1
|
Kang CK, Kim AR. Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants. iScience 2024; 27:108747. [PMID: 38222110 PMCID: PMC10784702 DOI: 10.1016/j.isci.2023.108747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/29/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024] Open
Abstract
Massively parallel reporter assay measures transcriptional activities of various cis-regulatory modules (CRMs) in a single experiment. We developed a thermodynamic computational model framework that calculates quantitative levels of gene expression directly from regulatory DNA sequences. Using the framework, we investigated the molecular mechanisms of cis-regulatory mutations of a synthetic enhancer that cause abnormal gene expression. We found that, in a human cell line, competitive binding between family transcription factors (TFs) with slightly different binding preferences significantly increases the accuracy of recapitulating the transcriptional effects of thousands of single- or multi-mutations. We also discovered that even if various harmful mutations occurred in an activator binding site, CRM could stably maintain or even increase gene expression through a certain form of competitive binding between family TFs. These findings enhance understanding the effect of SNPs and indels on CRMs and would help building robust custom-designed CRMs for biologics production and gene therapy.
Collapse
Affiliation(s)
- Chan-Koo Kang
- School of Life Science, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Department of Advanced Convergence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
| | - Ah-Ram Kim
- School of Life Science, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Department of Advanced Convergence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Applied Artificial Intelligence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
| |
Collapse
|
2
|
Thompson KD, Suber W, Nicholas R, Arnosti DN. Long-range repression by ecdysone receptor on complex enhancers of the insulin receptor gene. Fly (Austin) 2023; 17:2242238. [PMID: 37621079 PMCID: PMC10461493 DOI: 10.1080/19336934.2023.2242238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/26/2023] Open
Abstract
The insulin signalling pathway is evolutionarily conserved throughout metazoans, playing key roles in development, growth, and metabolism. Misregulation of this pathway is associated with a multitude of disease states including diabetes, cancer, and neurodegeneration. The human insulin receptor gene (INSR) is widely expressed throughout development and was previously described as a 'housekeeping' gene. Yet, there is abundant evidence that this gene is expressed in a cell-type specific manner, with dynamic regulation in response to environmental signals. The Drosophila insulin-like receptor gene (InR) is homologous to the human INSR gene and was previously shown to be regulated by multiple transcriptional elements located primarily within the introns of the gene. These elements were roughly defined in ~1.5 kbp segments, but we lack an understanding of the potential detailed mechanisms of their regulation. We characterized the substructure of these cis-regulatory elements in Drosophila S2 cells, focusing on regulation through the ecdysone receptor (EcR) and the dFOXO transcription factor. By identifying specific locations of activators and repressors within 300 bp subelements, we show that some previously identified enhancers consist of relatively compact clusters of activators, while others have a distributed architecture not amenable to further reduction. In addition, these assays uncovered a long-range repressive action of unliganded EcR. The complex transcriptional circuitry likely endows InR with a highly flexible and tissue-specific response to tune insulin signalling. Further studies will provide insights to demonstrate the impact of natural variation in this gene's regulation, applicable to human genetic studies.
Collapse
Affiliation(s)
- Katie D. Thompson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Will Suber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Rachel Nicholas
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - David N. Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
3
|
Raicu AM, Castanheira P, Arnosti DN. Retinoblastoma protein activity revealed by CRISPRi study of divergent Rbf1 and Rbf2 paralogs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541454. [PMID: 37293052 PMCID: PMC10245722 DOI: 10.1101/2023.05.19.541454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Retinoblastoma tumor suppressor proteins regulate the key transition from G1 to S phase of the cell cycle. The mammalian Rb family comprises Rb, p107, and p130, with overlapping and unique roles in gene regulation. Drosophila experienced an independent gene duplication event, leading to the Rbf1 and Rbf2 paralogs. To uncover the significance of paralogy in the Rb family, we used CRISPRi. We engineered dCas9 fusions to Rbf1 and Rbf2, and deployed them to gene promoters in developing Drosophila tissue to study their relative impacts on gene expression. On some genes, both Rbf1 and Rbf2 mediate potent repression, in a highly distance-dependent manner. In other cases, the two proteins have different effects on phenotype and gene expression, indicating different functional potential. In a direct comparison of Rb activity on endogenous genes and transiently transfected reporters, we found that only qualitative, but not key quantitative aspects of repression were conserved, indicating that the native chromatin environment generates context-specific effects of Rb activity. Our study uncovers the complexity of Rb-mediated transcriptional regulation in a living organism, which is clearly impacted by the different promoter landscapes and the evolution of the Rb proteins themselves.
Collapse
Affiliation(s)
- Ana-Maria Raicu
- Cell and Molecular Biology Program, Michigan State University, East Lansing, MI
| | - Patricia Castanheira
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| |
Collapse
|
4
|
Banisch TU, Slaidina M, Gupta S, Ho M, Gilboa L, Lehmann R. A transitory signaling center controls timing of primordial germ cell differentiation. Dev Cell 2021; 56:1742-1755.e4. [PMID: 34081907 PMCID: PMC8330407 DOI: 10.1016/j.devcel.2021.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/07/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
Organogenesis requires exquisite spatiotemporal coordination of cell morphogenesis, migration, proliferation, and differentiation of multiple cell types. For gonads, this involves complex interactions between somatic and germline tissues. During Drosophila ovary morphogenesis, primordial germ cells (PGCs) either are sequestered in stem cell niches and are maintained in an undifferentiated germline stem cell state or transition directly toward differentiation. Here, we identify a mechanism that links hormonal triggers of somatic tissue morphogenesis with PGC differentiation. An early ecdysone pulse initiates somatic swarm cell (SwC) migration, positioning these cells close to PGCs. A second hormone peak activates Torso-like signal in SwCs, which stimulates the Torso receptor tyrosine kinase (RTK) signaling pathway in PGCs promoting their differentiation by de-repression of the differentiation gene, bag of marbles. Thus, systemic temporal cues generate a transitory signaling center that coordinates ovarian morphogenesis with stem cell self-renewal and differentiation programs, highlighting a more general role for such centers in reproductive and developmental biology.
Collapse
Affiliation(s)
- Torsten U Banisch
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA.
| | - Maija Slaidina
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Selena Gupta
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Megan Ho
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Lilach Gilboa
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ruth Lehmann
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
5
|
Abstract
Key discoveries in Drosophila have shaped our understanding of cellular "enhancers." With a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory elements, whose actions are critical for the complex spatial/temporal transcriptional regulation of gene expression in metazoa. The powerful combination of genetics, molecular biology, and genomics available in Drosophila has provided an arena in which the developmental role of enhancers can be explored. Enhancers are characterized by diverse low- or high-throughput assays, which are challenging to interpret, as not all of these methods of identifying enhancers produce concordant results. As a model metazoan, the fly offers important advantages to comprehensive analysis of the central functions that enhancers play in gene expression, and their critical role in mediating the production of phenotypes from genotype and environmental inputs. A major challenge moving forward will be obtaining a quantitative understanding of how these cis-regulatory elements operate in development and disease.
Collapse
Affiliation(s)
- Stephen Small
- Department of Biology, Developmental Systems Training Program, New York University, 10003 and
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| |
Collapse
|
6
|
Yokoshi M, Segawa K, Fukaya T. Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication. Mol Cell 2020; 78:224-235.e5. [DOI: 10.1016/j.molcel.2020.02.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/19/2019] [Accepted: 02/05/2020] [Indexed: 12/21/2022]
|
7
|
Gisselbrecht SS, Palagi A, Kurland JV, Rogers JM, Ozadam H, Zhan Y, Dekker J, Bulyk ML. Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts. Mol Cell 2019; 77:324-337.e8. [PMID: 31704182 DOI: 10.1016/j.molcel.2019.10.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/15/2019] [Accepted: 10/01/2019] [Indexed: 12/26/2022]
Abstract
A major challenge in biology is to understand how complex gene expression patterns are encoded in the genome. While transcriptional enhancers have been studied extensively, few transcriptional silencers have been identified, and they remain poorly understood. Here, we used a novel strategy to screen hundreds of sequences for tissue-specific silencer activity in whole Drosophila embryos. Almost all of the transcriptional silencers that we identified were also active enhancers in other cellular contexts. These elements are bound by more transcription factors than non-silencers. A subset of these silencers forms long-range contacts with promoters. Deletion of a silencer caused derepression of its target gene. Our results challenge the common practice of treating enhancers and silencers as separate classes of regulatory elements and suggest the possibility that thousands or more bifunctional CRMs remain to be discovered in Drosophila and 104-105 in humans.
