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Al Asafen H, Beseli A, Chen HY, Hiremath S, Williams CM, Reeves GT. Dynamics of BMP signaling and stable gene expression in the early Drosophila embryo. Biol Open 2024; 13:bio061646. [PMID: 39207258 PMCID: PMC11381920 DOI: 10.1242/bio.061646] [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: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/04/2024] Open
Abstract
In developing tissues, morphogen gradients are thought to initialize gene expression patterns. However, the relationship between the dynamics of morphogen-encoded signals and gene expression decisions is largely unknown. Here we examine the dynamics of the Bone Morphogenetic Protein (BMP) pathway in Drosophila blastoderm-stage embryos. In this tissue, the BMP pathway is highly dynamic: it begins as a broad and weak signal on the dorsal half of the embryo, then 20-30 min later refines into a narrow, intense peak centered on the dorsal midline. This dynamical progression of the BMP signal raises questions of how it stably activates target genes. Therefore, we performed live imaging of the BMP signal and found that dorsal-lateral cells experience only a short transient in BMP signaling, after which the signal is lost completely. Moreover, we measured the transcriptional response of the BMP target gene pannier in live embryos and found it to remain activated in dorsal-lateral cells, even after the BMP signal is lost. Our findings may suggest that the BMP pathway activates a memory, or 'ratchet' mechanism that may sustain gene expression.
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Affiliation(s)
- Hadel Al Asafen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Aydin Beseli
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Hung-Yuan Chen
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843,USA
| | - Sharva Hiremath
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695,USA
- North Carolina Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695,USA
| | - Cranos M Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC 27695,USA
- North Carolina Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695,USA
| | - Gregory T Reeves
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843,USA
- Interdisciplinary Graduate Program in Genetics, Texas A&M University, College Station, TX 77843,USA
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2
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Akiyama T, Raftery LA, Wharton KA. Bone morphogenetic protein signaling: the pathway and its regulation. Genetics 2024; 226:iyad200. [PMID: 38124338 PMCID: PMC10847725 DOI: 10.1093/genetics/iyad200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023] Open
Abstract
In the mid-1960s, bone morphogenetic proteins (BMPs) were first identified in the extracts of bone to have the remarkable ability to induce heterotopic bone. When the Drosophila gene decapentaplegic (dpp) was first identified to share sequence similarity with mammalian BMP2/BMP4 in the late-1980s, it became clear that secreted BMP ligands can mediate processes other than bone formation. Following this discovery, collaborative efforts between Drosophila geneticists and mammalian biochemists made use of the strengths of their respective model systems to identify BMP signaling components and delineate the pathway. The ability to conduct genetic modifier screens in Drosophila with relative ease was critical in identifying the intracellular signal transducers for BMP signaling and the related transforming growth factor-beta/activin signaling pathway. Such screens also revealed a host of genes that encode other core signaling components and regulators of the pathway. In this review, we provide a historical account of this exciting time of gene discovery and discuss how the field has advanced over the past 30 years. We have learned that while the core BMP pathway is quite simple, composed of 3 components (ligand, receptor, and signal transducer), behind the versatility of this pathway lies multiple layers of regulation that ensures precise tissue-specific signaling output. We provide a sampling of these discoveries and highlight many questions that remain to be answered to fully understand the complexity of BMP signaling.
