-quality complete genome sequences are available, many efforts are focusing on the "second genomic code", namely the code that determines how the precise temporal and spatial expression of each gene in the genome is achieved. In this regard, the elucidation of transcription regulatory networks that describe combined transcriptional circuits for an organism of interest has become valuable to our understanding of gene expression at a systems level. Such networks describe physical and regulatory interactions between transcription factors (TFs) and the target genes they regulate under different developmental, physiological, or pathological conditions. The mapping of high-quality transcription regulatory networks depends not only on the accuracy of the experimental or computational method chosen, but also relies on the quality of TF predictions. Moreover, the total repertoire of TFs is not only determined by the protein-coding capacity of the genome, but also by different protein properties, including dimerization, co-factor interactions and post-translational modifications. Here, we discuss the factors that influence TF functionality and, hence, the functionality of the networks in which they operate.
Collapse
Affiliation(s)
- Christian A Grove
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | |
Collapse
|
127
|
Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJM, Montgomery SB, Bergman CM. Text-mining assisted regulatory annotation. Genome Biol 2008; 9:R31. [PMID: 18271954 PMCID: PMC2374703 DOI: 10.1186/gb-2008-9-2-r31] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2007] [Revised: 12/21/2007] [Accepted: 02/13/2008] [Indexed: 12/17/2022] Open
Abstract
Text-mining technologies can be integrated with genome annotation systems, increasing the availability of annotated cis-regulatory data. Background Decoding transcriptional regulatory networks and the genomic cis-regulatory logic implemented in their control nodes is a fundamental challenge in genome biology. High-throughput computational and experimental analyses of regulatory networks and sequences rely heavily on positive control data from prior small-scale experiments, but the vast majority of previously discovered regulatory data remains locked in the biomedical literature. Results We develop text-mining strategies to identify relevant publications and extract sequence information to assist the regulatory annotation process. Using a vector space model to identify Medline abstracts from papers likely to have high cis-regulatory content, we demonstrate that document relevance ranking can assist the curation of transcriptional regulatory networks and estimate that, minimally, 30,000 papers harbor unannotated cis-regulatory data. In addition, we show that DNA sequences can be extracted from primary text with high cis-regulatory content and mapped to genome sequences as a means of identifying the location, organism and target gene information that is critical to the cis-regulatory annotation process. Conclusion Our results demonstrate that text-mining technologies can be successfully integrated with genome annotation systems, thereby increasing the availability of annotated cis-regulatory data needed to catalyze advances in the field of gene regulation.
Collapse
Affiliation(s)
- Stein Aerts
- Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000, Belgium.
| | | | | | | | | | | | | | | | | |
Collapse
|
128
|
Vermeirssen V, Deplancke B, Barrasa MI, Reece-Hoyes JS, Arda HE, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Brent MR, Walhout AJM. Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nat Methods 2007; 4:659-64. [PMID: 17589517 DOI: 10.1038/nmeth1063] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 05/23/2007] [Indexed: 11/09/2022]
Abstract
Yeast one-hybrid (Y1H) assays provide a gene-centered method for the identification of interactions between gene promoters and regulatory transcription factors (TFs). To date, Y1H assays have involved library screens that are relatively expensive and laborious. We present two Y1H strategies that allow immediate prey identification: matrix assays that use an array of 755 individual Caenorhabditis elegans TFs, and smart-pool assays that use TF multiplexing. Both strategies simplify the Y1H pipeline and reduce the cost of protein-DNA interaction identification. We used a Steiner triple system (STS) to create smart pools of 4-25 TFs. Notably, we uniplexed a small number of highly connected TFs to allow efficient assay deconvolution. Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well.