Collapse
Affiliation(s)
- Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Palagi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Doctoral School of Life and Health Sciences, University of Nice Sophia Antipolis, 06560 Valbonne, France
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
8
|
Barr K, Reinitz J, Radulescu O. An in silico analysis of robust but fragile gene regulation links enhancer length to robustness. PLoS Comput Biol 2019; 15:e1007497. [PMID: 31730659 PMCID: PMC6881076 DOI: 10.1371/journal.pcbi.1007497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/27/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Organisms must ensure that expression of genes is directed to the appropriate tissues at the correct times, while simultaneously ensuring that these gene regulatory systems are robust to perturbation. This idea is captured by a mathematical concept called r-robustness, which says that a system is robust to a perturbation in up to r - 1 randomly chosen parameters. r-robustness implies that the biological system has a small number of sensitive parameters and that this number can be used as a robustness measure. In this work we use this idea to investigate the robustness of gene regulation using a sequence level model of the Drosophila melanogaster gene even-skipped. We consider robustness with respect to mutations of the enhancer sequence and with respect to changes of the transcription factor concentrations. We find that gene regulation is r-robust with respect to mutations in the enhancer sequence and identify a number of sensitive nucleotides. In both natural and in silico predicted enhancers, the number of nucleotides that are sensitive to mutation correlates negatively with the length of the sequence, meaning that longer sequences are more robust. The exact degree of robustness obtained is dependent not only on DNA sequence, but also on the local concentration of regulatory factors. We find that gene regulation can be remarkably sensitive to changes in transcription factor concentrations at the boundaries of expression features, while it is robust to perturbation elsewhere.
Collapse
Affiliation(s)
- Kenneth Barr
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - John Reinitz
- Departments of Statistics, Ecology & Evolution, Molecular Genetics & Cell Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Ovidiu Radulescu
- LPHI UMR CNRS 5235, University of Montpellier, Montpellier, France
| |
Collapse
|
9
|
Grover S, Williams ME, Kaiser R, Hughes JT, Gresham L, Rebeiz M, Williams TM. Augmentation of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait. Dev Biol 2018; 441:159-175. [PMID: 29981311 PMCID: PMC6075670 DOI: 10.1016/j.ydbio.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 11/16/2022]
Abstract
A challenge for evolutionary research is to uncover how new morphological traits evolve the coordinated spatial and temporal expression patterns of genes that govern their formation during development. Detailed studies are often limited to characterizing how one or a few genes contributed to a trait's emergence, and thus our knowledge of how entire GRNs evolve their coordinated expression of each gene remains unresolved. The melanic color patterns decorating the male abdominal tergites of Drosophila (D.) melanogaster evolved in part by novel expression patterns for genes acting at the terminus of a pigment metabolic pathway, driven by cis-regulatory elements (CREs) with distinct mechanisms of Hox regulation. Here, we examined the expression and evolutionary histories of two important enzymes in this pathway, encoded by the pale and Ddc genes. We found that while both genes exhibit dynamic patterns of expression, a robust pattern of Ddc expression specifically evolved in the lineage of fruit flies with pronounced melanic abdomens. Derived Ddc expression requires the activity of a CRE previously shown to activate expression in response to epidermal wounding. We show that a binding site for the Grainy head transcription factor that promotes the ancestral wound healing function of this CRE is also required for abdominal activity. Together with previous findings in this system, our work shows how the GRN for a novel trait emerged by assembling unique yet similarly functioning CREs from heterogeneous starting points.
Collapse
Affiliation(s)
- Sumant Grover
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Melissa E Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Rebecca Kaiser
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Jesse T Hughes
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Lauren Gresham
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Thomas M Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA; The Integrative Science and Engineering Center, University of Dayton, 300 College Park, Dayton, OH 45469, USA.
| |
Collapse
|
10
|
Samee MAH, Lydiard-Martin T, Biette KM, Vincent BJ, Bragdon MD, Eckenrode KB, Wunderlich Z, Estrada J, Sinha S, DePace AH. Quantitative Measurement and Thermodynamic Modeling of Fused Enhancers Support a Two-Tiered Mechanism for Interpreting Regulatory DNA. Cell Rep 2018; 21:236-245. [PMID: 28978476 DOI: 10.1016/j.celrep.2017.09.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/30/2017] [Accepted: 09/08/2017] [Indexed: 02/07/2023] Open
Abstract
Computational models of enhancer function generally assume that transcription factors (TFs) exert their regulatory effects independently, modeling an enhancer as a "bag of sites." These models fail on endogenous loci that harbor multiple enhancers, and a "two-tier" model appears better suited: in each enhancer TFs work independently, and the total expression is a weighted sum of their expression readouts. Here, we test these two opposing views on how cis-regulatory information is integrated. We fused two Drosophila blastoderm enhancers, measured their readouts, and applied the above two models to these data. The two-tier mechanism better fits these readouts, suggesting that these fused enhancers comprise multiple independent modules, despite having sequence characteristics typical of single enhancers. We show that short-range TF-TF interactions are not sufficient to designate such modules, suggesting unknown underlying mechanisms. Our results underscore that mechanisms of how modules are defined and how their outputs are combined remain to be elucidated.
Collapse
Affiliation(s)
- Md Abul Hassan Samee
- Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tara Lydiard-Martin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kelly M Biette
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ben J Vincent
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Meghan D Bragdon
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kelly B Eckenrode
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zeba Wunderlich
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Javier Estrada
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
11
|
Barr KA, Martinez C, Moran JR, Kim AR, Ramos AF, Reinitz J. Synthetic enhancer design by in silico compensatory evolution reveals flexibility and constraint in cis-regulation. BMC SYSTEMS BIOLOGY 2017; 11:116. [PMID: 29187214 PMCID: PMC5708098 DOI: 10.1186/s12918-017-0485-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/09/2017] [Indexed: 11/12/2022]
Abstract
BACKGROUND Models that incorporate specific chemical mechanisms have been successful in describing the activity of Drosophila developmental enhancers as a function of underlying transcription factor binding motifs. Despite this, the minimum set of mechanisms required to reconstruct an enhancer from its constituent parts is not known. Synthetic biology offers the potential to test the sufficiency of known mechanisms to describe the activity of enhancers, as well as to uncover constraints on the number, order, and spacing of motifs. RESULTS Using a functional model and in silico compensatory evolution, we generated putative synthetic even-skipped stripe 2 enhancers with varying degrees of similarity to the natural enhancer. These elements represent the evolutionary trajectories of the natural stripe 2 enhancer towards two synthetic enhancers designed ab initio. In the first trajectory, spatially regulated expression was maintained, even after more than a third of binding sites were lost. In the second, sequences with high similarity to the natural element did not drive expression, but a highly diverged sequence about half the length of the minimal stripe 2 enhancer drove ten times greater expression. Additionally, homotypic clusters of Zelda or Stat92E motifs, but not Bicoid, drove expression in developing embryos. CONCLUSIONS Here, we present a functional model of gene regulation to test the degree to which the known transcription factors and their interactions explain the activity of the Drosophila even-skipped stripe 2 enhancer. Initial success in the first trajectory showed that the gene regulation model explains much of the function of the stripe 2 enhancer. Cases where expression deviated from prediction indicates that undescribed factors likely act to modulate expression. We also showed that activation driven Bicoid and Hunchback is highly sensitive to spatial organization of binding motifs. In contrast, Zelda and Stat92E drive expression from simple homotypic clusters, suggesting that activation driven by these factors is less constrained. Collectively, the 40 sequences generated in this work provides a powerful training set for building future models of gene regulation.
Collapse
Affiliation(s)
- Kenneth A Barr
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Zoology 111, 1101 E 57th St, Chicago, 60637, Illinois, USA.
