1
|
Ghotbi E, Ye P, Ervin T, Kum A, Benes J, Jones RS. Polycomb-group recruitment to a Drosophila target gene is the default state that is inhibited by a transcriptional activator. SCIENCE ADVANCES 2021; 7:7/29/eabg1556. [PMID: 34272248 PMCID: PMC8284896 DOI: 10.1126/sciadv.abg1556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Abstract
Polycomb-group (PcG) proteins are epigenetic regulators that maintain the transcriptional repression of target genes following their initial repression by transcription factors. PcG target genes are repressed in some cells, but active in others. Therefore, a mechanism must exist by which PcG proteins distinguish between the repressed and active states and only assemble repressive chromatin environments at target genes that are repressed. Here, we present experimental evidence that the repressed state of a Drosophila PcG target gene, giant (gt), is not identified by the presence of a repressor. Rather, de novo establishment of PcG-mediated silencing at gt is the default state that is prevented by the presence of an activator or coactivator, which may inhibit the catalytic activity of Polycomb-repressive complex 2 (PRC2).
Collapse
Affiliation(s)
- Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Piao Ye
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Taylor Ervin
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Anni Kum
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
| |
Collapse
|
2
|
Alhaj Abed J, Ghotbi E, Ye P, Frolov A, Benes J, Jones RS. De novo recruitment of Polycomb-group proteins in Drosophila embryos. Development 2018; 145:dev.165027. [PMID: 30389849 DOI: 10.1242/dev.165027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 10/29/2018] [Indexed: 12/24/2022]
Abstract
Polycomb-group (PcG)-mediated transcriptional repression of target genes can be delineated into two phases. First, following initial repression of target genes by gene-specific transcription factors, PcG proteins recognize the repressed state and assume control of the genes' repression. Second, once the silenced state is established, PcG proteins may maintain repression through an indefinite number of cell cycles. Little is understood about how PcG proteins initially recognize the repressed state of target genes and the steps leading to de novo establishment of PcG-mediated repression. We describe a genetic system in which a Drosophila PcG target gene, giant (gt), is ubiquitously repressed during early embryogenesis by a maternally expressed transcription factor, and show the temporal recruitment of components of three PcG protein complexes: PhoRC, PRC1 and PRC2. We show that de novo PcG recruitment follows a temporal hierarchy in which PhoRC stably localizes at the target gene at least 1 h before stable recruitment of PRC2 and concurrent trimethylation of histone H3 at lysine 27 (H3K27me3). The presence of PRC2 and increased levels of H3K27me3 are found to precede stable binding by PRC1.
Collapse
Affiliation(s)
- Jumana Alhaj Abed
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Elnaz Ghotbi
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Piao Ye
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Alexander Frolov
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Judith Benes
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Richard S Jones
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| |
Collapse
|
3
|
Niedner A, Müller M, Moorthy BT, Jansen RP, Niessing D. Role of Loc1p in assembly and reorganization of nuclear ASH1 messenger ribonucleoprotein particles in yeast. Proc Natl Acad Sci U S A 2013; 110:E5049-58. [PMID: 24324176 PMCID: PMC3876240 DOI: 10.1073/pnas.1315289111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Directional transport of mRNA is a universal feature in eukaryotes, requiring the assembly of motor-dependent RNA-transport particles. The cytoplasmic transport of mRNAs is preceded by the nuclear assembly of pre-messenger ribonucleoprotein particles (mRNPs). In budding yeast, the asymmetric synthesis of HO 1 (ASH1) pre-mRNP originates already cotranscriptionally and passes through the nucleolus before its nuclear export. The nucleolar localization of ASH1 mRNA protein 1 (Loc1p) is required for efficient ASH1 mRNA localization. Immunoprecipitation experiments have revealed that Loc1p forms cocomplexes with other components of the ASH1 transport complex. However, it remains unclear how Loc1p is recruited into this mRNP and why Loc1p is important for ASH1 mRNA localization. Here we demonstrate that Loc1p undergoes a direct and specific interaction with the ASH1 mRNA-binding Swi5p-dependent HO expression protein 2 (She2p). This cocomplex shows higher affinity and specificity for RNA bearing localization elements than the individual proteins. It also stabilizes the otherwise transient binding of She2p to ASH1 mRNA, suggesting that cooperative mRNA binding of Loc1p with She2p is the required nuclear function of Loc1p for ASH1 mRNA localization. After nuclear export, myosin-bound She3p joins the ASH1 mRNP to form a highly specific cocomplex with She2p and ASH1 mRNA. Because Loc1p is found only in the nucleus, it must be removed from the complex directly before or after export. In vitro and in vivo experiments indicate that the synergistic interaction of She2p and She3p displaces Loc1p from the ASH1 complex, allowing free Loc1p to rapidly reenter the nucle(ol)us. Together these findings suggest an ordered process of nuclear assembly and reorganization for the maturation of localizing ASH1 mRNPs.