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Affiliation(s)
- Takuya Akiyama
- Department of Biology, Rich and Robin Porter Cancer Research Center, The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN 47809, USA
| | - Laurel A Raftery
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - Kristi A Wharton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
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3
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Schmidt-Ott U, Kwan CW. How two extraembryonic epithelia became one: serosa and amnion features and functions of Drosophila's amnioserosa. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210265. [PMID: 36252222 PMCID: PMC9574642 DOI: 10.1098/rstb.2021.0265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/30/2022] [Indexed: 01/19/2023] Open
Abstract
The conservation of gene networks that specify and differentiate distinct tissues has long been a subject of great interest to evolutionary developmental biologists, but the question of how pre-existing tissue-specific developmental trajectories merge is rarely asked. During the radiation of flies, two extraembryonic epithelia, known as serosa and amnion, evolved into one, called amnioserosa. This unique extraembryonic epithelium is found in fly species of the group Schizophora, including the genetic model organism Drosophila melanogaster, and has been studied in depth. Close relatives of this group develop a serosa and a rudimentary amnion. The scuttle fly Megaselia abdita has emerged as an excellent model organism to study this extraembryonic tissue organization. In this review, development and functions of the extraembryonic tissue complements of Drosophila and Megaselia are compared. It is concluded that the amnioserosa combines cells, genetic pathway components and functions that were previously associated either with serosa development or amnion development. The composite developmental trajectory of the amnioserosa raises the question of whether merging tissue-specific gene networks is a common evolutionary process. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
- Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, 1027 East 57th Street, Chicago, IL 60637, USA
| | - Chun Wai Kwan
- Laboratory for Epithelial Morphogenesis, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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4
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Schloop AE, Bandodkar PU, Reeves GT. Formation, interpretation, and regulation of the Drosophila Dorsal/NF-κB gradient. Curr Top Dev Biol 2019; 137:143-191. [PMID: 32143742 DOI: 10.1016/bs.ctdb.2019.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The morphogen gradient of the transcription factor Dorsal in the early Drosophila embryo has become one of the most widely studied tissue patterning systems. Dorsal is a Drosophila homolog of mammalian NF-κB and patterns the dorsal-ventral axis of the blastoderm embryo into several tissue types by spatially regulating upwards of 100 zygotic genes. Recent studies using fluorescence microscopy and live imaging have quantified the Dorsal gradient and its target genes, which has paved the way for mechanistic modeling of the gradient. In this review, we describe the mechanisms behind the initiation of the Dorsal gradient and its regulation of target genes. The main focus of the review is a discussion of quantitative and computational studies of the Dl gradient system, including regulation of the Dl gradient. We conclude with a discussion of potential future directions.
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Affiliation(s)
- Allison E Schloop
- Genetics Program, North Carolina State University, Raleigh, NC, United States
| | - Prasad U Bandodkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - Gregory T Reeves
- Genetics Program, North Carolina State University, Raleigh, NC, United States; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States.
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5
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Dunipace L, Ákos Z, Stathopoulos A. Coacting enhancers can have complementary functions within gene regulatory networks and promote canalization. PLoS Genet 2019; 15:e1008525. [PMID: 31830033 PMCID: PMC6932828 DOI: 10.1371/journal.pgen.1008525] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/26/2019] [Accepted: 11/15/2019] [Indexed: 11/18/2022] Open
Abstract
Developmental genes are often regulated by multiple enhancers exhibiting similar spatiotemporal outputs, which are generally considered redundantly acting though few have been studied functionally. Using CRISPR-Cas9, we created deletions of two enhancers, brk5' and brk3', that drive similar but not identical expression of the gene brinker (brk) in early Drosophila embryos. Utilizing both in situ hybridization and quantitative mRNA analysis, we investigated the changes in the gene network state caused by the removal of one or both of the early acting enhancers. brk5' deletion generally phenocopied the gene mutant, including expansion of the BMP ligand decapentaplegic (dpp) as well as inducing variability in amnioserosa tissue cell number suggesting a loss of canalization. In contrast, brk3' deletion presented unique phenotypes including dorsal expansion of several ventrally expressed genes and a decrease in amnioserosa cell number. Similarly, deletions were made for two enhancers associated with the gene short-gastrulation (sog), sog.int and sog.dist, demonstrating that they also exhibit distinct patterning phenotypes and affect canalization. In summary, this study shows that similar gene expression driven by coacting enhancers can support distinct, and sometimes complementary, functions within gene regulatory networks and, moreover, that phenotypes associated with individual enhancer deletion mutants can provide insight into new gene functions.
