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Tu M, Ge B, Li J, Pan Y, Zhao B, Han J, Wu J, Zhang K, Liu G, Hou M, Yue M, Han X, Sun T, An Y. Emerging biological functions of Twist1 in cell differentiation. Dev Dyn 2024. [PMID: 39254141 DOI: 10.1002/dvdy.736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 08/03/2024] [Accepted: 08/14/2024] [Indexed: 09/11/2024] Open
Abstract
Twist1 is required for embryonic development and expresses after birth in mesenchymal stem cells derived from mesoderm, where it governs mesenchymal cell development. As a well-known regulator of epithelial-mesenchymal transition or embryonic organogenesis, Twist1 is important in a variety of developmental systems, including mesoderm formation, neurogenesis, myogenesis, cranial neural crest cell migration, and differentiation. In this review, we first highlight the physiological significance of Twist1 in cell differentiation, including osteogenic, chondrogenic, and myogenic differentiation, and then detail its probable molecular processes and signaling pathways. On this premise, we summarize the significance of Twist1 in distinct developmental disorders and diseases to provide a reference for studies on cell differentiation/development-related diseases.
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Affiliation(s)
- Mengjie Tu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Bingqian Ge
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jiali Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yanbing Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Binbin Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jiayang Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jialin Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Kaifeng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Guangchao Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Mengwen Hou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Man Yue
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Xu Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Tiantian Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yang An
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
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2
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Zheng C, Allen KO, Liu T, Solodin NM, Meyer MB, Salem K, Tsourkas PK, McIlwain SJ, Vera JM, Cromwell ER, Ozers MS, Fowler AM, Alarid ET. Elevated GRHL2 Imparts Plasticity in ER-Positive Breast Cancer Cells. Cancers (Basel) 2024; 16:2906. [PMID: 39199676 PMCID: PMC11353109 DOI: 10.3390/cancers16162906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 09/01/2024] Open
Abstract
Estrogen receptor (ER)-positive breast cancer is characterized by late recurrences following initial treatment. The epithelial cell fate transcription factor Grainyhead-like protein 2 (GRHL2) is overexpressed in ER-positive breast cancers and is linked to poorer prognosis as compared to ER-negative breast cancers. To understand how GRHL2 contributes to progression, GRHL2 was overexpressed in ER-positive cells. We demonstrated that elevated GRHL2 imparts plasticity with stem cell- and dormancy-associated traits. RNA sequencing and immunocytochemistry revealed that high GRHL2 not only strengthens the epithelial identity but supports a hybrid epithelial to mesenchymal transition (EMT). Proliferation and tumor studies exhibited a decrease in growth and an upregulation of dormancy markers, such as NR2F1 and CDKN1B. Mammosphere assays and flow cytometry revealed enrichment of stem cell markers CD44 and ALDH1, and increased self-renewal capacity. Cistrome analyses revealed a change in transcription factor motifs near GRHL2 sites from developmental factors to those associated with disease progression. Together, these data support the idea that the plasticity and properties induced by elevated GRHL2 may provide a selective advantage to explain the association between GRHL2 and breast cancer progression.
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Affiliation(s)
- Christy Zheng
- McArdle Laboratory for Cancer Research, Department of Oncology, Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kaelyn O. Allen
- McArdle Laboratory for Cancer Research, Department of Oncology, Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Tianrui Liu
- McArdle Laboratory for Cancer Research, Department of Oncology, Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Natalia M. Solodin
- McArdle Laboratory for Cancer Research, Department of Oncology, Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Mark B. Meyer
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kelley Salem
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Phillipos K. Tsourkas
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sean J. McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jessica M. Vera
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Erika R. Cromwell
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Mary Szatkowski Ozers
- McArdle Laboratory for Cancer Research, Department of Oncology, Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Proteovista LLC, Madison, WI 53719, USA
| | - Amy M. Fowler
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
- Department of Medical Physics, University of Wisconsin-Madison, WI 53705, USA
- Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Elaine T. Alarid
- McArdle Laboratory for Cancer Research, Department of Oncology, Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
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Balasubramanian D, Borges Pinto P, Grasso A, Vincent S, Tarayre H, Lajoignie D, Ghavi-Helm Y. Enhancer-promoter interactions can form independently of genomic distance and be functional across TAD boundaries. Nucleic Acids Res 2024; 52:1702-1719. [PMID: 38084924 PMCID: PMC10899756 DOI: 10.1093/nar/gkad1183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 02/29/2024] Open
Abstract
Topologically Associating Domains (TADs) have been suggested to facilitate and constrain enhancer-promoter interactions. However, the role of TAD boundaries in effectively restricting these interactions remains unclear. Here, we show that a significant proportion of enhancer-promoter interactions are established across TAD boundaries in Drosophila embryos, but that developmental genes are strikingly enriched in intra- but not inter-TAD interactions. We pursued this observation using the twist locus, a master regulator of mesoderm development, and systematically relocated one of its enhancers to various genomic locations. While this developmental gene can establish inter-TAD interactions with its enhancer, the functionality of these interactions remains limited, highlighting the existence of topological constraints. Furthermore, contrary to intra-TAD interactions, the formation of inter-TAD enhancer-promoter interactions is not solely driven by genomic distance, with distal interactions sometimes favored over proximal ones. These observations suggest that other general mechanisms must exist to establish and maintain specific enhancer-promoter interactions across large distances.
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Affiliation(s)
- Deevitha Balasubramanian
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
- Indian Institute of Science Education and Research (IISER) Tirupati; Tirupati 517507 Andhra Pradesh, India
| | - Pedro Borges Pinto
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Alexia Grasso
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Séverine Vincent
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Hélène Tarayre
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Damien Lajoignie
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique UMR5242, Université Claude Bernard-Lyon 1; 69364 Lyon, France
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Ji S, Zhou X, Hoffmann JA. Toll-mediated airway homeostasis is essential for fly survival upon injection of RasV12-GFP oncogenic cells. Cell Rep 2024; 43:113677. [PMID: 38236774 DOI: 10.1016/j.celrep.2024.113677] [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: 08/15/2023] [Revised: 11/08/2023] [Accepted: 01/01/2024] [Indexed: 03/02/2024] Open
Abstract
Toll signaling is well known for its pivotal role in the host response against the invasion of external pathogens. Here, we investigate the potential involvement of Toll signaling in the intersection between the host and oncogenic cells. We show that loss of myeloid differentiation factor 88 (Myd88) leads to drastic fly death after the injection of RasV12-GFP oncogenic cells. Transcriptomic analyses show that challenging flies with oncogenic cells or bacteria leads to distinct inductions of Myd88-dependent genes. We note that downregulation of Myd88 in the tracheal system accounts for fly mortality, and ectopic tracheal complementation of Myd88 rescues the survival defect in Myd88 loss-of-function mutants following RasV12-GFP injection. Further, molecular and genetic evidence indicate that Toll signaling modulates fly resistance to RasV12-GFP cells through mediating airway function in a rolled-dependent manner. Collectively, our data indicate a critical role of Toll signaling in tracheal homeostasis and host survival after the injection of oncogenic cells.
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Affiliation(s)
- Shanming Ji
- Insect Models of Innate Immunity (M3I; 9022), Institute of Molecular and Cellular Biology, CNRS, 67084 Strasbourg, France
| | - Xiaojing Zhou
- Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 511436, China
| | - Jules A Hoffmann
- Insect Models of Innate Immunity (M3I; 9022), Institute of Molecular and Cellular Biology, CNRS, 67084 Strasbourg, France; Institute for Advanced Study, University of Strasbourg, 67000 Strasbourg, France; Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 511436, China.