Collapse
Affiliation(s)
- Annika Niedner
- Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University, 81377 Munich, Germany; and
| | - Marisa Müller
- Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University, 81377 Munich, Germany; and
| | - Balaji T. Moorthy
- Interfaculty Institute of Biochemistry, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany
| | - Ralf-Peter Jansen
- Interfaculty Institute of Biochemistry, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany
| | - Dierk Niessing
- Group Intracellular Transport and RNA Biology, Institute of Structural Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians University, 81377 Munich, Germany; and
| |
Collapse
|
4
|
Saunders A, Core LJ, Sutcliffe C, Lis JT, Ashe HL. Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. Genes Dev 2013; 27:1146-58. [PMID: 23699410 DOI: 10.1101/gad.215459.113] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cascades of zygotic gene expression pattern the anterior-posterior (AP) and dorsal-ventral (DV) axes of the early Drosophila embryo. Here, we used the global run-on sequencing assay (GRO-seq) to map the genome-wide RNA polymerase distribution during early Drosophila embryogenesis, thus providing insights into how genes are regulated. We identify widespread promoter-proximal pausing yet show that the presence of paused polymerase does not necessarily equate to direct regulation through pause release to productive elongation. Our data reveal that a subset of early Zelda-activated genes is regulated at the level of polymerase recruitment, whereas other Zelda target and axis patterning genes are predominantly regulated through pause release. In contrast to other signaling pathways, we found that bone morphogenetic protein (BMP) target genes are collectively more highly paused than BMP pathway components and show that BMP target gene expression requires the pause-inducing negative elongation factor (NELF) complex. Our data also suggest that polymerase pausing allows plasticity in gene activation throughout embryogenesis, as transiently repressed and transcriptionally silenced genes maintain and lose promoter polymerases, respectively. Finally, we provide evidence that the major effect of pausing is on the levels, rather than timing, of transcription. These data are discussed in terms of the efficiency of transcriptional activation required across cell populations during developmental time constraints.
Collapse
Affiliation(s)
- Abbie Saunders
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | | | | | | | | |
Collapse
|
5
|
Ten Tusscher KHWJ. Mechanisms and constraints shaping the evolution of body plan segmentation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:54. [PMID: 23708840 DOI: 10.1140/epje/i2013-13054-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 05/07/2013] [Indexed: 06/02/2023]
Abstract
Segmentation of the major body axis into repeating units is arguably one of the major inventions in the evolution of animal body plan pattering. It is found in current day vertebrates, annelids and arthropods. Most segmented animals seem to use a clock-and-wavefront type mechanism in which oscillations emanating from a posterior growth zone become transformed into an anterior posterior sequence of segments. In contrast, few animals such as Drosophila use a complex gene regulatory hierarchy to simultaneously subdivide their entire body axis into segments. Here I discuss how in silico models simulating the evolution of developmental patterning can be used to investigate the forces and constraints that helped shape these two developmental modes. I perform an analysis of a series of previous simulation studies, exploiting the similarities and differences in their outcomes in relation to model characteristics to elucidate the circumstances and constraints likely to have been important for the evolution of sequential and simultaneous segmentation modes. The analysis suggests that constraints arising from the involved growth process and spatial patterning signal--posterior elongation producing a propagating wavefront versus a tissue wide morphogen gradient--and the evolutionary history--ancestral versus derived segmentation mode--strongly shaped both segmentation mechanisms. Furthermore, this implies that these patterning types are to be expected rather than random evolutionary outcomes and supports the likelihood of multiple parallel evolutionary origins.