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Affiliation(s)
- Leslie Dunipace
- California Institute of Technology, Pasadena, CA, United States of America
| | - Zsuzsa Ákos
- California Institute of Technology, Pasadena, CA, United States of America
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6
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Chayengia M, Veikkolainen V, Jevtic M, Pyrowolakis G. Sequence environment of BMP-dependent activating elements controls transcriptional responses to Dpp signaling in Drosophila. Development 2019; 146:dev.176107. [PMID: 31110028 DOI: 10.1242/dev.176107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/14/2019] [Indexed: 11/20/2022]
Abstract
Intercellular signaling pathways activate transcription factors, which, along with tissue-specific co-factors, regulate expression of target genes. Responses to TGFβ/BMP signals are mediated by Smad proteins, which form complexes and accumulate in the nucleus to directly bind and regulate enhancers of BMP targets upon signaling. In Drosophila, gene activation by BMP signaling often requires, in addition to direct input by Smads, the signal-dependent removal of the transcriptional repressor Brk. Previous studies on enhancers of BMP-activated genes have defined a BMP-responsive motif, the AE, which integrates activatory and repressive input by the Smad complex and Brk, respectively. Here, we address whether sequence variations within the core AE sequences might endow the motif with additional properties accounting for qualitative and quantitative differences in BMP responses, including tissue specificity of transcriptional activation and differential sensitivity to Smad and Brk inputs. By analyzing and cross-comparing three distinct BMP-responsive enhancers from the genes wit and D ad in two different epithelia, the wing imaginal disc and the follicular epithelium, we demonstrate that differences in the AEs contribute neither to the observed tissue-restriction of BMP responses nor to differences in the utilization of the Smad and Brk branches for transcriptional activation. Rather, our results suggest that the cis-environment of the BMP-response elements not only dictates tissue specificity but also differential sensitivity to the two BMP mediators.
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Affiliation(s)
- Mrinal Chayengia
- Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany.,Research Training Program GRK 1104, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany.,Institute for Biology I, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany
| | - Ville Veikkolainen
- Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany.,Institute for Biology I, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany
| | - Milica Jevtic
- Institute for Biology I, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - George Pyrowolakis
- Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany .,Institute for Biology I, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany.,Center for Biological Systems Analysis, Albert-Ludwigs-University of Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany
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7
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Kim AR, Choi EB, Kim MY, Choi KW. Angiotensin-converting enzyme Ance is cooperatively regulated by Mad and Pannier in Drosophila imaginal discs. Sci Rep 2017; 7:13174. [PMID: 29030610 PMCID: PMC5640665 DOI: 10.1038/s41598-017-13487-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/26/2017] [Indexed: 02/02/2023] Open
Abstract
Angiotensin-converting enzyme (ACE) is an evolutionarily conserved peptidyl dipeptidase. Mammalian ACE converts angiotensin I to the active vasoconstrictor angiotensin II, thus playing a critical role for homeostasis of the renin-angiotensin system. In Drosophila, the ACE homolog Ance is expressed in specific regions of developing organs, but its regulatory mechanism has not been identified. Here we provide evidence that Ance expression is regulated by a combination of Mad and Pannier (Pnr) in imaginal discs. We demonstrate that Ance expression in eye and wing discs depends on Dpp signaling. The Mad binding site of Ance regulatory region is essential for Ance expression. Ance expression in imaginal discs is also regulated by the GATA family transcription factor Pnr. Pnr directly regulates Ance expression by binding to a GATA site of Ance enhancer. In addition, Pnr and Mad physically and genetically interact. Ance null mutants are morphologically normal but show genetic interaction with dpp mutants. Furthermore, we show that human SMAD2 and GATA4 physically interact and ACE expression in HEK293 cells is regulated by SMAD2 and GATA4. Taken together, this study reveals a cooperative mechanism of Ance regulation by Mad and Pnr. Our data also suggest a conserved transcriptional regulation of human ACE.
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Affiliation(s)
- Ah-Ram Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Eun-Bee Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Mi-Young Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea.