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5
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Janssen R, Budd GE. New insights into mesoderm and endoderm development, and the nature of the onychophoran blastopore. Front Zool 2024; 21:2. [PMID: 38267986 PMCID: PMC10809584 DOI: 10.1186/s12983-024-00521-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Early during onychophoran development and prior to the formation of the germ band, a posterior tissue thickening forms the posterior pit. Anterior to this thickening forms a groove, the embryonic slit, that marks the anterior-posterior orientation of the developing embryo. This slit is by some authors considered the blastopore, and thus the origin of the endoderm, while others argue that the posterior pit represents the blastopore. This controversy is of evolutionary significance because if the slit represents the blastopore, then this would support the amphistomy hypothesis that suggests that a slit-like blastopore in the bilaterian ancestor evolved into protostomy and deuterostomy. RESULTS In this paper, we summarize our current knowledge about endoderm and mesoderm development in onychophorans and provide additional data on early endoderm- and mesoderm-determining marker genes such as Blimp, Mox, and the T-box genes. CONCLUSION We come to the conclusion that the endoderm of onychophorans forms prior to the development of the embryonic slit, and thus that the slit is not the primary origin of the endoderm. It is thus unlikely that the embryonic slit represents the blastopore. We suggest instead that the posterior pit indeed represents the lips of the blastopore, and that the embryonic slit (and surrounding tissue) represents a morphologically superficial archenteron-like structure. We conclude further that both endoderm and mesoderm development are under control of conserved gene regulatory networks, and that many of the features found in arthropods including the model Drosophila melanogaster are likely derived.
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Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden.
| | - Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
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Anjum AA, Lin MJ, Jin L, Li GQ. Twist is required for muscle development of the adult legs in Henosepilachna vigintioctopunctata. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22063. [PMID: 37920138 DOI: 10.1002/arch.22063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/04/2023]
Abstract
Although muscle development has been widely studied in Drosophila melanogaster, it was a great challenge to apply to developmental processes of other insect muscles. This study was focused on the functional characterization of a basic helix-loop-helix transcription factor gene twist in an herbivorous ladybird Henosepilachna vigintioctopunctata. Its transcript (Hvtwist) levels were detected in all developmental stages. RNA interference (RNAi)-aided knockdown of Hvtwist at the penultimate larval instar stage impaired pupation, and caused a deformed adult in the legs. The tarsi were malformed and did not support the bodies in an upright position. The climbing ability was impaired. Moreover, around 50% of the impaired adults had a malformed elytrum. In addition, they consumed less foliage and did not lay eggs. A hematoxylin-eosin staining of the leg demonstrated that the tibial extensor (TE) and the tibial flexor (TF) muscles were originated from the femurs while levator and depressor muscles of the tarsus (TL and TD) were located in the tibia in the control adults, in which tarsal segments were devoid of muscles. RNAi treatment specific to Hvtwist expression markedly impaired TE and TF muscles in the femurs, and prevented the development of TL and TD muscles in the tibia. Therefore, our findings demonstrate Twist plays a vital role in the myogenesis in H. vigintioctopunctata adult legs.
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Affiliation(s)
- Ahmad Ali Anjum
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Meng-Jiao Lin
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lin Jin
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Qing Li
- Department of Entomology, Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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7
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Kapil S, Sobti RC, Kaur T. Prediction and analysis of cis-regulatory elements in Dorsal and Ventral patterning genes of Tribolium castaneum and its comparison with Drosophila melanogaster. Mol Cell Biochem 2024; 479:109-125. [PMID: 37004638 DOI: 10.1007/s11010-023-04712-4] [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: 12/26/2022] [Accepted: 03/15/2023] [Indexed: 04/04/2023]
Abstract
Insect embryonic development and morphology are characterized by their anterior-posterior and dorsal-ventral (DV) patterning. In Drosophila embryos, DV patterning is mediated by a dorsal protein gradient which activates twist and snail proteins, the important regulators of DV patterning. To activate or repress gene expression, some regulatory proteins bind in clusters to their target gene at sites known as cis-regulatory elements or enhancers. To understand how variations in gene expression in different lineages might lead to different phenotypes, it is necessary to understand enhancers and their evolution. Drosophila melanogaster has been widely studied to understand the interactions between transcription factors and the transcription factor binding sites. Tribolium castaneum is an upcoming model animal which is catching the interest of biologists and the research on the enhancer mechanisms in the insect's axes patterning is still in infancy. Therefore, the current study was designed to compare the enhancers of DV patterning in the two insect species. The sequences of ten proteins involved in DV patterning of D. melanogaster were obtained from Flybase. The protein sequences of T. castaneum orthologous to those obtained from D. melanogaster were acquired from NCBI BLAST, and these were then converted to DNA sequences which were modified by adding 20 kb sequences both upstream and downstream to the gene. These modified sequences were used for further analysis. Bioinformatics tools (Cluster-Buster and MCAST) were used to search for clusters of binding sites (enhancers) in the modified DV genes. The results obtained showed that the transcription factors in Drosophila melanogaster and Tribolium castaneum are nearly identical; however, the number of binding sites varies between the two species, indicating transcription factor binding site evolution, as predicted by two different computational tools. It was observed that dorsal, twist, snail, zelda, and Supressor of Hairless are the transcription factors responsible for the regulation of DV patterning in the two insect species.
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Affiliation(s)
- Subham Kapil
- Department of Zoology, DAV University, Jalandhar, India
| | | | - Tejinder Kaur
- Department of Zoology, DAV University, Jalandhar, India.
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Lai YT, Sasamura T, Kuroda J, Maeda R, Nakamura M, Hatori R, Ishibashi T, Taniguchi K, Ooike M, Taguchi T, Nakazawa N, Hozumi S, Okumura T, Aigaki T, Inaki M, Matsuno K. The Drosophila AWP1 ortholog Doctor No regulates JAK/STAT signaling for left-right asymmetry in the gut by promoting receptor endocytosis. Development 2023; 150:293490. [PMID: 36861793 PMCID: PMC10112927 DOI: 10.1242/dev.201224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 02/09/2023] [Indexed: 03/03/2023]
Abstract
Many organs of Drosophila show stereotypical left-right (LR) asymmetry; however, the underlying mechanisms remain elusive. Here, we have identified an evolutionarily conserved ubiquitin-binding protein, AWP1/Doctor No (Drn), as a factor required for LR asymmetry in the embryonic anterior gut. We found that drn is essential in the circular visceral muscle cells of the midgut for JAK/STAT signaling, which contributes to the first known cue for anterior gut lateralization via LR asymmetric nuclear rearrangement. Embryos homozygous for drn and lacking its maternal contribution showed phenotypes similar to those with depleted JAK/STAT signaling, suggesting that Drn is a general component of JAK/STAT signaling. Absence of Drn resulted in specific accumulation of Domeless (Dome), the receptor for ligands in the JAK/STAT signaling pathway, in intracellular compartments, including ubiquitylated cargos. Dome colocalized with Drn in wild-type Drosophila. These results suggest that Drn is required for the endocytic trafficking of Dome, which is a crucial step for activation of JAK/STAT signaling and the subsequent degradation of Dome. The roles of AWP1/Drn in activating JAK/STAT signaling and in LR asymmetric development may be conserved in various organisms.