- Department of Ecology and Evolution, The University of Chicago, Chicago, 60637, Illinois, USA.
| | - Carlos Martinez
- Department Biochemistry and Molecular Genetics, Northwestern University, Chicago, 60611, Illinois, USA
| | - Jennifer R Moran
- Department Human Genetics, The University of Chicago, Chicago, 60637, Illinois, USA
- Institute for Genomics & Systems Biology, The University of Chicago, Chicago, 60637, Illinois, USA
| | - Ah-Ram Kim
- School of Life Science, Handong Global University, Pohang, 37554, Gyeongbuk, South Korea
| | - Alexandre F Ramos
- Departamento de Radiologia - Faculdade de Medicina, Universidade de São Paulo & Instituto do Câncer do Estado de São Paulo, São Paulo, SP CEP, 05403-911, Brazil
- Escola de Artes, Ciências e Humanidades & Núcleo de Estudos Interdisciplinares em Sistemas Complexos, Universidade de São Paulo, Av. Arlindo Béttio, São Paulo, 1000 CEP 03828-000, SP, Brazil
| | - John Reinitz
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Zoology 111, 1101 E 57th St, Chicago, 60637, Illinois, USA
- Department of Ecology and Evolution, The University of Chicago, Chicago, 60637, Illinois, USA
- Institute for Genomics & Systems Biology, The University of Chicago, Chicago, 60637, Illinois, USA
- Department Statistics, The University of Chicago, 5747 S. Ellis Avenue Jones 312, Chicago, 60637, IL, USA
| |
Collapse
|
12
|
A Looping-Based Model for Quenching Repression. PLoS Comput Biol 2017; 13:e1005337. [PMID: 28085884 PMCID: PMC5279812 DOI: 10.1371/journal.pcbi.1005337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/30/2017] [Accepted: 12/29/2016] [Indexed: 12/18/2022] Open
Abstract
We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain’s termini reduces the probability of looping, even for chains much longer than the protrusion–chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. The reduced probability of looping can be explained via an eclipse-like model, which provides a novel inhibitory mechanism. We test the eclipse model on two possible transcription-factor occupancy states of the D. melanogastereve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns. Biological regulation-at-a-distance, whereby a transcription factor (TF) is able to generate susbstantial regulatory effects on gene expression even though it may be bound a large distance away from its target (500 bp–1 Mbp), is only partially understood. Using a biophysical model and a computer simulation that take dsDNA and TF volumes into account, we identify a downregulatory mechanism which functions at large distances, whereby a TF bound within ∼ 150 bp from an activator decreases the probability of looping-based interaction between the activator and the distant core promoter. This “eclipse” mechanism provides insight into the question of how enhancer architecture dictates gene expression.
Collapse
|
13
|
Crocker J, Tsai A, Stern DL. A Fully Synthetic Transcriptional Platform for a Multicellular Eukaryote. Cell Rep 2017; 18:287-296. [DOI: 10.1016/j.celrep.2016.12.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 12/07/2016] [Indexed: 01/12/2023] Open
|
14
|
Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J. Drosophila poised enhancers are generated during tissue patterning with the help of repression. Genome Res 2016; 27:64-74. [PMID: 27979994 PMCID: PMC5204345 DOI: 10.1101/gr.209486.116] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022]
Abstract
Histone modifications are frequently used as markers for enhancer states, but how to interpret enhancer states in the context of embryonic development is not clear. The poised enhancer signature, involving H3K4me1 and low levels of H3K27ac, has been reported to mark inactive enhancers that are poised for future activation. However, future activation is not always observed, and alternative reasons for the widespread occurrence of this enhancer signature have not been investigated. By analyzing enhancers during dorsal-ventral (DV) axis formation in the Drosophila embryo, we find that the poised enhancer signature is specifically generated during patterning in the tissue where the enhancers are not induced, including at enhancers that are known to be repressed by a transcriptional repressor. These results suggest that, rather than serving exclusively as an intermediate step before future activation, the poised enhancer state may be a mark for spatial regulation during tissue patterning. We discuss the possibility that the poised enhancer state is more generally the result of repression by transcriptional repressors.
Collapse
Affiliation(s)
- Nina Koenecke
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Qiye He
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Samuel Meier
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,University of Kansas Medical Center, Department of Pathology, Kansas City, Kansas 66160, USA
| |
Collapse
|
15
|
Esposito E, Lim B, Guessous G, Falahati H, Levine M. Mitosis-associated repression in development. Genes Dev 2016; 30:1503-8. [PMID: 27401553 PMCID: PMC4949323 DOI: 10.1101/gad.281188.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/13/2016] [Indexed: 11/25/2022]
Abstract
Transcriptional repression is a pervasive feature of animal development. Here, we employ live-imaging methods to visualize the Snail repressor, which establishes the boundary between the presumptive mesoderm and neurogenic ectoderm of early Drosophila embryos. Snail target enhancers were attached to an MS2 reporter gene, permitting detection of nascent transcripts in living embryos. The transgenes exhibit initially broad patterns of transcription but are refined by repression in the mesoderm following mitosis. These observations reveal a correlation between mitotic silencing and Snail repression. We propose that mitosis and other inherent discontinuities in transcription boost the activities of sequence-specific repressors, such as Snail.
Collapse
Affiliation(s)
- Emilia Esposito
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, University of California at Berkeley, Berkeley, California 94720, USA
| | - Bomyi Lim
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Ghita Guessous
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - Hanieh Falahati
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
16
|
El-Sherif E, Levine M. Shadow Enhancers Mediate Dynamic Shifts of Gap Gene Expression in the Drosophila Embryo. Curr Biol 2016; 26:1164-9. [PMID: 27112292 DOI: 10.1016/j.cub.2016.02.054] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 02/16/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022]
Abstract
Drosophila patterning genes often contain pairs of primary and shadow enhancers that possess overlapping activities [1-5]. It has been suggested that this regulatory "redundancy" helps ensure reliable activation of gene expression under stressful conditions such as increases in temperature [4, 5]. There is also evidence that shadow enhancers help produce sharp on/off boundaries of gene expression in response to small changes in the levels of regulatory factors, such as the maternal Bicoid gradient [6, 7]. Here, we use live-imaging methods to visualize the temporal dynamics of the gap genes Kruppel and knirps, which are essential for the patterning of the thorax and abdomen, respectively [8, 9]. Previous analyses of fixed embryos suggested anterior shifts of the Kruppel and knirps expression patterns [10]. Here, we use computational visualization methods to reveal the precise temporal dynamics of these shifts and further suggest that shadow enhancers are crucial for this process. We discuss potential mechanisms for enhancer dominance, whereby one enhancer represses the other to foster temporal dynamics.
Collapse
Affiliation(s)
- Ezzat El-Sherif
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Levine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
17
|
Bertolino E, Reinitz J, Manu. The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Dev Biol 2016; 413:128-44. [PMID: 26945717 DOI: 10.1016/j.ydbio.2016.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 01/13/2016] [Accepted: 02/15/2016] [Indexed: 11/25/2022]
Abstract
C/EBPα plays an instructive role in the macrophage-neutrophil cell-fate decision and its expression is necessary for neutrophil development. How Cebpa itself is regulated in the myeloid lineage is not known. We decoded the cis-regulatory logic of Cebpa, and two other myeloid transcription factors, Egr1 and Egr2, using a combined experimental-computational approach. With a reporter design capable of detecting both distal enhancers and silencers, we analyzed 46 putative cis-regulatory modules (CRMs) in cells representing myeloid progenitors, and derived early macrophages or neutrophils. In addition to novel enhancers, this analysis revealed a surprisingly large number of silencers. We determined the regulatory roles of 15 potential transcriptional regulators by testing 32,768 alternative sequence-based transcriptional models against CRM activity data. This comprehensive analysis allowed us to infer the cis-regulatory logic for most of the CRMs. Silencer-mediated repression of Cebpa was found to be effected mainly by TFs expressed in non-myeloid lineages, highlighting a previously unappreciated contribution of long-distance silencing to hematopoietic lineage resolution. The repression of Cebpa by multiple factors expressed in alternative lineages suggests that hematopoietic genes are organized into densely interconnected repressive networks instead of hierarchies of mutually repressive pairs of pivotal TFs. More generally, our results demonstrate that de novo cis-regulatory dissection is feasible on a large scale with the aid of transcriptional modeling. Current address: Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
Collapse
Affiliation(s)
- Eric Bertolino
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA.
| | - John Reinitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Statistics, The University of Chicago, Chicago, IL 60637, USA; Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Manu
- Department of Ecology and Evolution and Institute of Genomics and Systems Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Biology, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, ND 58202-9019, USA.
| |
Collapse
|
18
|
Hoermann A, Cicin-Sain D, Jaeger J. A quantitative validated model reveals two phases of transcriptional regulation for the gap gene giant in Drosophila. Dev Biol 2016; 411:325-338. [DOI: 10.1016/j.ydbio.2016.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/22/2015] [Accepted: 01/08/2016] [Indexed: 01/05/2023]
|
19
|
Brunwasser-Meirom M, Pollak Y, Goldberg S, Levy L, Atar O, Amit R. Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression. Nat Commun 2016; 7:10407. [PMID: 26832446 PMCID: PMC4740811 DOI: 10.1038/ncomms10407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 12/02/2015] [Indexed: 01/20/2023] Open
Abstract
We explore a model for 'quenching-like' repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model's predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10-11 bp insertions or deletions (INDELs) and sensitive to 5-6 bp INDELs. We test this prediction on 61 σ(54)-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers' sequences to the DNA's helical repeat.