Collapse
Affiliation(s)
- Vanessa Vermeirssen
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
129
|
Vermeirssen V, Barrasa MI, Hidalgo CA, Babon JAB, Sequerra R, Doucette-Stamm L, Barabási AL, Walhout AJ. Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res 2007; 17:1061-71. [PMID: 17513831 PMCID: PMC1899117 DOI: 10.1101/gr.6148107] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription regulatory networks play a pivotal role in the development, function, and pathology of metazoan organisms. Such networks are comprised of protein-DNA interactions between transcription factors (TFs) and their target genes. An important question pertains to how the architecture of such networks relates to network functionality. Here, we show that a Caenorhabditis elegans core neuronal protein-DNA interaction network is organized into two TF modules. These modules contain TFs that bind to a relatively small number of target genes and are more systems specific than the TF hubs that connect the modules. Each module relates to different functional aspects of the network. One module contains TFs involved in reproduction and target genes that are expressed in neurons as well as in other tissues. The second module is enriched for paired homeodomain TFs and connects to target genes that are often exclusively neuronal. We find that paired homeodomain TFs are specifically expressed in C. elegans and mouse neurons, indicating that the neuronal function of paired homeodomains is evolutionarily conserved. Taken together, we show that a core neuronal C. elegans protein-DNA interaction network possesses TF modules that relate to different functional aspects of the complete network.
Collapse
Affiliation(s)
- Vanessa Vermeirssen
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - M. Inmaculada Barrasa
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - César A. Hidalgo
- Center for Complex Network Research, Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jenny Aurielle B. Babon
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | | | | | - Albert-László Barabási
- Center for Complex Network Research, Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Albertha J.M. Walhout
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Corresponding author.E-mail ; fax (508) 856-5460
| |
Collapse
|
130
|
Katzen F. Gateway®recombinational cloning: a biological operating system. Expert Opin Drug Discov 2007; 2:571-89. [DOI: 10.1517/17460441.2.4.571] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
131
|
Richardt S, Lang D, Reski R, Frank W, Rensing SA. PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. PLANT PHYSIOLOGY 2007; 143:1452-66. [PMID: 17337525 PMCID: PMC1851845 DOI: 10.1104/pp.107.095760] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Diversification of transcription-associated protein (TAP) families during land plant evolution is a key process yielding increased complexity of plant life. Understanding the evolutionary relationships between these genes is crucial to gain insight into plant evolution. We have determined a substantial set of TAPs that are focused on, but not limited to, land plants using PSI-BLAST searches and subsequent filtering and clustering steps. Phylogenies were created in an automated way using a combination of distance and maximum likelihood methods. Comparison of the data to previously published work confirmed their accuracy and usefulness for the majority of gene families. Evidence is presented that the flowering plant apical stem cell regulator WUSCHEL evolved from an ancestral homeobox gene that was already present after the water-to-land transition. The presence of distinct expanded gene families, such as COP1 and HIT in moss, is discussed within the evolutionary backdrop. Comparative analyses revealed that almost all angiosperm transcription factor families were already present in the earliest land plants, whereas many are missing among unicellular algae. A global analysis not only of transcription factors but also of transcriptional regulators and novel putative families is presented. A wealth of data about plant TAP families and all data accrued throughout their automated detection and analysis are made available via the PlanTAPDB Web interface. Evolutionary relationships of these genes are readily accessible to the nonexpert at a mouse-click. Initial analyses of selected gene families revealed that PlanTAPDB can easily be exerted for knowledge discovery.
Collapse
Affiliation(s)
- Sandra Richardt
- Plant Biotechnology, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany
| | | | | | | | | |
Collapse
|
132
|
Zhao G, Schriefer LA, Stormo GD. Identification of muscle-specific regulatory modules in Caenorhabditis elegans. Genome Res 2007; 17:348-57. [PMID: 17284674 PMCID: PMC1800926 DOI: 10.1101/gr.5989907] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transcriptional regulation is the major regulatory mechanism that controls the spatial and temporal expression of genes during development. This is carried out by transcription factors (TFs), which recognize and bind to their cognate binding sites. Recent studies suggest a modular organization of TF-binding sites, in which clusters of transcription-factor binding sites cooperate in the regulation of downstream gene expression. In this study, we report our computational identification and experimental verification of muscle-specific cis-regulatory modules in Caenorhabditis elegans. We first identified a set of motifs that are correlated with muscle-specific gene expression. We then predicted muscle-specific regulatory modules based on clusters of those motifs with characteristics similar to a collection of well-studied modules in other species. The method correctly identifies 88% of the experimentally characterized modules with a positive predictive value of at least 65%. The prediction accuracy of muscle-specific expression on an independent test set is highly significant (P<0.0001). We performed in vivo experimental tests of 12 predicted modules, and 10 of those drive muscle-specific gene expression. These results suggest that our method is highly accurate in identifying functional sequences important for muscle-specific gene expression and is a valuable tool for guiding experimental designs.