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Affiliation(s)
- Yi-Ting Lai
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takeshi Sasamura
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Junpei Kuroda
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Reo Maeda
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Mitsutoshi Nakamura
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Ryo Hatori
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tomoki Ishibashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kiichiro Taniguchi
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Masashi Ooike
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Tomohiro Taguchi
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Naotaka Nakazawa
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Shunya Hozumi
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takashi Okumura
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Toshiro Aigaki
- Department of Biological Science, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo 192-0397, Japan
| | - Mikiko Inaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kenji Matsuno
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Galupa R, Alvarez-Canales G, Borst NO, Fuqua T, Gandara L, Misunou N, Richter K, Alves MRP, Karumbi E, Perkins ML, Kocijan T, Rushlow CA, Crocker J. Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development. Dev Cell 2023; 58:51-62.e4. [PMID: 36626871 PMCID: PMC9860173 DOI: 10.1016/j.devcel.2022.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Developmental enhancers bind transcription factors and dictate patterns of gene expression during development. Their molecular evolution can underlie phenotypical evolution, but the contributions of the evolutionary pathways involved remain little understood. Here, using mutation libraries in Drosophila melanogaster embryos, we observed that most point mutations in developmental enhancers led to changes in gene expression levels but rarely resulted in novel expression outside of the native pattern. In contrast, random sequences, often acting as developmental enhancers, drove expression across a range of cell types; random sequences including motifs for transcription factors with pioneer activity acted as enhancers even more frequently. Our findings suggest that the phenotypic landscapes of developmental enhancers are constrained by enhancer architecture and chromatin accessibility. We propose that the evolution of existing enhancers is limited in its capacity to generate novel phenotypes, whereas the activity of de novo elements is a primary source of phenotypic novelty.
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Affiliation(s)
- Rafael Galupa
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | | | | | - Timothy Fuqua
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lautaro Gandara
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Natalia Misunou
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Esther Karumbi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Tin Kocijan
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Justin Crocker
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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10
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Rodriguez K, Do A, Senay-Aras B, Perales M, Alber M, Chen W, Reddy GV. Concentration-dependent transcriptional switching through a collective action of cis-elements. SCIENCE ADVANCES 2022; 8:eabo6157. [PMID: 35947668 PMCID: PMC9365274 DOI: 10.1126/sciadv.abo6157] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Gene expression specificity of homeobox transcription factors has remained paradoxical. WUSCHEL activates and represses CLAVATA3 transcription at lower and higher concentrations, respectively. We use computational modeling and experimental analysis to investigate the properties of the cis-regulatory module. We find that intrinsically each cis-element can only activate CLAVATA3 at a higher WUSCHEL concentration. However, together, they repress CLAVATA3 at higher WUSCHEL and activate only at lower WUSCHEL, showing that the concentration-dependent interactions among cis-elements regulate both activation and repression. Biochemical experiments show that two adjacent functional cis-elements bind WUSCHEL with higher affinity and dimerize at relatively lower levels. Moreover, increasing the distance between cis-elements prolongs WUSCHEL monomer binding window, resulting in higher CLAVATA3 activation. Our work showing a constellation of optimally spaced cis-elements of defined affinities determining activation and repression thresholds in regulating CLAVATA3 transcription provides a previously unknown mechanism of cofactor-independent regulation of transcription factor binding in mediating gene expression specificity.
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Affiliation(s)
- Kevin Rodriguez
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Albert Do
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Betul Senay-Aras
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Mariano Perales
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Weitao Chen
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - G. Venugopala Reddy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
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11
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Hegde S, Sreejan A, Gadgil CJ, Ratnaparkhi GS. SUMOylation of Dorsal attenuates Toll/NF-κB signaling. Genetics 2022; 221:iyac081. [PMID: 35567478 PMCID: PMC9252280 DOI: 10.1093/genetics/iyac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
In Drosophila, Toll/NF-κB signaling plays key roles in both animal development and in host defense. The activation, intensity, and kinetics of Toll signaling are regulated by posttranslational modifications such as phosphorylation, SUMOylation, or ubiquitination that target multiple proteins in the Toll/NF-κB cascade. Here, we have generated a CRISPR-Cas9 edited Dorsal (DL) variant that is SUMO conjugation resistant. Intriguingly, embryos laid by dlSCR mothers overcome dl haploinsufficiency and complete the developmental program. This ability appears to be a result of higher transcriptional activation by DLSCR. In contrast, SUMOylation dampens DL transcriptional activation, ultimately conferring robustness to the dorso-ventral program. In the larval immune response, dlSCR animals show an increase in crystal cell numbers, stronger activation of humoral defense genes, and high cactus levels. A mathematical model that evaluates the contribution of the small fraction of SUMOylated DL (1-5%) suggests that it acts to block transcriptional activation, which is driven primarily by DL that is not SUMO conjugated. Our findings define SUMO conjugation as an important regulator of the Toll signaling cascade, in both development and host defense. Our results broadly suggest that SUMO attenuates DL at the level of transcriptional activation. Furthermore, we hypothesize that SUMO conjugation of DL may be part of a Ubc9-dependent mechanism that restrains Toll/NF-κB signaling.
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Affiliation(s)
- Sushmitha Hegde
- Biology, Indian Institute of Science Education & Research, Pune 411008, India
| | - Ashley Sreejan
- Chemical Engineering and Process Development Division, CSIR—National Chemical Laboratory, Pune 411008, India
| | - Chetan J Gadgil
- Chemical Engineering and Process Development Division, CSIR—National Chemical Laboratory, Pune 411008, India
- CSIR—Institute of Genomics and Integrative Biology, New Delhi 110020, India
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12
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Macabenta F, Sun HT, Stathopoulos A. BMP-gated cell-cycle progression drives anoikis during mesenchymal collective migration. Dev Cell 2022; 57:1683-1693.e3. [PMID: 35709766 PMCID: PMC9339487 DOI: 10.1016/j.devcel.2022.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 05/02/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022]
Abstract
Tissue homeostasis involves the elimination of abnormal cells to avoid compromised patterning and function. Although quality control through cell competition is well studied in epithelial tissues, it is unknown if and how homeostasis is regulated in mesenchymal collectives. Here, we demonstrate that collectively migrating Drosophila muscle precursors utilize both fibroblast growth factor (FGF) and bone morphogenetic protein (BMP) signaling to promote homeostasis via anoikis, a form of cell death in response to substrate de-adhesion. Cell-cycle-regulated expression of the cell death gene head involution defective is responsible for caudal visceral mesoderm (CVM) anoikis. The secreted BMP ligand drives cell-cycle progression via a visceral mesoderm-specific cdc25/string enhancer to synchronize collective proliferation, as well as apoptosis of cells that have lost access to substrate-derived FGF. Perturbation of BMP-dependent cell-cycle progression is sufficient to confer anoikis resistance to mismigrating cells and thus facilitate invasion of other tissues. This BMP-gated cell-cycle checkpoint defines a quality control mechanism during mesenchymal collective migration.