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8
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Target genes of Dpp/BMP signaling pathway revealed by transcriptome profiling in the early D. melanogaster embryo. Gene 2016; 591:191-200. [DOI: 10.1016/j.gene.2016.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 01/23/2023]
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9
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Koenecke N, Johnston J, Gaertner B, Natarajan M, Zeitlinger J. Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. Genome Biol 2016; 17:196. [PMID: 27678375 PMCID: PMC5037609 DOI: 10.1186/s13059-016-1057-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/05/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear. RESULTS Using DV patterning as a test system, we develop a simple and effective method to identify tissue-specific enhancers de novo. We sample a broad set of candidate enhancer regions using data on CREB-binding protein co-factor binding or ATAC-seq chromatin accessibility, and then identify those regions with significant differences in histone acetylation between tissues. This method identifies hundreds of novel DV enhancers and outperforms ChIP-seq data of relevant transcription factors when benchmarked with mRNA expression data and transgenic reporter assays. These DV enhancers allow the de novo discovery of the relevant transcription factor motifs involved in DV patterning and contain additional motifs that are evolutionarily conserved and for which the corresponding transcription factors are expressed in a DV-biased fashion. Finally, we identify novel target genes of the regulatory network, implicating morphogenesis genes as early targets of DV patterning. CONCLUSIONS Taken together, our approach has expanded our knowledge of the DV patterning network even further and is a general method to identify enhancers in any developmental system, including mammalian development.
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Affiliation(s)
- Nina Koenecke
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,Present address: Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Malini Natarajan
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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10
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Kutejova E, Sasai N, Shah A, Gouti M, Briscoe J. Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs. Dev Cell 2016; 36:639-53. [PMID: 26972603 PMCID: PMC4819439 DOI: 10.1016/j.devcel.2016.02.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 12/29/2015] [Accepted: 02/12/2016] [Indexed: 01/01/2023]
Abstract
In the vertebrate neural tube, a morphogen-induced transcriptional network produces multiple molecularly distinct progenitor domains, each generating different neuronal subtypes. Using an in vitro differentiation system, we defined gene expression signatures of distinct progenitor populations and identified direct gene-regulatory inputs corresponding to locations of specific transcription factor binding. Combined with targeted perturbations of the network, this revealed a mechanism in which a progenitor identity is installed by active repression of the entire transcriptional programs of other neural progenitor fates. In the ventral neural tube, sonic hedgehog (Shh) signaling, together with broadly expressed transcriptional activators, concurrently activates the gene expression programs of several domains. The specific outcome is selected by repressive input provided by Shh-induced transcription factors that act as the key nodes in the network, enabling progenitors to adopt a single definitive identity from several initially permitted options. Together, the data suggest design principles relevant to many developing tissues. Specific vertebrate neural progenitor populations generated in vitro Gene expression dynamics, transcription factor binding assessed in neural progenitors Progenitor fate selected by repressors blocking entire programs of other identities Repressors counteract non-selective morphogen and pan-neural activatory inputs
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Affiliation(s)
- Eva Kutejova
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Noriaki Sasai
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Ankita Shah
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Mina Gouti
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - James Briscoe
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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11
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Bier E, De Robertis EM. BMP gradients: A paradigm for morphogen-mediated developmental patterning. Science 2015; 348:aaa5838. [DOI: 10.1126/science.aaa5838] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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12
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BMP-dependent gene repression cascade in Drosophila eggshell patterning. Dev Biol 2015; 400:258-65. [PMID: 25704512 DOI: 10.1016/j.ydbio.2015.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 01/19/2015] [Accepted: 02/10/2015] [Indexed: 12/17/2022]
Abstract
Bone Morphogenetic Proteins (BMPs) signal by activating Smad transcription factors to control a number of decisions during animal development. In Drosophila, signaling by the BMP ligand Decapentaplegic (Dpp) involves the activity of brinker (brk) which, in most contexts, is repressed by Dpp. Brk encodes a transcription factor which represses BMP signaling output by antagonizing Smad-dependent target gene activation. Here, we study BMP-dependent gene regulation during Drosophila oogenesis by following the signal transmission from Dpp to its target broad (br), a gene with a crucial function in eggshell patterning. We identify regulatory sequences that account for expression of both brk and br, and connect these to the transcription factors of the pathway. We show that Dpp directly regulates brk transcription through Smad- and Schnurri (Shn)-dependent repression. Brk is epistatic to Dpp in br expression and activates br indirectly, through removal of a repressor, which is yet to be identified. Our work provides first cis-regulatory insights into transcriptional interpretation of BMP signaling in eggshell morphogenesis and defines a transcriptional cascade that connects Dpp to target gene regulation.