Collapse
Affiliation(s)
- K H W J Ten Tusscher
- Theoretical Biology and Bioinformactics Group, Utrecht University, Padualaan 8, 3584, CH Utrecht, The Netherlands.
| |
Collapse
|
6
|
Jansen RP, Niessing D. Assembly of mRNA-protein complexes for directional mRNA transport in eukaryotes--an overview. Curr Protein Pept Sci 2012; 13:284-93. [PMID: 22708485 PMCID: PMC3474952 DOI: 10.2174/138920312801619493] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 01/10/2012] [Accepted: 01/20/2012] [Indexed: 12/11/2022]
Abstract
At all steps from transcription to translation, RNA-binding proteins play important roles in determining mRNA function. Initially it was believed that for the vast majority of transcripts the role of RNA-binding proteins is limited to general functions such as splicing and translation. However, work from recent years showed that members of this class of proteins also recognize several mRNAs via cis-acting elements for their incorporation into large motor-containing particles. These particles are transported to distant subcellular sites, where they become subsequently translated. This process, called mRNA localization, occurs along microtubules or actin filaments, and involves kinesins, dyneins, as well as myosins. Although mRNA localization has been detected in a large number of organisms from fungi to humans, the underlying molecular machineries are not well understood. In this review we will outline general principles of mRNA localization and highlight three examples, for which a comparably large body of information is available. The first example is She2p/She3p-dependent localization of ASH1 mRNA in budding yeast. It is particularly well suited to highlight the interdependence between different steps of mRNA localization. The second example is Staufen-dependent localization of oskar mRNA in the Drosophila embryo, for which the importance of nuclear events for cytoplasmic localization and translational control has been clearly demonstrated. The third example summarizes Egalitarian/Bicaudal D-dependent mRNA transport events in the oocyte and embryo of Drosophila. We will highlight general themes and differences, point to similarities in other model systems, and raise open questions that might be answered in the coming years.
Collapse
Affiliation(s)
- Ralf-Peter Jansen
- Interfaculty Institute for Biochemistry, University of Tübingen, Tübingen, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, München, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, München, Germany
| |
Collapse
|
7
|
Andrioli LP. Toward new Drosophila paradigms. Genesis 2012; 50:585-98. [DOI: 10.1002/dvg.22019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 11/07/2022]
|
8
|
Papatsenko D. Stripe formation in the early fly embryo: principles, models, and networks. Bioessays 2009; 31:1172-80. [DOI: 10.1002/bies.200900096] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
9
|
Li CW, Chen BS. Stochastic Spatio-Temporal Dynamic Model for Gene/Protein Interaction Network in Early Drosophila Development. GENE REGULATION AND SYSTEMS BIOLOGY 2009. [DOI: 10.1177/117762500900300001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order to investigate the possible mechanisms for eve stripe formation of Drosophila embryo, a spatio-temporal gene/protein interaction network model is proposed to mimic dynamic behaviors of protein synthesis, protein decay, mRNA decay, protein diffusion, transcription regulations and autoregulation to analyze the interplay of genes and proteins at different compartments in early embryogenesis. In this study, we use the maximum likelihood (ML) method to identify the stochastic 3-D Embryo Space-Time (3-DEST) dynamic model for gene/protein interaction network via 3-D mRNA and protein expression data and then use the Akaike Information Criterion (AIC) to prune the gene/protein interaction network. The identified gene/protein interaction network allows us not only to analyze the dynamic interplay of genes and proteins on the border of eve stripes but also to infer that eve stripes are established and maintained by network motifs built by the cooperation between transcription regulations and diffusion mechanisms in early embryogenesis. Literature reference with the wet experiments of gene mutations provides a clue for validating the identified network. The proposed spatio-temporal dynamic model can be extended to gene/protein network construction of different biological phenotypes, which depend on compartments, e.g. postnatal stem/progenitor cell differentiation.