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Affiliation(s)
- Frank Macabenta
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Hsuan-Te Sun
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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13
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Shields A, Amcheslavsky A, Brown E, Lee TV, Nie Y, Tanji T, Ip YT, Bergmann A. Toll-9 interacts with Toll-1 to mediate a feedback loop during apoptosis-induced proliferation in Drosophila. Cell Rep 2022; 39:110817. [PMID: 35584678 PMCID: PMC9211775 DOI: 10.1016/j.celrep.2022.110817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/25/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022] Open
Abstract
Drosophila Toll-1 and all mammalian Toll-like receptors regulate innate immunity. However, the functions of the remaining eight Toll-related proteins in Drosophila are not fully understood. Here, we show that Drosophila Toll-9 is necessary and sufficient for a special form of compensatory proliferation after apoptotic cell loss (undead apoptosis-induced proliferation [AiP]). Mechanistically, for AiP, Toll-9 interacts with Toll-1 to activate the intracellular Toll-1 pathway for nuclear translocation of the NF-κB-like transcription factor Dorsal, which induces expression of the pro-apoptotic genes reaper and hid. This activity contributes to the feedback amplification loop that operates in undead cells. Given that Toll-9 also functions in loser cells during cell competition, we define a general role of Toll-9 in cellular stress situations leading to the expression of pro-apoptotic genes that trigger apoptosis and apoptosis-induced processes such as AiP. This work identifies conceptual similarities between cell competition and AiP.
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Affiliation(s)
- Alicia Shields
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Alla Amcheslavsky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Elizabeth Brown
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Tom V Lee
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yingchao Nie
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Takahiro Tanji
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Y Tony Ip
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andreas Bergmann
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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14
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Rose M, Domsch K, Bartle-Schultheis J, Reim I, Schaub C. Twist regulates Yorkie activity to guide lineage reprogramming of syncytial alary muscles. Cell Rep 2022; 38:110295. [DOI: 10.1016/j.celrep.2022.110295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/25/2021] [Accepted: 01/04/2022] [Indexed: 11/28/2022] Open
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15
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Multiple Risk Factors for Heart Disease: A Challenge to the Ethnopharmacological Use of Croton urucurana Baill. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6580458. [PMID: 34819983 PMCID: PMC8608512 DOI: 10.1155/2021/6580458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022]
Abstract
Croton urucurana Baill. is a native Brazilian tree, popularly known as "sangra-d'água" or "sangue-de-dragão," based on the red resinous sap of the trunk. Its use has been transmitted through generations based on popular tradition that attributes analgesic, anti-inflammatory, and cardioprotective properties to the tree. However, its cardioprotective effects have not yet been scientifically investigated. Thus, the present study investigated the pharmacological response to an ethanol-soluble fraction from the leaves of C. urucurana in Wistar rats exposed to smoking and dyslipidemia, two important cardiovascular risk factors. The extract was evaluated by high-performance liquid chromatography. Wistar rats received a 0.5% cholesterol-enriched diet and were exposed to cigarette smoke (9 cigarettes/day for 10 weeks). During the last 5 weeks, the animals were orally treated with vehicle (negative control group), C. urucurana extract (30, 100, and 300 mg/kg), or simvastatin (2.5 mg/kg) + enalapril (15 mg/kg). One group of rats that was not exposed to these risk factors was also evaluated (basal group). Electrocardiograms and systolic, diastolic, and mean blood pressure were measured. Blood was collected to measure total cholesterol, triglycerides, urea, and creatinine. The heart and kidneys were collected and processed for oxidative status and histopathological evaluation. The phytochemical analysis revealed different classes of flavonoids and condensed tannins. The model induced dyslipidemia and cardiac and renal oxidative stress and increased levels of urea and creatinine in the negative control group. Treatment with the C. urucurana extract (300 mg/kg) and simvastatin + enalapril decreased cholesterol and triglyceride levels. In contrast to simvastatin + enalapril treatment, the C. urucurana extract exerted cardiac and renal antioxidant effects. No alterations of electrocardiograms, blood pressure, or histopathology were observed between groups. These findings indicate that C. urucurana exerts lipid-lowering, renal, and cardioprotective effects against oxidative stress in a preclinical model of multiple risk factors for heart disease.
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16
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Rich A, Glotzer M. Small GTPases modulate intrinsic and extrinsic forces that control epithelial folding in Drosophila embryos. Small GTPases 2021; 12:416-428. [PMID: 33985411 DOI: 10.1080/21541248.2021.1926879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Epithelial folding is a common means to execute morphogenetic movements. The gastrulating Drosophila embryo offers many examples of epithelial folding events, including the ventral, cephalic, and dorsal furrows. Each of these folding events is associated with changes in intracellular contractility and/or cytoskeleton structures that autonomously promote epithelial folding. Here, we review accumulating evidence that suggests the progression and final form of ventral, cephalic, and dorsal furrows are also influenced by the behaviour of cells neighbouring these folds. We further discuss the prevalence and importance of junctional rearrangements during epithelial folding events, suggesting adherens junction components are prime candidates to modulate the transmission of the intercellular forces that influence folding events. Finally, we discuss how recently developed methods that enable precise spatial and/or temporal control of protein activity allow direct testing of molecular models of morphogenesis in vivo.
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Affiliation(s)
- Ashley Rich
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.,Department of Cell Biology, Duke University School of Medicine, Durham, NC, USA
| | - Michael Glotzer
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
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17
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Stapornwongkul KS, Vincent JP. Generation of extracellular morphogen gradients: the case for diffusion. Nat Rev Genet 2021; 22:393-411. [PMID: 33767424 DOI: 10.1038/s41576-021-00342-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Cells within developing tissues rely on morphogens to assess positional information. Passive diffusion is the most parsimonious transport model for long-range morphogen gradient formation but does not, on its own, readily explain scaling, robustness and planar transport. Here, we argue that diffusion is sufficient to ensure robust morphogen gradient formation in a variety of tissues if the interactions between morphogens and their extracellular binders are considered. A current challenge is to assess how the affinity for extracellular binders, as well as other biophysical and cell biological parameters, determines gradient dynamics and shape in a diffusion-based transport system. Technological advances in genome editing, tissue engineering, live imaging and in vivo biophysics are now facilitating measurement of these parameters, paving the way for mathematical modelling and a quantitative understanding of morphogen gradient formation and modulation.
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18
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Domsch K, Schröder J, Janeschik M, Schaub C, Lohmann I. The Hox Transcription Factor Ubx Ensures Somatic Myogenesis by Suppressing the Mesodermal Master Regulator Twist. Cell Rep 2021; 34:108577. [PMID: 33406430 DOI: 10.1016/j.celrep.2020.108577] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 10/25/2020] [Accepted: 12/08/2020] [Indexed: 02/03/2023] Open
Abstract
Early lineage-specific master regulators are essential for the specification of cell types. However, once cells are committed to a specific fate, it is critical to restrict the activity of such factors to enable differentiation. To date, it remains unclear how these factors are silenced. Using the Drosophila mesoderm as a model and a comparative genomic approach, we identify the Hox transcription factor Ultrabithorax (Ubx) to be critical for the repression of the master regulator Twist. Mesoderm-specific Ubx loss-of-function experiments using CRISPR-Cas9 and overexpression studies demonstrate that Ubx majorly impacts twist transcription. A mechanistic analysis reveals that Ubx requires the NK-homeodomain protein Tinman to bind to the twist promoter. Furthermore, we find these factor interactions to be critical for silencing by recruiting the Polycomb DNA binding protein Pleiohomeotic. Altogether, our data reveal that Ubx is a critical player in mediating the silencing of Twist, which is crucial for coordinated muscle differentiation.