Collapse
Affiliation(s)
- Michal Brunwasser-Meirom
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Yaroslav Pollak
- Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Lior Levy
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Orna Atar
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion—Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology, Haifa 32000, Israel
| |
Collapse
|
20
|
Abstract
The Drosophila blastoderm and the vertebrate neural tube are archetypal examples of morphogen-patterned tissues that create precise spatial patterns of different cell types. In both tissues, pattern formation is dependent on molecular gradients that emanate from opposite poles. Despite distinct evolutionary origins and differences in time scales, cell biology and molecular players, both tissues exhibit striking similarities in the regulatory systems that establish gene expression patterns that foreshadow the arrangement of cell types. First, signaling gradients establish initial conditions that polarize the tissue, but there is no strict correspondence between specific morphogen thresholds and boundary positions. Second, gradients initiate transcriptional networks that integrate broadly distributed activators and localized repressors to generate patterns of gene expression. Third, the correct positioning of boundaries depends on the temporal and spatial dynamics of the transcriptional networks. These similarities reveal design principles that are likely to be broadly applicable to morphogen-patterned tissues.
Collapse
Affiliation(s)
- James Briscoe
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stephen Small
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
| |
Collapse
|
21
|
Kok K, Ay A, Li LM, Arnosti DN. Genome-wide errant targeting by Hairy. eLife 2015; 4. [PMID: 26305409 PMCID: PMC4547095 DOI: 10.7554/elife.06394] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/24/2015] [Indexed: 01/08/2023] Open
Abstract
Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.
Collapse
Affiliation(s)
- Kurtulus Kok
- Genetics Program, Michigan State University, East Lansing, United States
| | - Ahmet Ay
- Departments of Biology and Mathematics, Colgate University, Hamilton, United States
| | - Li M Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - David N Arnosti
- Genetics Program, Michigan State University, East Lansing, United States
| |
Collapse
|
22
|
Holloway DM, Spirov AV. Mid-embryo patterning and precision in Drosophila segmentation: Krüppel dual regulation of hunchback. PLoS One 2015; 10:e0118450. [PMID: 25793381 PMCID: PMC4368514 DOI: 10.1371/journal.pone.0118450] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 12/15/2014] [Indexed: 12/26/2022] Open
Abstract
In early development, genes are expressed in spatial patterns which later define cellular identities and tissue locations. The mechanisms of such pattern formation have been studied extensively in early Drosophila (fruit fly) embryos. The gap gene hunchback (hb) is one of the earliest genes to be expressed in anterior-posterior (AP) body segmentation. As a transcriptional regulator for a number of downstream genes, the spatial precision of hb expression can have significant effects in the development of the body plan. To investigate the factors contributing to hb precision, we used fine spatial and temporal resolution data to develop a quantitative model for the regulation of hb expression in the mid-embryo. In particular, modelling hb pattern refinement in mid nuclear cleavage cycle 14 (NC14) reveals some of the regulatory contributions of simultaneously-expressed gap genes. Matching the model to recent data from wild-type (WT) embryos and mutants of the gap gene Krüppel (Kr) indicates that a mid-embryo Hb concentration peak important in thoracic development (at parasegment 4, PS4) is regulated in a dual manner by Kr, with low Kr concentration activating hb and high Kr concentration repressing hb. The processes of gene expression (transcription, translation, transport) are intrinsically random. We used stochastic simulations to characterize the noise generated in hb expression. We find that Kr regulation can limit the positional variability of the Hb mid-embryo border. This has been recently corroborated in experimental comparisons of WT and Kr- mutant embryos. Further, Kr regulation can decrease uncertainty in mid-embryo hb expression (i.e. contribute to a smooth Hb boundary) and decrease between-copy transcriptional variability within nuclei. Since many tissue boundaries are first established by interactions between neighbouring gene expression domains, these properties of Hb-Kr dynamics to diminish the effects of intrinsic expression noise may represent a general mechanism contributing to robustness in early development.
Collapse
Affiliation(s)
- David M. Holloway
- Mathematics Department, British Columbia Institute of Technology, Burnaby, B.C., V5G 3H2, Canada
- * E-mail:
| | - Alexander V. Spirov
- Computer Science, and Center of Excellence in Wireless and Information Technology, State University of New York, Stony Brook, Stony Brook, New York, United States of America
- The Sechenov Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia
| |
Collapse
|
23
|
Kearns NA, Pham H, Tabak B, Genga RM, Silverstein NJ, Garber M, Maehr R. Functional annotation of native enhancers with a Cas9-histone demethylase fusion. Nat Methods 2015; 12:401-403. [PMID: 25775043 PMCID: PMC4414811 DOI: 10.1038/nmeth.3325] [Citation(s) in RCA: 471] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/26/2015] [Indexed: 02/06/2023]
Abstract
Understanding of mammalian enhancer function is limited by the lack of a technology to rapidly and thoroughly test their cell type-specific function. Here, we use a nuclease-deficient (d)Cas9 histone demethylase fusion to functionally characterize previously described and novel enhancer elements for their roles in the embryonic stem cell state. Further, we distinguish the mechanism of action of dCas9-LSD1 at enhancers from previous dCas9-effectors.
Collapse
Affiliation(s)
- Nicola A Kearns
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Hannah Pham
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Barbara Tabak
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ryan M Genga
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Noah J Silverstein
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - René Maehr
- Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| |
Collapse
|
24
|
Abstract
BACKGROUND The detailed analysis of transcriptional regulation is crucially important for understanding biological processes. The gap gene network in Drosophila attracts large interest among researches studying mechanisms of transcriptional regulation. It implements the most upstream regulatory layer of the segmentation gene network. The knowledge of molecular mechanisms involved in gap gene regulation is far less complete than that of genetics of the system. Mathematical modeling goes beyond insights gained by genetics and molecular approaches. It allows us to reconstruct wild-type gene expression patterns in silico, infer underlying regulatory mechanism and prove its sufficiency. RESULTS We developed a new model that provides a dynamical description of gap gene regulatory systems, using detailed DNA-based information, as well as spatial transcription factor concentration data at varying time points. We showed that this model correctly reproduces gap gene expression patterns in wild type embryos and is able to predict gap expression patterns in Kr mutants and four reporter constructs. We used four-fold cross validation test and fitting to random dataset to validate the model and proof its sufficiency in data description. The identifiability analysis showed that most model parameters are well identifiable. We reconstructed the gap gene network topology and studied the impact of individual transcription factor binding sites on the model output. We measured this impact by calculating the site regulatory weight as a normalized difference between the residual sum of squares error for the set of all annotated sites and for the set with the site of interest excluded. CONCLUSIONS The reconstructed topology of the gap gene network is in agreement with previous modeling results and data from literature. We showed that 1) the regulatory weights of transcription factor binding sites show very weak correlation with their PWM score; 2) sites with low regulatory weight are important for the model output; 3) functional important sites are not exclusively located in cis-regulatory elements, but are rather dispersed through regulatory region. It is of importance that some of the sites with high functional impact in hb, Kr and kni regulatory regions coincide with strong sites annotated and verified in Dnase I footprint assays.