Collapse
Affiliation(s)
- Cheng-Wei Li
- Laboratory of Systems Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Bor-Sen Chen
- Laboratory of Systems Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| |
Collapse
|
10
|
The Drosophila gap gene giant has an anterior segment identity function mediated through disconnected and teashirt. Genetics 2008; 179:441-53. [PMID: 18493063 DOI: 10.1534/genetics.107.084988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The C2H2 zinc-finger-containing transcription factors encoded by the disconnected (disco) and teashirt (tsh) genes contribute to the regionalization of the Drosophila embryo by establishing fields in which specific Homeotic complex (Hom-C) proteins can function. In Drosophila embryos, disco and the paralogous disco-related (disco-r) are expressed throughout most of the epidermis of the head segments, but only in small patches in the trunk segments. Conversely, tsh is expressed extensively in the trunk segments, with little or no accumulation in the head segments. Little is known about the regulation of these genes; for example, what limits their expression to these domains? Here, we report the regulatory effects of gap genes on the spatial expression of disco, disco-r, and tsh during Drosophila embryogenesis. The data shed new light on how mutations in giant (gt) affect patterning within the anterior gt domain, demonstrating homeotic function in this domain. However, the homeosis does not occur through altered expression of the Hom-C genes but through changes in the regulation of disco and tsh.
Collapse
|
11
|
Wu J, Xie J. Computation-based discovery of cis-regulatory modules by hidden Markov model. J Comput Biol 2008; 15:279-90. [PMID: 18333759 DOI: 10.1089/cmb.2008.0024] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A key component in genome sequence analysis is the identification of regions of the genome that contain regulatory information. In higher eukaryotes, this information is organized into modular units called cis-regulatory modules. Each module contains multiple binding sites for a specific combination of several transcription factors. In this article, we propose a hidden Markov model (HMM) to identify transcription factor binding sites (TFBSs) and cis-regulatory modules (CRMs). For a given genomic sequence, we first select potential TFBSs from a large database (e.g., TRANSFAC), then construct an HMM where the TFBSs are only counted when they occur within a specialized CRM state. The novel features of the proposed method include that it does not assume a small set of TFBSs for a given gene; on the other hand, the method utilizes information from a large collection of well-characterized TFBSs and therefore is computationally more efficient and robust than the de novo methods. Our approach is applied to three data sets with experimentally evaluated TFBSs. The method shows better specificity and sensitivity than other similar computational tools in identifying CRMs and TFBSs. The executable codes of our programs and module predictions across the fly Drosophila genome are available at www.stat.purdue.edu/~ jingwu/module/.
Collapse
Affiliation(s)
- Jing Wu
- Department of Statistics, Purdue University, West Lafayette, Indiana 47907, USA
| | | |
Collapse
|
12
|
Blanco J, Gehring WJ. Analysis of twin of eyeless regulation during early embryogenesis in Drosophila melanogaster. Gene Expr Patterns 2008; 8:523-7. [DOI: 10.1016/j.gep.2008.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 05/27/2008] [Accepted: 06/01/2008] [Indexed: 11/27/2022]
|
13
|
Hannenhalli S. Eukaryotic transcription factor binding sites--modeling and integrative search methods. Bioinformatics 2008; 24:1325-31. [PMID: 18426806 DOI: 10.1093/bioinformatics/btn198] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
A comprehensive knowledge of transcription factor binding sites (TFBS) is important for a mechanistic understanding of transcriptional regulation as well as for inferring gene regulatory networks. Because the DNA motif recognized by a transcription factor is typically short and degenerate, computational approaches for identifying binding sites based only on the sequence motif inevitably suffer from high error rates. Current state-of-the-art techniques for improving computational identification of binding sites can be broadly categorized into two classes: (1) approaches that aim to improve binding motif models by extracting maximal sequence information from experimentally determined binding sites and (2) approaches that supplement binding motif models with additional genomic or other attributes (such as evolutionary conservation). In this review we will discuss recent attempts to improve computational identification of TFBS through these two types of approaches and conclude with thoughts on future development.