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Affiliation(s)
- Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany.
| | - Julia Schröder
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany
| | - Matthias Janeschik
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany
| | - Christoph Schaub
- Erlangen-Nürnberg University, Developmental Biology, 91058 Erlangen, Germany
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, 69120 Heidelberg, Germany
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19
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Rich A, Fehon RG, Glotzer M. Rho1 activation recapitulates early gastrulation events in the ventral, but not dorsal, epithelium of Drosophila embryos. eLife 2020; 9:56893. [PMID: 33200987 PMCID: PMC7717907 DOI: 10.7554/elife.56893] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/16/2020] [Indexed: 12/27/2022] Open
Abstract
Ventral furrow formation, the first step in Drosophila gastrulation, is a well-studied example of tissue morphogenesis. Rho1 is highly active in a subset of ventral cells and is required for this morphogenetic event. However, it is unclear whether spatially patterned Rho1 activity alone is sufficient to recapitulate all aspects of this morphogenetic event, including anisotropic apical constriction and coordinated cell movements. Here, using an optogenetic probe that rapidly and robustly activates Rho1 in Drosophila tissues, we show that Rho1 activity induces ectopic deformations in the dorsal and ventral epithelia of Drosophila embryos. These perturbations reveal substantial differences in how ventral and dorsal cells, both within and outside the zone of Rho1 activation, respond to spatially and temporally identical patterns of Rho1 activation. Our results demonstrate that an asymmetric zone of Rho1 activity is not sufficient to recapitulate ventral furrow formation and reveal that additional, ventral-specific factors contribute to the cell- and tissue-level behaviors that emerge during ventral furrow formation.
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Affiliation(s)
- Ashley Rich
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, United States
| | - Richard G Fehon
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, United States
| | - Michael Glotzer
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, United States
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20
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Sun J, Macabenta F, Akos Z, Stathopoulos A. Collective Migrations of Drosophila Embryonic Trunk and Caudal Mesoderm-Derived Muscle Precursor Cells. Genetics 2020; 215:297-322. [PMID: 32487692 PMCID: PMC7268997 DOI: 10.1534/genetics.120.303258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 04/17/2020] [Indexed: 01/06/2023] Open
Abstract
Mesoderm migration in the Drosophila embryo is a highly conserved, complex process that is required for the formation of specialized tissues and organs, including the somatic and visceral musculature. In this FlyBook chapter, we will compare and contrast the specification and migration of cells originating from the trunk and caudal mesoderm. Both cell types engage in collective migrations that enable cells to achieve new positions within developing embryos and form distinct tissues. To start, we will discuss specification and early morphogenetic movements of the presumptive mesoderm, then focus on the coordinate movements of the two subtypes trunk mesoderm and caudal visceral mesoderm, ending with a comparison of these processes including general insights gained through study.
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Affiliation(s)
- Jingjing Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Frank Macabenta
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Zsuzsa Akos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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21
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Bandodkar PU, Al Asafen H, Reeves GT. Spatiotemporal control of gene expression boundaries using a feedforward loop. Dev Dyn 2020; 249:369-382. [PMID: 31925874 DOI: 10.1002/dvdy.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND A feedforward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen-mediated tissue patterning. However, most morphogen gradients also evolve in time. RESULTS We studied the spatiotemporal behavior of a coherent FFL in two contexts: (a) a generic, oscillating morphogen gradient and (b) the dorsal-ventral patterning of the early Drosophila embryo by a gradient of the NF-κB homolog dorsal with its early target Twist. In both models, we found features in the dynamics of the intermediate node-phase difference and noise filtering-that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the dorsal gradient model, we also found that proper target gene expression was not possible without including the effect of maternal pioneer factor Zelda. CONCLUSIONS An FFL buffers fluctuation to changes in the morphogen signal ensuring stable gene expression boundaries.
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Affiliation(s)
- Prasad U Bandodkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Hadel Al Asafen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
| | - Gregory T Reeves
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina
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22
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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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23
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A Cell Density-Dependent Reporter in the Drosophila S2 Cells. Sci Rep 2019; 9:11868. [PMID: 31413273 PMCID: PMC6694118 DOI: 10.1038/s41598-019-47652-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/22/2019] [Indexed: 01/20/2023] Open
Abstract
Cell density regulates many aspects of cell properties and behaviors including metabolism, growth, cytoskeletal structure and locomotion. Importantly, the responses by cultured cells to density signals also uncover key mechanisms that govern animal development and diseases in vivo. Here we characterized a density-responsive reporter system in transgenic Drosophila S2 cells. We show that the reporter genes are strongly induced in a cell density-dependent and reporter-independent fashion. The rapid and reversible induction occurs at the level of mRNA accumulation. We show that multiple DNA elements within the transgene sequences, including a metal response element from the metallothionein gene, contribute to the reporter induction. The reporter induction correlates with changes in multiple cell density and growth regulatory pathways including hypoxia, apoptosis, cell cycle and cytoskeletal organization. Potential applications of such a density-responsive reporter will be discussed.
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24
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PLCε regulates prostate cancer mitochondrial oxidative metabolism and migration via upregulation of Twist1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:337. [PMID: 31383001 PMCID: PMC6683382 DOI: 10.1186/s13046-019-1323-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 07/14/2019] [Indexed: 12/17/2022]
Abstract
Background Metabolic rewiring is a common feature of many cancer types, including prostate cancer (PCa). Alterations in master genes lead to mitochondrial metabolic rewiring and provide an appealing target to inhibit cancer progression and improve survival. Phospholipase C (PLC)ε is a regulator of tumor generation and progression. However, its role in mitochondrial metabolism remains unclear. Methods The GEO, The Cancer Genome Atlas, and the GTEx databases were used to determine Twist1 mRNA levels in tumors and their non-tumor counterparts. Fifty-five PCa and 48 benign prostatic hypertrophy tissue samples were tested for the presence of PLCε and Twist1 immunohistochemically. An association between PLCε and Twist1 was determined by Pearson’s correlation analysis. PLCε was knocked down with a lentiviral short hairpin RNA. Mitochondrial activity was assessed by measuring the oxygen consumption rate. Western blotting analyses were used to measure levels of PPARβ, Twist1, phosphorylated (p)-Twist1, p-MEK, p-ERK, p-P38, and p-c-Jun N-terminal kinase (JNK). Cells were treated with inhibitors of MEK, JNK, and P38 MAPK, and an agonist and inhibitor of peroxisome proliferator activated receptor (PPAR) β, to evaluate which signaling pathways were involved in PLCε-mediated Twist1 expression. The stability of Twist1 was determined after blocking protein synthesis with cycloheximide. Reporter assays utilized E-cadherin or N-cadherin luciferase reporters under depletion of PLCε or Twist1. Transwell assays assessed cell migration. Finally, a nude mouse tumor xenograft assay was conducted to verify the role of PLCε in tumor formation. Results Our findings revealed that the expression of PLCε was positively associated with Twist1 in clinical PCa samples. PLCε knockdown promoted mitochondrial oxidative metabolism in PCa cells. Mechanistically, PLCε increased phosphorylation of Twist1 and stabilized the Twist1 protein through MAPK signaling. The transcriptional activity of Twist1, and the Twist1-mediated epithelial-to-mesenchymal transition, cell migration, and transcription regulation, were suppressed by PLCε knockdown and by blocking PPARβ nuclear translocation. The tumor xenograft assay demonstrated that PLCε depletion diminished PCa cell tumorigenesis. Conclusions These findings reveal an undiscovered physiological role for PLCε in the suppression of mitochondrial oxidative metabolism that has significant implications for understanding PCa occurrence and migration. Electronic supplementary material The online version of this article (10.1186/s13046-019-1323-8) contains supplementary material, which is available to authorized users.