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13
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Li XY, Harrison MM, Villalta JE, Kaplan T, Eisen MB. Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition. eLife 2014; 3. [PMID: 25313869 PMCID: PMC4358338 DOI: 10.7554/elife.03737] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022] Open
Abstract
We describe the genome-wide distributions and temporal dynamics of nucleosomes and post-translational histone modifications throughout the maternal-to-zygotic transition in embryos of Drosophila melanogaster. At mitotic cycle 8, when few zygotic genes are being transcribed, embryonic chromatin is in a relatively simple state: there are few nucleosome free regions, undetectable levels of the histone methylation marks characteristic of mature chromatin, and low levels of histone acetylation at a relatively small number of loci. Histone acetylation increases by cycle 12, but it is not until cycle 14 that nucleosome free regions and domains of histone methylation become widespread. Early histone acetylation is strongly associated with regions that we have previously shown to be bound in early embryos by the maternally deposited transcription factor Zelda, suggesting that Zelda triggers a cascade of events, including the accumulation of specific histone modifications, that plays a role in the subsequent activation of these sequences.
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Affiliation(s)
- Xiao-Yong Li
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, United States
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, United States
| | - Jacqueline E Villalta
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael B Eisen
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, United States
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14
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Hamaratoglu F, Affolter M, Pyrowolakis G. Dpp/BMP signaling in flies: from molecules to biology. Semin Cell Dev Biol 2014; 32:128-36. [PMID: 24813173 DOI: 10.1016/j.semcdb.2014.04.036] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/30/2014] [Indexed: 01/08/2023]
Abstract
Decapentaplegic (Dpp), the fly homolog of the secreted mammalian BMP2/4 signaling molecules, is involved in almost all aspects of fly development. Dpp has critical functions at all developmental stages, from patterning of the eggshell to the determination of adult intestinal stem cell identity. Here, we focus on recent findings regarding the transcriptional regulatory logic of the pathway, on a new feedback regulator, Pentagone, and on Dpp's roles in scaling and growth of the Drosophila wing.
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Affiliation(s)
- Fisun Hamaratoglu
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| | - Markus Affolter
- Growth & Development, Biozentrum, University of Basel, Basel, Switzerland
| | - George Pyrowolakis
- Institute for Biology I, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Centre for Biological Signaling Studies (BIOSS), Albert-Ludwigs-University of Freiburg, Freiburg, Germany
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15
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O'Keefe DD, Thomas S, Edgar BA, Buttitta L. Temporal regulation of Dpp signaling output in the Drosophila wing. Dev Dyn 2014; 243:818-32. [PMID: 24591046 DOI: 10.1002/dvdy.24122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 02/25/2014] [Accepted: 02/25/2014] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The Decapentaplegic (Dpp) signaling pathway is used in many developmental and homeostatic contexts, each time resulting in cellular responses particular to that biological niche. The flexibility of Dpp signaling is clearly evident in epithelial cells of the Drosophila wing imaginal disc. During larval stages of development, Dpp functions as a morphogen, patterning the wing developmental field and stimulating tissue growth. A short time later, however, as wing-epithelial cells exit the cell cycle and begin to differentiate, Dpp is a critical determinant of vein-cell fate. It is likely that the Dpp signaling pathway regulates different sets of target genes at these two developmental time points. RESULTS To identify mechanisms that temporally control the transcriptional output of Dpp signaling in this system, we have taken a gene expression profiling approach. We identified genes affected by Dpp signaling at late larval or early pupal developmental time points, thereby identifying patterning- and differentiation-specific downstream targets, respectively. CONCLUSIONS Analysis of target genes and transcription factor binding sites associated with these groups of genes revealed potential mechanisms by which target-gene specificity of the Dpp signaling pathway is temporally regulated. In addition, this approach revealed novel mechanisms by which Dpp affects the cellular differentiation of wing-veins.
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Affiliation(s)
- David D O'Keefe
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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