Collapse
Affiliation(s)
- Sridhar Hannenhalli
- Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, USA.
| |
Collapse
|
14
|
Haecker A, Qi D, Lilja T, Moussian B, Andrioli LP, Luschnig S, Mannervik M. Drosophila brakeless interacts with atrophin and is required for tailless-mediated transcriptional repression in early embryos. PLoS Biol 2007; 5:e145. [PMID: 17503969 PMCID: PMC1868043 DOI: 10.1371/journal.pbio.0050145] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 03/26/2007] [Indexed: 02/07/2023] Open
Abstract
Complex gene expression patterns in animal development are generated by the interplay of transcriptional activators and repressors at cis-regulatory DNA modules (CRMs). How repressors work is not well understood, but often involves interactions with co-repressors. We isolated mutations in the brakeless gene in a screen for maternal factors affecting segmentation of the Drosophila embryo. Brakeless, also known as Scribbler, or Master of thickveins, is a nuclear protein of unknown function. In brakeless embryos, we noted an expanded expression pattern of the Krüppel (Kr) and knirps (kni) genes. We found that Tailless-mediated repression of kni expression is impaired in brakeless mutants. Tailless and Brakeless bind each other in vitro and interact genetically. Brakeless is recruited to the Kr and kni CRMs, and represses transcription when tethered to DNA. This suggests that Brakeless is a novel co-repressor. Orphan nuclear receptors of the Tailless type also interact with Atrophin co-repressors. We show that both Drosophila and human Brakeless and Atrophin interact in vitro, and propose that they act together as a co-repressor complex in many developmental contexts. We discuss the possibility that human Brakeless homologs may influence the toxicity of polyglutamine-expanded Atrophin-1, which causes the human neurodegenerative disease dentatorubral-pallidoluysian atrophy (DRPLA).
Collapse
Affiliation(s)
- Achim Haecker
- Developmental Biology, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dai Qi
- Developmental Biology, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Tobias Lilja
- Developmental Biology, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bernard Moussian
- Abteilung Genetik, Max-Planck Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Luiz Paulo Andrioli
- Department of Genetics and Evolution, University of Sao Paulo, Sao Paulo, Brazil
| | - Stefan Luschnig
- Abteilung Genetik, Max-Planck Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Mattias Mannervik
- Developmental Biology, Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
15
|
Choe CP, Brown SJ. Evolutionary flexibility of pair-rule patterning revealed by functional analysis of secondary pair-rule genes, paired and sloppy-paired in the short-germ insect, Tribolium castaneum. Dev Biol 2006; 302:281-94. [PMID: 17054935 PMCID: PMC1800430 DOI: 10.1016/j.ydbio.2006.09.037] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 09/07/2006] [Accepted: 09/20/2006] [Indexed: 11/29/2022]
Abstract
In the Drosophila segmentation hierarchy, periodic expression of pair-rule genes translates gradients of regional information from maternal and gap genes into the segmental expression of segment polarity genes. In Tribolium, homologs of almost all the eight canonical Drosophila pair-rule genes are expressed in pair-rule domains, but only five have pair-rule functions. even-skipped, runt and odd-skipped act as primary pair-rule genes, while the functions of paired (prd) and sloppy-paired (slp) are secondary. Since secondary pair-rule genes directly regulate segment polarity genes in Drosophila, we analyzed Tc-prd and Tc-slp to determine the extent to which this paradigm is conserved in Tribolium. We found that the role of prd is conserved between Drosophila and Tribolium; it is required in both insects to activate engrailed in odd-numbered parasegments and wingless (wg) in even-numbered parasegments. Similarly, slp is required to activate wg in alternate parasegments and to maintain the remaining wg stripes in both insects. However, the parasegmental register for Tc-slp is opposite that of Drosophila slp1. Thus, while prd is functionally conserved, the fact that the register of slp function has evolved differently in the lineages leading to Drosophila and Tribolium reveals an unprecedented flexibility in pair-rule patterning.