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25
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Macabenta F, Stathopoulos A. Migrating cells control morphogenesis of substratum serving as track to promote directional movement of the collective. Development 2019; 146:dev.177295. [PMID: 31239242 DOI: 10.1242/dev.177295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022]
Abstract
In Drosophila embryos, caudal visceral mesoderm (CVM) cells undergo bilateral migration along the trunk visceral mesoderm (TVM) in order to form midgut muscles. Mutation of FGF receptor Heartless (Htl) has been shown to cause CVM migration defects, particularly midline crossing of the bilateral groups. Here, we show that htl mutants also exhibit TVM defects including contralateral merging. Both CVM mismigration and TVM contralateral merging are attenuated by restoring FGF signaling specifically in the CVM, suggesting that migrating CVM cells influence TVM morphogenesis; however, the inverse, supplying FGF to the TVM, does not rescue CVM mismigration. In addition, we show that FGF regulates integrin expression in both tissues, but only providing a source of integrin specifically to the TVM attenuates the contralateral merging phenotype. Finally, we demonstrate that the CVM influences cell shape in the TVM, and a loss of CVM results in TVM morphological defects. In summary, this study provides insight into how a migrating collective of cells can influence their tissue substrate and supports the view that morphogenesis of tissues during development is interdependent.
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Affiliation(s)
- Frank Macabenta
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
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26
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Yamini B. NF-κB, Mesenchymal Differentiation and Glioblastoma. Cells 2018; 7:cells7090125. [PMID: 30200302 PMCID: PMC6162779 DOI: 10.3390/cells7090125] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/14/2018] [Accepted: 08/30/2018] [Indexed: 12/11/2022] Open
Abstract
Although glioblastoma (GBM) has always been recognized as a heterogeneous tumor, the advent of largescale molecular analysis has enabled robust categorization of this malignancy into several specific subgroups. Among the subtypes designated by expression profiling, mesenchymal tumors have been associated with an inflammatory microenvironment, increased angiogenesis, and resistance to therapy. Nuclear factor-κB (NF-κB) is a ubiquitous transcription factor that plays a prominent role in mediating many of the central features associated with mesenchymal differentiation. This review summarizes the mechanisms by which NF-κB proteins and their co-regulating partners induce the transcriptional network that underlies the mesenchymal phenotype. Moreover, both the intrinsic changes within mesenchymal GBM cells and the microenvironmental factors that modify the overall NF-κB response are detailed.
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Affiliation(s)
- Bakhtiar Yamini
- Section of Neurosurgery Department of Surgery, The University of Chicago, Chicago, IL 60637, USA.
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27
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NF-κB/twist mediated regulation of colonic inflammation by lupeol in abating dextran sodium sulfate induced colitis in mice. J Funct Foods 2018. [DOI: 10.1016/j.jff.2017.12.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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28
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Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EEM. The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription. Genes Dev 2018; 32:42-57. [PMID: 29378788 PMCID: PMC5828394 DOI: 10.1101/gad.308619.117] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 12/21/2017] [Indexed: 12/03/2022]
Abstract
Here, Mikhaylichenko et al. investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. The authors demonstrate that while the timing of enhancer transcription is correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers and conclude that this is likely an inherent sequence property of the elements themselves. Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio–temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.
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Affiliation(s)
- Olga Mikhaylichenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Vladyslav Bondarenko
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Dermot Harnett
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Ignacio E Schor
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Matilda Males
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Rebecca R Viales
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), D-69117 Heidelberg, Germany
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29
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Zhao Z, Rahman MA, Chen ZG, Shin DM. Multiple biological functions of Twist1 in various cancers. Oncotarget 2017; 8:20380-20393. [PMID: 28099910 PMCID: PMC5386770 DOI: 10.18632/oncotarget.14608] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/01/2017] [Indexed: 01/05/2023] Open
Abstract
Twist1 is a well-known regulator of transcription during embryonic organogenesis in many species. In humans, Twist1 malfunction was first linked to Saethre-Chotzen syndrome and later identified to play an essential role in tumor initiation, stemness, angiogenesis, invasion, metastasis, and chemo-resistance in a variety of carcinomas, sarcomas, and hematological malignances. In this review, we will first focus on systematically elaborating the diverse pathological functions of Twist1 in various cancers, then delineating the intricate underlying network of molecular mechanisms, based on which we will summarize current therapeutic strategies in cancer treatment that target and modulate Twist1-involved signaling pathways. Most importantly, we will put special emphasis on revealing the independence and interdependency of these multiple biological functions of Twist1, piecing together the whole delicate picture of Twist1's diversified pathological roles in different cancers and providing new perspectives to guide future research.
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Affiliation(s)
- Zhixiang Zhao
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, United States of America.,Department of Dermatology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mohammad Aminur Rahman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, United States of America
| | - Zhuo G Chen
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, United States of America
| | - Dong M Shin
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, United States of America
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30
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Stepanik V, Dunipace L, Bae YK, Macabenta F, Sun J, Trisnadi N, Stathopoulos A. The migrations of Drosophila muscle founders and primordial germ cells are interdependent. Development 2017; 143:3206-15. [PMID: 27578182 DOI: 10.1242/dev.134346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 07/29/2016] [Indexed: 12/31/2022]
Abstract
Caudal visceral mesoderm (CVM) cells migrate from posterior to anterior of the Drosophila embryo as two bilateral streams of cells to support the specification of longitudinal muscles along the midgut. To accomplish this long-distance migration, CVM cells receive input from their environment, but little is known about how this collective cell migration is regulated. In a screen we found that wunen mutants exhibit CVM cell migration defects. Wunens are lipid phosphate phosphatases known to regulate the directional migration of primordial germ cells (PGCs). PGC and CVM cell types interact while PGCs are en route to the somatic gonadal mesoderm, and previous studies have shown that CVM impacts PGC migration. In turn, we found here that CVM cells exhibit an affinity for PGCs, localizing to the position of PGCs whether mislocalized or trapped in the endoderm. In the absence of PGCs, CVM cells exhibit subtle changes, including more cohesive movement of the migrating collective, and an increased number of longitudinal muscles is found at anterior sections of the larval midgut. These data demonstrate that PGC and CVM cell migrations are interdependent and suggest that distinct migrating cell types can coordinately influence each other to promote effective cell migration during development.