Collapse
Affiliation(s)
- Konstantin Kozlov
- St.Petersburg State Polytechnical University, Polytekhnicheskaya 29, 195251 St.Petersburg, Russia
| | - Vitaly Gursky
- Ioffe Physical-Technical Institute, RAS, Polytekhnicheskaya 26, 194021 St.Petersburg, Russia
| | - Ivan Kulakovskiy
- Engelhardt Institute of Molecular Biology, RAS, Vavilov 32, 119991 Moscow, Russia
| | - Maria Samsonova
- St.Petersburg State Polytechnical University, Polytekhnicheskaya 29, 195251 St.Petersburg, Russia
| |
Collapse
|
25
|
Llamusí B, Muñoz-Soriano V, Paricio N, Artero R. The use of whole-mount in situ hybridization to illustrate gene expression regulation. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 42:339-347. [PMID: 24979316 DOI: 10.1002/bmb.20807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 06/03/2023]
Abstract
In situ hybridization is a widely used technique for studying gene expression. Here, we describe two experiments addressed to postgraduate genetics students in which the effect of transcription factors on gene expression is analyzed in Drosophila embryos of different genotypes by whole-mount in situ hybridization. In one of the experiments, students analyzed the repressive effect of Snail over rhomboid expression using reporter lines containing different constructs of the rhomboid neuroectodermal enhancer fused to the lacZ gene. In the second experiment, the epistatic relationship between the cabut and decapentaplegic genes was analyzed. These simple experiments allowed students to (1) understand the role of transcription factors and cis-regulatory elements over gene expression regulation and (2) practice a widespread laboratory technique, in situ hybridization with nonradioactive labeled probes, to detect gene expression patterns. These experiments required 12 hr and were organized into four daily sessions that included the discussion of the results with students. Examples of the results obtained and their relevance are shown and discussed herein. The methods described in these laboratory exercises can be easily adapted to model organisms other than Drosophila.
Collapse
Affiliation(s)
- Beatriz Llamusí
- Department of Genetics, Faculty of Biology, Universitat de València, Valencia, Spain; INCLIVA Health Research Institute, Valencia, Spain
| | | | | | | |
Collapse
|
26
|
Martinez C, Rest JS, Kim AR, Ludwig M, Kreitman M, White K, Reinitz J. Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change. Mol Biol Evol 2014; 31:903-16. [PMID: 24408913 DOI: 10.1093/molbev/msu042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Upstream regulatory sequences that control gene expression evolve rapidly, yet the expression patterns and functions of most genes are typically conserved. To address this paradox, we have reconstructed computationally and resurrected in vivo the cis-regulatory regions of the ancestral Drosophila eve stripe 2 element and evaluated its evolution using a mathematical model of promoter function. Our feed-forward transcriptional model predicts gene expression patterns directly from enhancer sequence. We used this functional model along with phylogenetics to generate a set of possible ancestral eve stripe 2 sequences for the common ancestors of 1) D. simulans and D. sechellia; 2) D. melanogaster, D. simulans, and D. sechellia; and 3) D. erecta and D. yakuba. These ancestral sequences were synthesized and resurrected in vivo. Using a combination of quantitative and computational analysis, we find clear support for functional compensation between the binding sites for Bicoid, Giant, and Krüppel over the course of 40-60 My of Drosophila evolution. We show that this compensation is driven by a coupling interaction between Bicoid activation and repression at the anterior and posterior border necessary for proper placement of the anterior stripe 2 border. A multiplicity of mechanisms for binding site turnover exemplified by Bicoid, Giant, and Krüppel sites, explains how rapid sequence change may occur while maintaining the function of the cis-regulatory element.
Collapse
Affiliation(s)
- Carlos Martinez
- Institute for Genomics and Systems Biology, University of Chicago
| | | | | | | | | | | | | |
Collapse
|
27
|
Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EEM. A conserved role for Snail as a potentiator of active transcription. Genes Dev 2014; 28:167-81. [PMID: 24402316 PMCID: PMC3909790 DOI: 10.1101/gad.230953.113] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The transcription factors of the Snail family are key regulators of epithelial-mesenchymal transitions, cell morphogenesis, and tumor metastasis. Since its discovery in Drosophila ∼25 years ago, Snail has been extensively studied for its role as a transcriptional repressor. Here we demonstrate that Drosophila Snail can positively modulate transcriptional activation. By combining information on in vivo occupancy with expression profiling of hand-selected, staged snail mutant embryos, we identified 106 genes that are potentially directly regulated by Snail during mesoderm development. In addition to the expected Snail-repressed genes, almost 50% of Snail targets showed an unanticipated activation. The majority of "Snail-activated" genes have enhancer elements cobound by Twist and are expressed in the mesoderm at the stages of Snail occupancy. Snail can potentiate Twist-mediated enhancer activation in vitro and is essential for enhancer activity in vivo. Using a machine learning approach, we show that differentially enriched motifs are sufficient to predict Snail's regulatory response. In silico mutagenesis revealed a likely causative motif, which we demonstrate is essential for enhancer activation. Taken together, these data indicate that Snail can potentiate enhancer activation by collaborating with different activators, providing a new mechanism by which Snail regulates development.
Collapse
Affiliation(s)
- Martina Rembold
- Institute of Genetics, University of Cologne, 50674 Cologne, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Crocker J, Stern DL. TALE-mediated modulation of transcriptional enhancers in vivo. Nat Methods 2013; 10:762-7. [PMID: 23817068 PMCID: PMC3733453 DOI: 10.1038/nmeth.2543] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/03/2013] [Indexed: 01/26/2023]
Abstract
We tested whether Transcription Activator-Like Effectors (TALEs) can mediate repression and activation of endogenous enhancers in the Drosophila genome. TALE-repressors (TALERs) targeting each of the five even-skipped (eve) “stripe” enhancers generated repression specifically of the focal stripes. TALE-activators (TALEAs) targeting the eve promoter or eve enhancers caused increased expression primarily in cells normally activated by the promoter or targeted enhancer, respectfully. The phenotypic effects of TALER and TALEA expression in larvae and adults are consistent with the observed modulations of eve expression. In these assays, the Hairy repression domain did not exhibit previously described long-range transcriptional repression activity. The precise effects of the TALEAs support the view that repression acts in a dominant fashion on transcriptional activators and that the activity state of an enhancer influences TALE binding or the ability of VP16 to enhance transcription. TALEs thus provide a novel tool for detection and functional modulation of transcriptional enhancers in their native genomic context.
Collapse
Affiliation(s)
- Justin Crocker
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, Virginia, USA.
| | | |
Collapse
|
29
|
Li JV, Chien CD, Garee JP, Xu J, Wellstein A, Riegel AT. Transcriptional repression of AIB1 by FoxG1 leads to apoptosis in breast cancer cells. Mol Endocrinol 2013; 27:1113-27. [PMID: 23660594 DOI: 10.1210/me.2012-1353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The oncogene nuclear receptor coactivator amplified in breast cancer 1 (AIB1) is a transcriptional coactivator that is overexpressed in various types of human cancers. However, the molecular mechanisms controlling AIB1 expression in the majority of cancers remain unclear. In this study, we identified a novel interacting protein of AIB1, forkhead-box protein G1 (FoxG1), which is an evolutionarily conserved forkhead-box transcriptional corepressor. We show that FoxG1 expression is low in breast cancer cell lines and that low levels of FoxG1 are correlated with a worse prognosis in breast cancer. We also demonstrate that transient overexpression of FoxG1 can suppress endogenous levels of AIB1 mRNA and protein in MCF-7 breast cancer cells. Exogenously expressed FoxG1 in MCF-7 cells also leads to apoptosis that can be rescued in part by AIB1 overexpression. Using chromatin immunoprecipitation, we determined that FoxG1 is recruited to a region of the AIB1 gene promoter previously characterized to be responsible for AIB1-induced, positive autoregulation of transcription through the recruitment of an activating, multiprotein complex, involving AIB1, E2F transcription factor 1, and specificity protein 1. Increased FoxG1 expression significantly reduces the recruitment of AIB1, E2F transcription factor 1 and E1A-binding protein p300 to this region of the endogenous AIB1 gene promoter. Our data imply that FoxG1 can function as a pro-apoptotic factor in part through suppression of AIB1 coactivator transcription complex formation, thereby reducing the expression of the AIB1 oncogene.