Collapse
Affiliation(s)
| | - Susan J Brown
- *Corresponding author: Susan J Brown, Division of Biology, Kansas State University, Manhattan, KS 66506, USA, , Phone: (785) 532-3935, Fax: (785) 532-6653
| |
Collapse
|
16
|
Choe CP, Miller SC, Brown SJ. A pair-rule gene circuit defines segments sequentially in the short-germ insect Tribolium castaneum. Proc Natl Acad Sci U S A 2006; 103:6560-4. [PMID: 16611732 PMCID: PMC1564201 DOI: 10.1073/pnas.0510440103] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Drosophila, a hierarchy of maternal, gap, pair-rule, and segment polarity gene interactions regulates virtually simultaneous blastoderm segmentation. For the last decade, studies have focused on revealing the extent to which Drosophila segmentation mechanisms are conserved in other arthropods where segments are added sequentially from anterior to posterior in a cellular environment. Despite our increased knowledge of individual segmentation genes, details of their interactions in non-Drosophilid insects are not well understood. We analyzed the Tribolium orthologs of Drosophila pair-rule genes, which display pair-rule expression patterns. Tribolium castaneum paired (Tc-prd) and sloppy-paired (Tc-slp) genes produced pair-rule phenotypes when their transcripts were severely reduced by RNA interference. In contrast, similar analysis of T. castaneum even-skipped (Tc-eve), runt (Tc-run), or odd-skipped (Tc-odd) genes produced severely truncated, almost completely asegmental phenotypes. Analysis of interactions between pair-rule components revealed that Tc-eve, Tc-run, and Tc-odd form a three-gene circuit to regulate one another as well as their downstream targets, Tc-prd and Tc-slp. The complement of primary pair-rule genes in Tribolium differs from Drosophila in that it includes Tc-odd but not Tc-hairy. This gene circuit defines segments sequentially in double segment periodicity. Furthermore, this single mechanism functions in the early blastoderm stage and subsequently during germ-band elongation. The periodicity of the Tribolium pair-rule gene interactions reveals components of the genetic hierarchy that are regulated in a repetitive circuit or clock-like mechanism. This pair-rule gene circuit provides insight into short-germ segmentation in Tribolium that may be more generally applicable to segmentation in other arthropods.
Collapse
Affiliation(s)
- Chong Pyo Choe
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | - Sherry C. Miller
- Division of Biology, Kansas State University, Manhattan, KS 66506
| | - Susan J. Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506
- *To whom correspondence should be addressed. E-mail:
| |
Collapse
|
17
|
Tsuzuki S, Sekiguchi S, Kamimura M, Kiuchi M, Hayakawa Y. A cytokine secreted from the suboesophageal body is essential for morphogenesis of the insect head. Mech Dev 2005; 122:189-97. [PMID: 15652706 DOI: 10.1016/j.mod.2004.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 10/09/2004] [Accepted: 10/09/2004] [Indexed: 12/01/2022]
Abstract
The suboesophageal body of insects was identified over a century ago in the silkworm embryo, but its biological function is still unknown. We discovered that this tissue is differentiated in the earliest embryonic stages of the cabbage armyworm and secretes the insect cytokine, growth-blocking peptide (GBP), transiently from 24 to 60 h after oviposition when gastrulation is in progress. Over-expression of GBP, achieved by microinjection of the GBP gene driven by a cytomegalovirus (CMV) constitutive promoter, resulted in complex deformities of the procephalon (embryonic head). Severe abnormal phenotypes of the head structure were produced by silencing the GBP expression in the embryo by treating with GBP double-stranded RNA: the procephalon-containing optic lobes diminished and completely separated into bilateral halves. This indicates that GBP secreted from the suboesophageal body plays an essential role in the formation of the procephalic domain during early embryogenesis. The cytokine-induced fusion of bilateral procephalic lobes is thought to be evolutionarily conserved at least in insects, because of the widespread occurrence of the suboesophageal body in insect embryos.