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Affiliation(s)
- Vincent Stepanik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leslie Dunipace
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Young-Kyung Bae
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Frank Macabenta
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jingjing Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nathanie Trisnadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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31
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Feitosa NM, Pechmann M, Schwager EE, Tobias-Santos V, McGregor AP, Damen WGM, Nunes da Fonseca R. Molecular control of gut formation in the spider Parasteatoda tepidariorum. Genesis 2017; 55. [PMID: 28432834 DOI: 10.1002/dvg.23033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/23/2017] [Accepted: 03/16/2017] [Indexed: 12/16/2022]
Abstract
The development of a digestive system is an essential feature of bilaterians. Studies of the molecular control of gut formation in arthropods have been studied in detail in the fruit fly Drosophila melanogaster. However, little is known in other arthropods, especially in noninsect arthropods. To better understand the evolution of arthropod alimentary system, we investigate the molecular control of gut development in the spider Parasteatoda tepidariorum (Pt), the primary chelicerate model species for developmental studies. Orthologs of the ectodermal genes Pt-wingless (Pt-wg) and Pt-hedgehog (Pt-hh), of the endodermal genes, Pt-serpent (Pt-srp) and Pt-hepatocyte-nuclear factor-4 (Pt-hnf4) and of the mesodermal gene Pt-twist (Pt-twi) are expressed in the same germ layers during spider gut development as in D. melanogaster. Thus, our expression data suggest that the downstream molecular components involved in gut development in arthropods are conserved. However, Pt-forkhead (Pt-fkh) expression and function in spiders is considerably different from its D. melanogaster ortholog. Pt-fkh is expressed before gastrulation in a cell population that gives rise to endodermal and mesodermal precursors, suggesting a possible role for this factor in specification of both germ layers. To test this hypothesis, we knocked down Pt-fkh via RNA interference. Pt-fkh RNAi embryos not only fail to develop a proper gut, but also lack the mesodermal Pt-twi expressing cells. Thus, in spiders Pt-fkh specifies endodermal and mesodermal germ layers. We discuss the implications of these findings for the evolution and development of gut formation in Ecdysozoans.
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Affiliation(s)
- Natália Martins Feitosa
- Laboratório Integrado de Ciências Morfofuncionais, Núcleo em Ecologia e Desenvolvimento Socio-Ambiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, 27920-560, Brazil
| | - Matthias Pechmann
- Institute for Developmental Biology, University of Cologne, Cologne, North-Rhine Westphalia, 50674, Germany
| | - Evelyn E Schwager
- Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, Massachusetts, 01854
| | - Vitória Tobias-Santos
- Laboratório Integrado de Ciências Morfofuncionais, Núcleo em Ecologia e Desenvolvimento Socio-Ambiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, 27920-560, Brazil
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Wim G M Damen
- Department of Genetics, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena, 07743, Germany
| | - Rodrigo Nunes da Fonseca
- Laboratório Integrado de Ciências Morfofuncionais, Núcleo em Ecologia e Desenvolvimento Socio-Ambiental de Macaé (NUPEM), Campus Macaé, Universidade Federal do Rio de Janeiro (UFRJ), Macaé, Rio de Janeiro, 27920-560, Brazil.,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Universidade Federal do Rio de Janeiro (UFRJ), 21941-599 Rio de Janeiro, Rio de Janeiro, Brazil
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32
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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.
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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
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33
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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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34
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Initiation of diverse epigenetic states during nuclear programming of the Drosophila body plan. Proc Natl Acad Sci U S A 2016; 113:8735-40. [PMID: 27439862 DOI: 10.1073/pnas.1516450113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epigenetic patterns of histone modifications contribute to the maintenance of tissue-specific gene expression. Here, we show that such modifications also accompany the specification of cell identities by the NF-κB transcription factor Dorsal in the precellular Drosophila embryo. We provide evidence that the maternal pioneer factor, Zelda, is responsible for establishing poised RNA polymerase at Dorsal target genes before Dorsal-mediated zygotic activation. At the onset of cell specification, Dorsal recruits the CBP/p300 coactivator to the regulatory regions of defined target genes in the presumptive neuroectoderm, resulting in their histone acetylation and transcriptional activation. These genes are inactive in the mesoderm due to transcriptional quenching by the Snail repressor, which precludes recruitment of CBP and prevents histone acetylation. By contrast, inactivation of the same enhancers in the dorsal ectoderm is associated with Polycomb-repressed H3K27me3 chromatin. Thus, the Dorsal morphogen gradient produces three distinct histone signatures including two modes of transcriptional repression, active repression (hypoacetylation), and inactivity (H3K27me3). Whereas histone hypoacetylation is associated with a poised polymerase, H3K27me3 displaces polymerase from chromatin. Our results link different modes of RNA polymerase regulation to separate epigenetic patterns and demonstrate that developmental determinants orchestrate differential chromatin states, providing new insights into the link between epigenetics and developmental patterning.
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35
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Pettie KP, Dresch JM, Drewell RA. Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks. Mech Dev 2016; 141:51-61. [PMID: 27264535 DOI: 10.1016/j.mod.2016.06.001] [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: 11/19/2015] [Revised: 04/24/2016] [Accepted: 06/01/2016] [Indexed: 11/19/2022]
Abstract
In the development of the Drosophila embryo, gene expression is directed by the sequence-specific interactions of a large network of protein transcription factors (TFs) and DNA cis-regulatory binding sites. Once the identity of the typically 8-10bp binding sites for any given TF has been determined by one of several experimental procedures, the sequences can be represented in a position weight matrix (PWM) and used to predict the location of additional TF binding sites elsewhere in the genome. Often, alignments of large (>200bp) genomic fragments that have been experimentally determined to bind the TF of interest in Chromatin Immunoprecipitation (ChIP) studies are trimmed under the assumption that the majority of the binding sites are located near the center of all the aligned fragments. In this study, ChIP/chip datasets are analyzed using the corresponding PWMs for the well-studied TFs; CAUDAL, HUNCHBACK, KNIRPS and KRUPPEL, to determine the distribution of predicted binding sites. All four TFs are critical regulators of gene expression along the anterio-posterior axis in early Drosophila development. For all four TFs, the ChIP peaks contain multiple binding sites that are broadly distributed across the genomic region represented by the peak, regardless of the prediction stringency criteria used. This result suggests that ChIP peak trimming may exclude functional binding sites from subsequent analyses.