Collapse
Affiliation(s)
- Jordan V Li
- Department of Pharmacology, Lombardi Cancer Center, Georgetown University, Research Building E307, 3970 Reservoir Road Northwest, Washington, DC 20007-2197, USA
| | | | | | | | | | | |
Collapse
|
30
|
Kim AR, Martinez C, Ionides J, Ramos AF, Ludwig MZ, Ogawa N, Sharp DH, Reinitz J. Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic. PLoS Genet 2013; 9:e1003243. [PMID: 23468638 PMCID: PMC3585115 DOI: 10.1371/journal.pgen.1003243] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 11/30/2012] [Indexed: 01/19/2023] Open
Abstract
Rearrangements of about 2.5 kilobases of regulatory DNA located 5' of the transcription start site of the Drosophila even-skipped locus generate large-scale changes in the expression of even-skipped stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small "spacer" segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2-3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic cis-regulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein-DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other Drosophila genes; even-skipped enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of even-skipped regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that cis-regulatory "elements" are not elementary objects.
Collapse
Affiliation(s)
- Ah-Ram Kim
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Carlos Martinez
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - John Ionides
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre F. Ramos
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil
| | - Michael Z. Ludwig
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Nobuo Ogawa
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - David H. Sharp
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - John Reinitz
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, Department of Molecular Genetics and Cell Biology, and Institute of Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
31
|
Marsman J, Horsfield JA. Long distance relationships: enhancer-promoter communication and dynamic gene transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:1217-27. [PMID: 23124110 DOI: 10.1016/j.bbagrm.2012.10.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/18/2012] [Accepted: 10/22/2012] [Indexed: 11/27/2022]
Abstract
The three-dimensional regulation of gene transcription involves loop formation between enhancer and promoter elements, controlling spatiotemporal gene expression in multicellular organisms. Enhancers are usually located in non-coding DNA and can activate gene transcription by recruiting transcription factors, chromatin remodeling factors and RNA Polymerase II. Research over the last few years has revealed that enhancers have tell-tale characteristics that facilitate their detection by several approaches, although the hallmarks of enhancers are not always uniform. Enhancers likely play an important role in the activation of genes by functioning as a primary point of contact for transcriptional activators, and by making physical contact with gene promoters often by means of a chromatin loop. Although numerous transcriptional regulators participate in the formation of chromatin loops that bring enhancers into proximity with promoters, the mechanism(s) of enhancer-promoter connectivity remain enigmatic. Here we discuss enhancer function, review some of the many proteins shown to be involved in establishing enhancer-promoter loops, and describe the dynamics of enhancer-promoter contacts during development, differentiation and in specific cell types.
Collapse
Affiliation(s)
- Judith Marsman
- Department of Pathology, The University of Otago, Dunedin, New Zealand
| | | |
Collapse
|
32
|
Park KW, Hong JW. Mesodermal repression of single-minded in Drosophila embryo is mediated by a cluster of Snail-binding sites proximal to the early promoter. BMB Rep 2012; 45:577-82. [PMID: 23101512 DOI: 10.5483/bmbrep.2012.45.10.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
single-minded (sim) is a master regulatory gene that directs differentiation in the central nervous system during Drosophila embryogenesis. Recent identification of the mesectoderm enhancer (MSE) of sim has led to the hypothesis that two Snail (Sna)-binding sites in the MSE may repress sim expression in the presumptive mesoderm. We provide evidence here that three Sna-binding sites proximal to the sim promoter, but not those of the MSE, are responsible for the mesodermal repression of sim in vivo. Using transgenic embryos injected with lacZ transgenes, we showed that sim repression in the mesoderm requires the three promoter-proximal Sna-binding sites. These results suggest that Sna represses the mesectodermal expression of sim by directly repressing the nearby promoter, and not by quenching adjacent transcriptional activators in the MSE. These data also showed how the MSE, lacking the three proximal Sna-binding sites, reproduced the endogenous pattern of sim expression in transgenic embryos.
Collapse
Affiliation(s)
- Kye Won Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Korea
| | | |
Collapse
|
33
|
Transcriptional repression via antilooping in the Drosophila embryo. Proc Natl Acad Sci U S A 2012; 109:9460-4. [PMID: 22645339 DOI: 10.1073/pnas.1102625108] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcriptional repressors are thought to inhibit gene expression by interfering with the binding or function of RNA Polymerase II, perhaps by promoting local chromatin condensation. Here, we present evidence for a distinctive mechanism of repression, whereby sequence-specific repressors prevent the looping of distal enhancers to the promoter. Particular efforts focus on the Snail repressor, which plays a conserved role in promoting epithelial-mesenchyme transitions in both invertebrates and vertebrates, including mesoderm invagination in Drosophila, neural crest migration in vertebrates, and tumorigenesis in mammals. Chromosome conformation capture experiments were used to examine enhancer looping at Snail target genes in wild-type and mutant embryos. These studies suggest that the Snail repressor blocks the formation of fruitful enhancer-promoter interactions when bound to a distal enhancer. This higher-order mechanism of transcriptional repression has broad implications for the control of gene activity in metazoan development.
Collapse
|
34
|
Barolo S. Shadow enhancers: frequently asked questions about distributed cis-regulatory information and enhancer redundancy. Bioessays 2012; 34:135-41. [PMID: 22083793 PMCID: PMC3517143 DOI: 10.1002/bies.201100121] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper, in the form of a frequently asked questions page (FAQ), addresses outstanding questions about "shadow enhancers", quasi-redundant cis-regulatory elements, and their proposed roles in transcriptional control. Questions include: What exactly are shadow enhancers? How many genes have shadow/redundant/distributed enhancers? How redundant are these elements? What is the function of distributed enhancers? How modular are enhancers? Is it useful to study a single enhancer in isolation? In addition, a revised definition of "shadow enhancers" is proposed, and possible mechanisms of shadow enhancer function and evolution are discussed.
Collapse
Affiliation(s)
- Scott Barolo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
35
|
Abstract
Drosophila Groucho (Gro) is the founding member of a family of metazoan corepressors. Gro mediates repression through interactions with a myriad of DNA-binding repressor proteins to direct the silencing of genes involved in many developmental processes, including neurogenesis and patterning of the main body axis, as well as receptor tyrosine kinase/Ras/MAPK, Notch, Wingless (Wg)/Wnt, and Decapentaplegic (Dpp) signaling. Gro mediates repression by multiple molecular mechanisms, depending on the regulatory context. Because Gro is a broadly expressed nuclear factor, whereas its repressor partners display restricted temporal and spatial distribution, it was presumed that this corepressor played permissive rather than instructive roles in development. However, a wide range of studies demonstrates that this is not the case. Gro can sense and integrate many cellular inputs to modulate the expression of variety of genes, making it a versatile corepressor with crucial instructive roles in development and signaling.
Collapse
Affiliation(s)
- Wiam Turki-Judeh
- Department of Chemistry & Biochemistry and Molecular Biology Institute, University of California, Los Angeles, California, USA
| | | |
Collapse
|
36
|
Technau M, Knispel M, Roth S. Molecular mechanisms of EGF signaling-dependent regulation of pipe, a gene crucial for dorsoventral axis formation in Drosophila. Dev Genes Evol 2011; 222:1-17. [PMID: 22198544 PMCID: PMC3291829 DOI: 10.1007/s00427-011-0384-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 11/29/2011] [Indexed: 01/28/2023]
Abstract
During Drosophila oogenesis the expression of the sulfotransferase Pipe in ventral follicle cells is crucial for dorsoventral axis formation. Pipe modifies proteins that are incorporated in the ventral eggshell and activate Toll signaling which in turn initiates embryonic dorsoventral patterning. Ventral pipe expression is the result of an oocyte-derived EGF signal which down-regulates pipe in dorsal follicle cells. The analysis of mutant follicle cell clones reveals that none of the transcription factors known to act downstream of EGF signaling in Drosophila is required or sufficient for pipe regulation. However, the pipe cis-regulatory region harbors a 31-bp element which is essential for pipe repression, and ovarian extracts contain a protein that binds this element. Thus, EGF signaling does not act by down-regulating an activator of pipe as previously suggested but rather by activating a repressor. Surprisingly, this repressor acts independent of the common co-repressors Groucho or CtBP.