Collapse
Affiliation(s)
- Guoyan Zhao
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Lawrence A. Schriefer
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Gary D. Stormo
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Corresponding author.E-mail ; fax (314) 362-7855
| |
Collapse
|
133
|
Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics 2007; 8:27. [PMID: 17244357 PMCID: PMC1785375 DOI: 10.1186/1471-2164-8-27] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Accepted: 01/23/2007] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically. Transcription factors will form the core of any systems biology model of genome control and therefore the promoter activity of Promoterome inserts for C. elegans transcription factor genes was examined, in vivo, with a reporter gene approach. RESULTS Transgenic C. elegans strains were generated for 366 transcription factor promoter/gfp reporter gene fusions. GFP distributions were determined, and then summarized with reference to developmental stage and cell type. Reliability of these data was demonstrated by comparison to previously described gene product distributions. A detailed consideration of the results for one C. elegans transcription factor gene family, the Six family, comprising ceh-32, ceh-33, ceh-34 and unc-39 illustrates the value of these analyses. The high proportion of Promoterome reporter fusions that drove GFP expression, compared to previous studies, led to the hypothesis that transcription factor genes might be involved in local gene duplication events less frequently than other genes. Comparison of transcription factor genes of C. elegans and Caenorhabditis briggsae was therefore carried out and revealed very few examples of functional gene duplication since the divergence of these species for most, but not all, transcription factor gene families. CONCLUSION Examining reporter expression patterns for hundreds of promoters informs, and thereby improves, interpretation of this data type. Genes encoding transcription factors involved in intrinsic developmental control processes appear acutely sensitive to changes in gene dosage through local gene duplication, on an evolutionary time scale.
Collapse
|
134
|
EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression. BMC Genomics 2007; 8:21. [PMID: 17233892 PMCID: PMC1790901 DOI: 10.1186/1471-2164-8-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 01/18/2007] [Indexed: 11/21/2022] Open
Abstract
Background Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-centered methods can be used to systematically identify such interactions. We use high-throughput yeast one-hybrid assays as a gene-centered method to identify protein-DNA interactions between regulatory sequences (e.g. gene promoters) and transcription factors in the nematode Caenorhabditis elegans. We have already mapped several hundred protein-DNA interactions and analyzed the transcriptional consequences of some by examining differential gene expression of targets in the presence or absence of an upstream regulator. The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration. Description Here, we report the implementation of a C. elegans differential gene expression database (EDGEdb). This database enables the storage and retrieval of protein-DNA interactions and other data that relate to differential gene expression. Specifically, EDGEdb contains: i) sequence information of regulatory elements, including gene promoters, ii) sequence information of all 934 predicted transcription factors, their DNA binding domains, and, where available, their dimerization partners and consensus DNA binding sites, iii) protein-DNA interactions between regulatory elements and transcription factors, and iv) expression patterns conferred by regulatory elements, and how such patterns are affected by interacting transcription factors. Conclusion EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms. The database is available at .
Collapse
|
135
|
Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G. Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol 2007; 8:R15. [PMID: 17274809 PMCID: PMC1852409 DOI: 10.1186/gb-2007-8-2-r15] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 10/20/2006] [Accepted: 02/02/2007] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding elements (CNEs) are associated with genes that coordinate development, and have been proposed to act as transcriptional enhancers. Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates. RESULTS Here we report that nematode genomes contain an alternative set of CNEs that share sequence characteristics, but not identity, with their vertebrate counterparts. CNEs thus represent a very unusual class of sequences that are extremely conserved within specific animal lineages yet are highly divergent between lineages. Nematode CNEs are also associated with developmental regulatory genes, and include well-characterized enhancers and transcription factor binding sites, supporting the proposed function of CNEs as cis-regulatory elements. Most remarkably, 40 of 156 human CNE-associated genes with invertebrate orthologs are also associated with CNEs in both worms and flies. CONCLUSION A core set of genes that regulate development is associated with CNEs across three animal groups (worms, flies and vertebrates). We propose that these CNEs reflect the parallel evolution of alternative enhancers for a common set of developmental regulatory genes in different animal groups. This 're-wiring' of gene regulatory networks containing key developmental coordinators was probably a driving force during the evolution of animal body plans. CNEs may, therefore, represent the genomic traces of these 'hard-wired' core gene regulatory networks that specify the development of each alternative animal body plan.