Collapse
Affiliation(s)
- Seiji Tsuzuki
- Department of Applied Biological Science, Faculty of Agriculture, Saga University, Honjo-1, Saga 840-8502, Japan
| | | | | | | | | |
Collapse
|
18
|
Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A 2002; 99:757-62. [PMID: 11805330 PMCID: PMC117378 DOI: 10.1073/pnas.231608898] [Citation(s) in RCA: 435] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A major challenge in interpreting genome sequences is understanding how the genome encodes the information that specifies when and where a gene will be expressed. The first step in this process is the identification of regions of the genome that contain regulatory information. In higher eukaryotes, this cis-regulatory information is organized into modular units [cis-regulatory modules (CRMs)] of a few hundred base pairs. A common feature of these cis-regulatory modules is the presence of multiple binding sites for multiple transcription factors. Here, we evaluate the extent to which the tendency for transcription factor binding sites to be clustered can be used as the basis for the computational identification of cis-regulatory modules. By using published DNA binding specificity data for five transcription factors active in the early Drosophila embryo, we identified genomic regions containing unusually high concentrations of predicted binding sites for these factors. A significant fraction of these binding site clusters overlap known CRMs that are regulated by these factors. In addition, many of the remaining clusters are adjacent to genes expressed in a pattern characteristic of genes regulated by these factors. We tested one of the newly identified clusters, mapping upstream of the gap gene giant (gt), and show that it acts as an enhancer that recapitulates the posterior expression pattern of gt.
Collapse
Affiliation(s)
- Benjamin P Berman
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
Theoretical views on morphogen gradients have altered dramatically with the massive arrival of molecular data regarding the establishment of graded concentrations in the embryo, and the finely tuned reading by cells of these concentration levels. I review these new perspectives, and analyze in detail two models, one pertaining to the propagation of activin in Xenopus embryos, the other to the interpretation of retinoic acid levels into transcription patterns by nuclear receptors. The unifying threads that seem to emerge are the combinatorial uses of receptor subtypes, cooperativity and autocatalysis (positive feedback) to achieve specificity and reliability.
Collapse
Affiliation(s)
- M Kerszberg
- Neurobiologie Mole@a3culaire, CNRS UA D1284, Institut Pasteur, 25, rue du Docteur Roux, Paris, Cedex 15, F-75724, France
| |
Collapse
|
20
|
Carrera P, Abrell S, Kerber B, Walldorf U, Preiss A, Hoch M, Jäckle H. A modifier screen in the eye reveals control genes for Krüppel activity in the Drosophila embryo. Proc Natl Acad Sci U S A 1998; 95:10779-84. [PMID: 9724781 PMCID: PMC27972 DOI: 10.1073/pnas.95.18.10779] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/1998] [Indexed: 11/18/2022] Open
Abstract
Irregular facets (If) is a dominant mutation of Drosophila that results in small eyes with fused ommatidia. Previous results showed that the gene Krüppel (Kr), which is best known for its early segmentation function, is expressed ectopically in If mutant eye discs. However, it was not known whether ectopic Kr activity is either the cause or the result of the If mutation. Here, we show that If is a gain-of-function allele of Kr. We then used the If mutation in a genetic screen to identify dominant enhancers and suppressors of Kr activity on the third chromosome. Of 30 identified Kr-interacting loci, two were cloned, and we examined whether they also represent components of a natural Kr-dependent developmental pathway of the embryo. We show that the two genes, eyelid (eld) and extramacrochaetae (emc), which encode a Bright family-type DNA binding protein and a helix-loop-helix factor, respectively, are necessary to achieve the singling-out of a unique Kr-expressing cell during the development of the Malpighian tubules, the excretory organs of the fly. The results indicate that the Kr gain-of-function mutation If provides a tool to identify genes that are active during eye development and that a number of them function also in the control of Kr-dependent developmental processes.
Collapse
Affiliation(s)
- P Carrera
- Abteilung Molekulare Entwicklungsbiologie, Max-Planck-Institut für biophysikalische Chemie, Am Fassberg, D-37077 Göttingen, Germany
| | | | | | | | | | | | | |
Collapse
|