Collapse
Affiliation(s)
- Martin Technau
- Institute for Developmental Biology, Biocenter, University of Cologne, Zuelpicher Straße 47b, 50674, Cologne, Germany
| | | | | |
Collapse
|
37
|
Perry MW, Boettiger AN, Levine M. Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A 2011; 108:13570-5. [PMID: 21825127 PMCID: PMC3158186 DOI: 10.1073/pnas.1109873108] [Citation(s) in RCA: 165] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Segmentation of the Drosophila embryo begins with the establishment of spatially restricted gap gene-expression patterns in response to broad gradients of maternal transcription factors, such as Bicoid. Numerous studies have documented the fidelity of these expression patterns, even when embryos are subjected to genetic or environmental stress, but the underlying mechanisms for this transcriptional precision are uncertain. Here we present evidence that every gap gene contains multiple enhancers with overlapping activities to produce authentic patterns of gene expression. For example, a recently identified hunchback (hb) enhancer (located 5-kb upstream of the classic enhancer) ensures repression at the anterior pole. The combination of intronic and 5' knirps (kni) enhancers produces a faithful expression pattern, even though the intronic enhancer alone directs an abnormally broad expression pattern. We present different models for "enhancer synergy," whereby two enhancers with overlapping activities produce authentic patterns of gene expression.
Collapse
Affiliation(s)
| | | | - Michael Levine
- Center for Integrative Genomics, Division of Genetics, Genomics, and Development, and
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200
| |
Collapse
|
38
|
Abstract
Gap genes are involved in segment determination during the early development of the fruit fly Drosophila melanogaster as well as in other insects. This review attempts to synthesize the current knowledge of the gap gene network through a comprehensive survey of the experimental literature. I focus on genetic and molecular evidence, which provides us with an almost-complete picture of the regulatory interactions responsible for trunk gap gene expression. I discuss the regulatory mechanisms involved, and highlight the remaining ambiguities and gaps in the evidence. This is followed by a brief discussion of molecular regulatory mechanisms for transcriptional regulation, as well as precision and size-regulation provided by the system. Finally, I discuss evidence on the evolution of gap gene expression from species other than Drosophila. My survey concludes that studies of the gap gene system continue to reveal interesting and important new insights into the role of gene regulatory networks in development and evolution.
Collapse
Affiliation(s)
- Johannes Jaeger
- Centre de Regulació Genòmica, Universtitat Pompeu Fabra, Barcelona, Spain.
| |
Collapse
|
39
|
Cunha PMF, Sandmann T, Gustafson EH, Ciglar L, Eichenlaub MP, Furlong EEM. Combinatorial binding leads to diverse regulatory responses: Lmd is a tissue-specific modulator of Mef2 activity. PLoS Genet 2010; 6:e1001014. [PMID: 20617173 PMCID: PMC2895655 DOI: 10.1371/journal.pgen.1001014] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 06/01/2010] [Indexed: 11/26/2022] Open
Abstract
Understanding how complex patterns of temporal and spatial expression are regulated is central to deciphering genetic programs that drive development. Gene expression is initiated through the action of transcription factors and their cofactors converging on enhancer elements leading to a defined activity. Specific constellations of combinatorial occupancy are therefore often conceptualized as rigid binding codes that give rise to a common output of spatio-temporal expression. Here, we assessed this assumption using the regulatory input of two essential transcription factors within the Drosophila myogenic network. Mutations in either Myocyte enhancing factor 2 (Mef2) or the zinc-finger transcription factor lame duck (lmd) lead to very similar defects in myoblast fusion, yet the underlying molecular mechanism for this shared phenotype is not understood. Using a combination of ChIP-on-chip analysis and expression profiling of loss-of-function mutants, we obtained a global view of the regulatory input of both factors during development. The majority of Lmd-bound enhancers are co-bound by Mef2, representing a subset of Mef2's transcriptional input during these stages of development. Systematic analyses of the regulatory contribution of both factors demonstrate diverse regulatory roles, despite their co-occupancy of shared enhancer elements. These results indicate that Lmd is a tissue-specific modulator of Mef2 activity, acting as both a transcriptional activator and repressor, which has important implications for myogenesis. More generally, this study demonstrates considerable flexibility in the regulatory output of two factors, leading to additive, cooperative, and repressive modes of co-regulation. While genetic studies are essential to reveal the phenotypic relationships between genes, it is often very difficult to disentangle the molecular mechanism of two genes that phenocopy each other. In this study, we used global scale and single gene analysis to investigate the relationship between two transcription factors whose mutant embryos have a similar defect in myogenesis. In Drosophila, Mef2 mutant embryos display a block in myoblast fusion, which is very similar to what is observed in mutant embryos for lmd, a zinc-finger transcription factor. To understand the underlying nature of these defects we used ChIP-on-chip analysis to obtain a global view of their co-regulated enhancers, and we used expression profiling of mutant embryos to reveal their downstream transcriptional response. The results indicate that Lmd acts as a tissue specific modulator of Mef2 activity. Using in vivo and in vitro reporter assays, we show that co-binding to the same enhancer element can lead to diverse regulatory responses. The presence of Lmd has an additive, cooperative, or repressive effect on Mef2 activity, demonstrating that it acts as a molecular switch for gene expression during muscle differentiation. More broadly, our results highlight the difficulty in translating information on combinatorial binding data into a functional regulatory response.
Collapse
Affiliation(s)
| | | | | | - Lucia Ciglar
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | |
Collapse
|
40
|
Evolution of insect dorsoventral patterning mechanisms. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2009; 74:275-9. [PMID: 19843594 DOI: 10.1101/sqb.2009.74.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The dorsoventral (DV) patterning of the early Drosophila embryo depends on Dorsal, a maternal sequence-specific transcription factor related to mammalian NF-kappaB. Dorsal controls DV patterning through the differential regulation of approximately 50 target genes in a concentration-dependent manner. Whole-genome methods, including ChIP-chip and ChIP-seq assays, have identified approximately 100 Dorsal target enhancers, and more than one-third of these have been experimentally confirmed via transgenic embryo assays. Despite differences in DV patterning among divergent insects, a number of the Dorsal target enhancers are located in conserved positions relative to the associated transcription units. Thus, the evolution of novel patterns of gene expression might depend on the modification of old enhancers, rather than the invention of new ones. As many as half of all Dorsal target genes appear to contain "shadow" enhancers: a second enhancer that directs the same or similar expression pattern as the primary enhancer. Preliminary studies suggest that shadow enhancers might help to ensure resilience of gene expression in response to environmental and genetic perturbations. Finally, most Dorsal target genes appear to contain RNA polymerase II (pol II) prior to their activation. Stalled pol II fosters synchronous patterns of gene activation in the early embryo. In contrast, DV patterning genes lacking stalled pol II are initially activated in an erratic or stochastic fashion. It is possible that stalled pol II confers fitness to a population by ensuring coordinate deployment of the gene networks controlling embryogenesis.
Collapse
|
41
|
Groucho corepressor functions as a cofactor for the Knirps short-range transcriptional repressor. Proc Natl Acad Sci U S A 2009; 106:17314-9. [PMID: 19805071 DOI: 10.1073/pnas.0904507106] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the pervasive roles for repressors in transcriptional control, the range of action of these proteins on cis regulatory elements remains poorly understood. Knirps has essential roles in patterning the Drosophila embryo by means of short-range repression, an activity that is essential for proper regulation of complex transcriptional control elements. Short-range repressors function in a local fashion to interfere with the activity of activators or basal promoters within approximately 100 bp. In contrast, long-range repressors such as Hairy act over distances >1 kb. The functional distinction between these two classes of repressors has been suggested to stem from the differential recruitment of the CtBP corepressor to short-range repressors and Groucho to long-range repressors. Contrary to this differential recruitment model, we report that Groucho is a functional part of the Knirps short-range repression complex. The corepressor interaction is mediated via an eh-1 like motif present in the N terminus and a conserved region present in the central portion of Knirps. We also show that this interaction is important for the CtBP-independent repression activity of Knirps and is required for regulation of even-skipped. Our study uncovers a previously uncharacterized interaction between proteins previously thought to function in distinct repression pathways, and indicates that the Groucho corepressor can be differentially harnessed to execute short- and long-range repression.