Collapse
Affiliation(s)
- Tanya Vavouri
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Klaudia Walter
- MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, UK
| | - Walter R Gilks
- Department of Statistics, University of Leeds, Leeds LS2 9JT, UK
| | - Ben Lehner
- EMBL/CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), UPF, C/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| |
Collapse
|
136
|
Kerry S, TeKippe M, Gaddis NC, Aballay A. GATA transcription factor required for immunity to bacterial and fungal pathogens. PLoS One 2006; 1:e77. [PMID: 17183709 PMCID: PMC1762309 DOI: 10.1371/journal.pone.0000077] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Accepted: 11/12/2006] [Indexed: 12/20/2022] Open
Abstract
In the past decade, Caenorhabditis elegans has been used to dissect several genetic pathways involved in immunity; however, little is known about transcription factors that regulate the expression of immune effectors. C. elegans does not appear to have a functional homolog of the key immune transcription factor NF-κB. Here we show that that the intestinal GATA transcription factor ELT-2 is required for both immunity to Salmonella enterica and expression of a C-type lectin gene, clec-67, which is expressed in the intestinal cells and is a good marker of S. enterica infection. We also found that ELT-2 is required for immunity to Pseudomonas aeruginosa, Enterococcus faecalis, and Cryptococcus neoformans. Lack of immune inhibition by DAF-2, which negatively regulates the FOXO transcription factor DAF-16, rescues the hypersusceptibility to pathogens phenotype of elt-2(RNAi) animals. Our results indicate that ELT-2 is part of a multi-pathogen defense pathway that regulates innate immunity independently of the DAF-2/DAF-16 signaling pathway.
Collapse
|
137
|
Fukushige T, Brodigan TM, Schriefer LA, Waterston RH, Krause M. Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development. Genes Dev 2006; 20:3395-406. [PMID: 17142668 PMCID: PMC1698447 DOI: 10.1101/gad.1481706] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Myogenic regulatory factors (MRFs) are required for mammalian skeletal myogenesis. In contrast, bodywall muscle is readily detectable in Caenorhabditis elegans embryos lacking activity of the lone MRF ortholog HLH-1, indicating that additional myogenic factors must function in the nematode. We find that two additional C. elegans proteins, UNC-120/SRF and HND-1/HAND, can convert naïve blastomeres to muscle when overproduced ectopically in the embryo. In addition, we have used genetic null mutants to demonstrate that both of these factors act in concert with HLH-1 to regulate myogenesis. Loss of all three factors results in embryos that lack detectable bodywall muscle differentiation, identifying this trio as a set that is both necessary and sufficient for bodywall myogenesis in C. elegans. In mammals, SRF and HAND play prominent roles in regulating smooth and cardiac muscle development. That C. elegans bodywall muscle development is dependent on transcription factors that are associated with all three types of mammalian muscle supports a theory that all animal muscle types are derived from a common ancestral contractile cell type.
Collapse
Affiliation(s)
- Tetsunari Fukushige
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Thomas M. Brodigan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Robert H. Waterston
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Michael Krause
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
- Corresponding author.E-MAIL ; FAX (301) 496-0201
| |
Collapse
|
138
|
Walhout AJM. Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res 2006; 16:1445-54. [PMID: 17053092 DOI: 10.1101/gr.5321506] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Metazoan genomes contain thousands of protein-coding and noncoding RNA genes, most of which are differentially expressed, i.e., at different locations or at different times during development, function, or pathology of the organism. Differential gene expression is achieved in part by the action of regulatory transcription factors (TFs) that bind to cis-regulatory elements that are often located in or near their target genes. Each TF likely regulates many targets in the context of intricate transcription regulatory networks. Up to 10% of a genome may encode TFs, but only a handful of these have been studied in detail. Here, I will discuss the different steps involved in the mapping and analysis of transcription regulatory networks, including the identification of network nodes (TFs and their target sequences) and edges (TF-TF dimers and TF-DNA target interactions), integration with other data types, and network properties and emerging principles that provide insights into differential gene expression.
Collapse
Affiliation(s)
- Albertha J M Walhout
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
| |
Collapse
|
139
|
Deplancke B, Vermeirssen V, Arda HE, Martinez NJ, Walhout AJM. Gateway-compatible yeast one-hybrid screens. Cold Spring Harb Protoc 2006; 2006:2006/5/pdb.prot4590. [PMID: 22485967 DOI: 10.1101/pdb.prot4590] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
INTRODUCTIONProtein-DNA interactions (PDIs) between transcription factors (TFs) and their target genes form the backbone of transcription regulatory networks. Such PDIs can be identified with either a TF or a gene as a starting point. The Gateway-compatible yeast one-hybrid (Y1H) system provides a high-throughput, gene-centered method for the identification of interactions between a "DNA bait" (e.g., cis-regulatory DNA elements or gene promoters) and "protein preys" (e.g., TFs). The Y1H system is a genetic system to detect PDIs based on selection of reporter gene expression in yeast. DNA baits are fused by Gateway cloning to two reporter genes, HIS3 and lacZ, and the resulting DNA bait::reporter constructs are subsequently integrated into the genome of the host yeast strain. After integration, baits are examined for self-activation (i.e., their ability to drive reporter gene expression in the absence of an exogenous prey protein). Subsequently, each DNA bait is screened for interacting proteins by transforming a library of preys into the corresponding Y1H DNA bait yeast strain. Preys are hybrid proteins composed of a protein from the organism of interest and a heterologous transcription activation domain. When a prey protein binds to the DNA bait, the heterologous activation domain activates reporter gene expression. Thus, physical interactions between both repressors and activators and their DNA targets can be identified.
Collapse
Affiliation(s)
- Bart Deplancke
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | |
Collapse
|
140
|
Materna SC, Howard-Ashby M, Gray RF, Davidson EH. The C2H2 zinc finger genes of Strongylocentrotus purpuratus and their expression in embryonic development. Dev Biol 2006; 300:108-20. [PMID: 16997293 DOI: 10.1016/j.ydbio.2006.08.032] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/04/2006] [Accepted: 08/16/2006] [Indexed: 11/21/2022]
Abstract
The C2H2 zinc finger is one of the most abundant protein domains and is thought to have been extensively replicated in diverse animal clades. Some well-studied proteins that contain this domain are transcriptional regulators. As part of an attempt to delineate all transcription factors encoded in the Strongylocentrotus purpuratus genome, we identified the C2H2 zinc finger genes indicated in the sequence, and examined their involvement in embryonic development. We found 377 zinc finger genes in the sea urchin genome, about half the number found in mice or humans. Their expression was measured by quantitative PCR. Up to the end of gastrulation less than a third of these genes is expressed, and about 75% of the expressed genes are maternal; both parameters distinguish these from all other classes of regulatory genes as measured in other studies. Spatial expression pattern was determined by whole mount in situ hybridization for 43 genes transcribed at a sufficient level, and localized expression was observed in diverse embryonic tissues. These genes may execute important regulatory functions in development. However, the functional meaning of the majority of this large gene family remains undefined.
Collapse
Affiliation(s)
- Stefan C Materna
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | |
Collapse
|
141
|
Deplancke B, Mukhopadhyay A, Ao W, Elewa AM, Grove CA, Martinez NJ, Sequerra R, Doucette-Stamm L, Reece-Hoyes JS, Hope IA, Tissenbaum HA, Mango SE, Walhout AJM. A gene-centered C. elegans protein-DNA interaction network. Cell 2006; 125:1193-205. [PMID: 16777607 DOI: 10.1016/j.cell.2006.04.038] [Citation(s) in RCA: 192] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Revised: 02/27/2006] [Accepted: 04/12/2006] [Indexed: 11/16/2022]
Abstract
Transcription regulatory networks consist of physical and functional interactions between transcription factors (TFs) and their target genes. The systematic mapping of TF-target gene interactions has been pioneered in unicellular systems, using "TF-centered" methods (e.g., chromatin immunoprecipitation). However, metazoan systems are less amenable to such methods. Here, we used "gene-centered" high-throughput yeast one-hybrid (Y1H) assays to identify 283 interactions between 72 C. elegans digestive tract gene promoters and 117 proteins. The resulting protein-DNA interaction (PDI) network is highly connected and enriched for TFs that are expressed in the digestive tract. We provide functional annotations for approximately 10% of all worm TFs, many of which were previously uncharacterized, and find ten novel putative TFs, illustrating the power of a gene-centered approach. We provide additional in vivo evidence for multiple PDIs and illustrate how the PDI network provides insights into metazoan differential gene expression at a systems level.