Collapse
|
42
|
Reece-Hoyes JS, Deplancke B, Barrasa MI, Hatzold J, Smit RB, Arda HE, Pope PA, Gaudet J, Conradt B, Walhout AJM. The C. elegans Snail homolog CES-1 can activate gene expression in vivo and share targets with bHLH transcription factors. Nucleic Acids Res 2009; 37:3689-98. [PMID: 19372275 PMCID: PMC2699517 DOI: 10.1093/nar/gkp232] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Snail-type transcription factors (TFs) are found in numerous metazoan organisms and function in a plethora of cellular and developmental processes including mesoderm and neuronal development, apoptosis and cancer. So far, Snail-type TFs are exclusively known as transcriptional repressors. They repress gene expression by recruiting transcriptional co-repressors and/or by preventing DNA binding of activators from the basic helix-loop-helix (bHLH) family of TFs to CAGGTG E-box sequences. Here we report that the Caenorhabditis elegans Snail-type TF CES-1 can activate transcription in vivo. Moreover, we provide results that suggest that CES-1 can share its binding site with bHLH TFs, in different tissues, rather than only occluding bHLH DNA binding. Together, our data indicate that there are at least two types of CES-1 target genes and, therefore, that the molecular function of Snail-type TFs is more plastic than previously appreciated.
Collapse
Affiliation(s)
- John S Reece-Hoyes
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
de-Leon SBT, Davidson EH. Modeling the dynamics of transcriptional gene regulatory networks for animal development. Dev Biol 2009; 325:317-28. [PMID: 19028486 PMCID: PMC4100934 DOI: 10.1016/j.ydbio.2008.10.043] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2008] [Revised: 10/14/2008] [Accepted: 10/21/2008] [Indexed: 01/04/2023]
Abstract
The dynamic process of cell fate specification is regulated by networks of regulatory genes. The architecture of the network defines the temporal order of specification events. To understand the dynamic control of the developmental process, the kinetics of mRNA and protein synthesis and the response of the cis-regulatory modules to transcription factor concentration must be considered. Here we review mathematical models for mRNA and protein synthesis kinetics which are based on experimental measurements of the rates of the relevant processes. The model comprises the response functions of cis-regulatory modules to their transcription factor inputs, by incorporating binding site occupancy and its dependence on biologically measurable quantities. We use this model to simulate gene expression, to distinguish between cis-regulatory execution of "AND" and "OR" logic functions, rationalize the oscillatory behavior of certain transcriptional auto-repressors and to show how linked subcircuits can be dealt with. Model simulations display the effects of mutation of binding sites, or perturbation of upstream gene expression. The model is a generally useful tool for understanding gene regulation and the dynamics of cell fate specification.
Collapse
Affiliation(s)
| | - Eric H. Davidson
- Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
44
|
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster. BMC Genomics 2009; 10:9. [PMID: 19128496 PMCID: PMC2631479 DOI: 10.1186/1471-2164-10-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 01/07/2009] [Indexed: 12/31/2022] Open
Abstract
Background The promoter is a critical necessary transcriptional cis-regulatory element. In addition to its role as an assembly site for the basal transcriptional apparatus, the promoter plays a key part in mediating temporal and spatial aspects of gene expression through differential binding of transcription factors and selective interaction with distal enhancers. Although many genes have multiple promoters, little attention has been focused on how these relate to one another; nor has much study been directed at relationships between promoters of adjacent genes. Results We have undertaken a systematic investigation of Drosophila promoters. We divided promoters into three groups: unique promoters, first alternative promoters (the most 5' of a gene's multiple promoters), and downstream alternative promoters (the remaining alternative promoters 3' to the first). We observed distinct nucleotide distribution and sequence motif preferences among these three classes. We also investigated the promoters of neighboring genes and found that a greater than expected number of adjacent genes have similar sequence motif profiles, which may allow the genes to be regulated in a coordinated fashion. Consistent with this, there is a positive correlation between similar promoter motifs and related gene expression profiles for these genes. Conclusions Our results suggest that different regulatory mechanisms may apply to each of the three promoter classes, and provide a mechanism for "gene expression neighborhoods," local clusters of co-expressed genes. As a whole, our data reveal an unexpected complexity of genomic organization at the promoter level with respect to both alternative and neighboring promoters.
Collapse
|
45
|
Bonn S, Furlong EE. cis-Regulatory networks during development: a view of Drosophila. Curr Opin Genet Dev 2008; 18:513-20. [DOI: 10.1016/j.gde.2008.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 09/16/2008] [Accepted: 09/20/2008] [Indexed: 10/21/2022]
|
46
|
Hare EE, Peterson BK, Eisen MB. A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids. PLoS Genet 2008; 4:e1000268. [PMID: 19043550 PMCID: PMC2582681 DOI: 10.1371/journal.pgen.1000268] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Emily E. Hare
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Brant K. Peterson
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, United States of America
- * E-mail:
| |
Collapse
|
47
|
Abstract
Quantitative measurements of the Hunchback transcription factor in Drosophila embryos show that its target genes can respond with a high degree of precision to the exact level of the protein, simulating a continuous, analog readout, while other target genes show a combinatorial effect, resembling a Boolean logic element.
Collapse
Affiliation(s)
- Sandhya Payankaulam
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | | |
Collapse
|
48
|
Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB. Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet 2008; 4:e1000106. [PMID: 18584029 PMCID: PMC2430619 DOI: 10.1371/journal.pgen.1000106] [Citation(s) in RCA: 215] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 05/22/2008] [Indexed: 12/31/2022] Open
Abstract
The gene expression pattern specified by an animal regulatory sequence is generally viewed as arising from the particular arrangement of transcription factor binding sites it contains. However, we demonstrate here that regulatory sequences whose binding sites have been almost completely rearranged can still produce identical outputs. We sequenced the even-skipped locus from six species of scavenger flies (Sepsidae) that are highly diverged from the model species Drosophila melanogaster, but share its basic patterns of developmental gene expression. Although there is little sequence similarity between the sepsid eve enhancers and their well-characterized D. melanogaster counterparts, the sepsid and Drosophila enhancers drive nearly identical expression patterns in transgenic D. melanogaster embryos. We conclude that the molecular machinery that connects regulatory sequences to the transcription apparatus is more flexible than previously appreciated. In exploring this diverse collection of sequences to identify the shared features that account for their similar functions, we found a small number of short (20-30 bp) sequences nearly perfectly conserved among the species. These highly conserved sequences are strongly enriched for pairs of overlapping or adjacent binding sites. Together, these observations suggest that the local arrangement of binding sites relative to each other is more important than their overall arrangement into larger units of cis-regulatory function.
Collapse
Affiliation(s)
- Emily E. Hare
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Brant K. Peterson
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America
| | - Venky N. Iyer
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Center for Integrative Genomics, University of California Berkeley, Berkeley, California, United States of America
- Genomics Division, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- California Institute for Quantitative Biosciences, Berkeley, California, United States of America
| |
Collapse
|
49
|
Drosophila Ebi mediates Snail-dependent transcriptional repression through HDAC3-induced histone deacetylation. EMBO J 2008; 27:898-909. [PMID: 18309295 DOI: 10.1038/emboj.2008.26] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 02/07/2008] [Indexed: 01/14/2023] Open
Abstract
The Drosophila Snail protein is a transcriptional repressor that is necessary for mesoderm formation. Here, we identify the Ebi protein as an essential Snail co-repressor. In ebi mutant embryos, Snail target genes are derepressed in the presumptive mesoderm. Ebi and Snail interact both genetically and physically. We identify a Snail domain that is sufficient for Ebi binding, and which functions independently of another Snail co-repressor, Drosophila CtBP. This Ebi interaction domain is conserved among all insect Snail-related proteins, is a potent repression domain and is required for Snail function in transgenic embryos. In mammalian cells, the Ebi homologue TBL1 is part of the NCoR/SMRT-HDAC3 (histone deacetylase 3) co-repressor complex. We found that Ebi interacts with Drosophila HDAC3, and that HDAC3 knockdown or addition of a HDAC inhibitor impairs Snail-mediated repression in cells. In the early embryo, Ebi is recruited to a Snail target gene in a Snail-dependent manner, which coincides with histone hypoacetylation. Our results demonstrate that Snail requires the combined activities of Ebi and CtBP, and indicate that histone deacetylation is a repression mechanism in early Drosophila development.
Collapse
|
50
|
Abstract
High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned?
Collapse
Affiliation(s)
- Mike Levine
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.
| |
Collapse
|