Collapse
Affiliation(s)
- Bart Deplancke
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, 01605, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
142
|
Broitman-Maduro G, Lin KTH, Hung WWK, Maduro MF. Specification of the C. elegans MS blastomere by the T-box factor TBX-35. Development 2006; 133:3097-106. [PMID: 16831832 DOI: 10.1242/dev.02475] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In C. elegans, many mesodermal cell types are made by descendants of the progenitor MS, born at the seven-cell stage of embryonic development. Descendants of MS contribute to body wall muscle and to the posterior half of the pharynx. We have previously shown that MS is specified by the activity of the divergent MED-1,2 GATA factors. We report that the MED-1,2 target gene tbx-35, which encodes a T-box transcription factor, specifies the MS fate. Embryos homozygous for a putative tbx-35-null mutation fail to generate MS-derived pharynx and body muscle, and instead generate ectopic PAL-1-dependent muscle and hypodermis, tissues normally made by the C blastomere. Conversely, overexpression of tbx-35 results in the generation of ectopic pharynx and muscle tissue. The MS and E sister cells are made different by transduction of a Wnt/MAPK/Src pathway signal through the nuclear effector TCF/POP-1. We show that in E, tbx-35 is repressed in a Wnt-dependent manner that does not require activity of TCF/POP-1, suggesting that an additional nuclear Wnt effector functions in E to repress MS development. Genes of the T-box family are known to function in protostomes and deuterostomes in the specification of mesodermal fates. Our results show that this role has been evolutionarily conserved in the early C. elegans embryo, and that a progenitor of multiple tissue types can be specified by a surprisingly simple gene cascade.
Collapse
Affiliation(s)
- Gina Broitman-Maduro
- Department of Biology, University of California, Riverside, Riverside, CA 92521, USA
| | | | | | | |
Collapse
|
143
|
O’Rourke D, Baban D, Demidova M, Mott R, Hodgkin J. Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum. Genome Res 2006; 16:1005-16. [PMID: 16809667 PMCID: PMC1524860 DOI: 10.1101/gr.50823006] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interaction between the nematode Caenorhabditis elegans and a Gram-positive bacterial pathogen, Microbacterium nematophilum, provides a model for an innate immune response in nematodes. This pathogen adheres to the rectal and post-anal cuticle of the worm, causing slowed growth, constipation, and a defensive swelling response of rectal hypodermal cells. To explore the genomic responses that the worm activates after pathogenic attack we used microarray analysis of transcriptional changes induced after 6-h infection, comparing virulent with avirulent infection. We defined 89 genes with statistically significant expression changes of at least twofold, of which 68 were up-regulated and 21 were down-regulated. Among the former, those encoding C-type lectin domains were the most abundant class. Many of the 89 genes exhibit genomic clustering, and we identified one large cluster of 62 genes, of which most were induced in response to infection. We tested 41 of the induced genes for involvement in immunity using mutants or RNAi, finding that six of these are required for the swelling response and five are required more generally for defense. Our results indicate that C-type lectins and other putative pathogen-recognition molecules are important for innate immune defense in C. elegans. We also found significant induction of genes encoding lysozymes, proteases, and defense-related proteins, as well as various domains of unknown function. The genes induced during infection by M. nematophilum appear largely distinct from genes induced by other pathogens, suggesting that C. elegans mounts pathogen-specific responses to infection.
Collapse
Affiliation(s)
- Delia O’Rourke
- Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Dilair Baban
- MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Maria Demidova
- Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Jonathan Hodgkin
- Genetics Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Corresponding author.E-mail ; fax 44-1865-275318
| |
Collapse
|