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Affiliation(s)
- Kade P Pettie
- Department of Biology, Amherst College, Amherst, MA 01002, United States
| | - Jacqueline M Dresch
- Department of Mathematics and Computer Science, Clark University, 950 Main Street, Worcester, MA 01610, United States
| | - Robert A Drewell
- Biology Department, Clark University, 950 Main Street, Worcester, MA 01610, United States
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36
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Sayal R, Dresch JM, Pushel I, Taylor BR, Arnosti DN. Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo. eLife 2016; 5. [PMID: 27152947 PMCID: PMC4859806 DOI: 10.7554/elife.08445] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 04/04/2016] [Indexed: 01/02/2023] Open
Abstract
Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal architecture and cis-regulatory grammar remain elusive. Here, we describe an extensive, quantitative perturbation analysis targeting the dorsal-ventral patterning gene regulatory network (GRN) controlled by Drosophila NF-κB homolog Dorsal. To understand transcription factor interactions on enhancers, we employed an ensemble of mathematical models, testing effects of cooperativity, repression, and factor potency. Models trained on the dataset correctly predict activity of evolutionarily divergent regulatory regions, providing insights into spatial relationships between repressor and activator binding sites. Importantly, the collective predictions of sets of models were effective at novel enhancer identification and characterization. Our study demonstrates how experimental dataset and modeling can be effectively combined to provide quantitative insights into cis-regulatory information on a genome-wide scale. DOI:http://dx.doi.org/10.7554/eLife.08445.001 DNA contains regions known as genes, which may be “transcribed” to produce the RNA molecules that act as templates for building proteins and regulate cell activity. Proteins called transcription factors can bind to specific sequences of DNA to influence whether nearby genes are transcribed. For example, so-called enhancer regions of DNA contain several binding sites for transcription factors, and this binding activates gene transcription. Little is known about how the transcription factor binding sites are organized in enhancer regions, which makes it difficult to use DNA sequence information alone to predict the regulation of genes. A transcription factor called Dorsal controls the activity of a network of genes that plays a crucial role in the development of fruit fly embryos. Dorsal binds to the enhancer region of a gene called rhomboid, which has been well studied and is known to be a fairly typical example of an enhancer region. To understand the regulatory information encoded in the DNA sequences of enhancers, Sayal, Dresch et al. have now used a technique called perturbation analysis to investigate the interactions that are likely to occur between Dorsal and other transcription factors as they bind to the rhomboid enhancer. This technique involves systematically mutating the enhancer to remove different combinations of transcription factor binding sites and quantitatively investigating the effect this has on gene activity. A large set of mathematical models were then trained using this data and shown to correctly predict the activity of a range of other gene regulatory regions. The collective predictions of the models identified new enhancer regions and revealed details about how different types of transcription factor binding sites are arranged within enhancers. As we enter an era where the DNA sequences of entire human populations are increasingly accessible, we would like to know the functional significance of changes in gene regulatory regions. Sayal, Dresch et al. show that the regulatory properties of specific control proteins are accessible by employing quantitative experiments and mathematical models. Similar studies will be required to learn how mutations found across the genome may alter gene expression, leading to better diagnosis and treatment of disease. DOI:http://dx.doi.org/10.7554/eLife.08445.002
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Affiliation(s)
- Rupinder Sayal
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Biochemistry, DAV University, Jalandhar, India
| | - Jacqueline M Dresch
- Department of Mathematics, Michigan State University, East Lansing, United States.,Department of Mathematics and Computer Science, Clark University, Worcester, United States
| | - Irina Pushel
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Stowers Institute for Medical Research, Kansas City, United States
| | - Benjamin R Taylor
- Department of Computer Science and Engineering, Michigan State University, East Lansing, United States.,School of Computer Science, Georgia Institute of Technology, Atlanta, United States
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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37
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Sharma R, Beer K, Iwanov K, Schmöhl F, Beckmann PI, Schröder R. The single fgf receptor gene in the beetle Tribolium castaneum codes for two isoforms that integrate FGF8- and Branchless-dependent signals. Dev Biol 2015; 402:264-75. [PMID: 25864412 DOI: 10.1016/j.ydbio.2015.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/16/2022]
Abstract
The precise regulation of cell-cell communication by numerous signal-transduction pathways is fundamental for many different processes during embryonic development. One important signalling pathway is the evolutionary conserved fibroblast-growth-factor (FGF)-pathway that controls processes like cell migration, axis specification and mesoderm formation in vertebrate and invertebrate animals. In the model insect Drosophila, the FGF ligand / receptor combinations of FGF8 (Pyramus and Thisbe) / Heartless (Htl) and Branchless (Bnl) / Breathless (Btl) are required for the migration of mesodermal cells and for the formation of the tracheal network respectively with both the receptors functioning independently of each other. However, only a single fgf-receptor gene (Tc-fgfr) has been identified in the genome of the beetle Tribolium. We therefore asked whether both the ligands Fgf8 and Bnl could transduce their signal through a common FGF-receptor in Tribolium. Indeed, we found that the function of the single Tc-fgfr gene is essential for mesoderm differentiation as well as for the formation of the tracheal network during early development. Ligand specific RNAi for Tc-fgf8 and Tc-bnl resulted in two distinct non-overlapping phenotypes of impaired mesoderm differentiation and abnormal formation of the tracheal network in Tc-fgf8- and Tc-bnl(RNAi) embryos respectively. We further show that the single Tc-fgfr gene encodes at least two different receptor isoforms that are generated through alternative splicing. We in addition demonstrate through exon-specific RNAi their distinct tissue-specific functions. Finally, we discuss the structure of the fgf-receptor gene from an evolutionary perspective.
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Affiliation(s)
- Rahul Sharma
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Katharina Beer
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Katharina Iwanov
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Felix Schmöhl
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Paula Indigo Beckmann
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Reinhard Schröder
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany.
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38
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Peng H, Myers EW. Constructing 5D developing gene expression patterns without live animal imaging. Biomed Eng Lett 2014. [DOI: 10.1007/s13534-014-0167-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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39
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Mazari AMA, Dahlberg O, Mannervik B, Mannervik M. Overexpression of glutathione transferase E7 in Drosophila differentially impacts toxicity of organic isothiocyanates in males and females. PLoS One 2014; 9:e110103. [PMID: 25329882 PMCID: PMC4199631 DOI: 10.1371/journal.pone.0110103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 09/16/2014] [Indexed: 11/18/2022] Open
Abstract
Organic isothiocyanates (ITCs) are allelochemicals produced by plants in order to combat insects and other herbivores. The compounds are toxic electrophiles that can be inactivated and conjugated with intracellular glutathione in reactions catalyzed by glutathione transferases (GSTs). The Drosophila melanogaster GSTE7 was heterologously expressed in Escherichia coli and purified for functional studies. The enzyme showed high catalytic activity with various isothiocyanates including phenethyl isothiocyanate (PEITC) and allyl isothiocyanate (AITC), which in millimolar dietary concentrations conferred toxicity to adult D. melanogaster leading to death or a shortened life-span of the flies. In situ hybridization revealed a maternal contribution of GSTE7 transcripts to embryos, and strongest zygotic expression in the digestive tract. Transgenesis involving the GSTE7 gene controlled by an actin promoter produced viable flies expressing the GSTE7 transcript ubiquitously. Transgenic females show a significantly increased survival when subjected to the same PEITC treatment as the wild-type flies. By contrast, transgenic male flies show a significantly lower survival rate. Oviposition activity was enhanced in transgenic flies. The effect was significant in transgenic females reared in the absence of ITCs as well as in the presence of 0.15 mM PEITC or 1 mM AITC. Thus the GSTE7 transgene elicits responses to exposure to ITC allelochemicals which differentially affect life-span and fecundity of male and female flies.
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Affiliation(s)
- Aslam M. A. Mazari
- Department of Neurochemistry, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Olle Dahlberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bengt Mannervik
- Department of Neurochemistry, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail: (BM); (MM)
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- * E-mail: (BM); (MM)
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40
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Analytic approaches to stochastic gene expression in multicellular systems. Biophys J 2014; 105:2629-40. [PMID: 24359735 DOI: 10.1016/j.bpj.2013.10.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 10/16/2013] [Indexed: 11/22/2022] Open
Abstract
Deterministic thermodynamic models of the complex systems, which control gene expression in metazoa, are helping researchers identify fundamental themes in the regulation of transcription. However, quantitative single cell studies are increasingly identifying regulatory mechanisms that control variability in expression. Such behaviors cannot be captured by deterministic models and are poorly suited to contemporary stochastic approaches that rely on continuum approximations, such as Langevin methods. Fortunately, theoretical advances in the modeling of transcription have assembled some general results that can be readily applied to systems being explored only through a deterministic approach. Here, I review some of the recent experimental evidence for the importance of genetically regulating stochastic effects during embryonic development and discuss key results from Markov theory that can be used to model this regulation. I then discuss several pairs of regulatory mechanisms recently investigated through a Markov approach. In each case, a deterministic treatment predicts no difference between the mechanisms, but the statistical treatment reveals the potential for substantially different distributions of transcriptional activity. In this light, features of gene regulation that seemed needlessly complex evolutionary baggage may be appreciated for their key contributions to reliability and precision of gene expression.
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41
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Gregor T, Garcia HG, Little SC. The embryo as a laboratory: quantifying transcription in Drosophila. Trends Genet 2014; 30:364-75. [PMID: 25005921 DOI: 10.1016/j.tig.2014.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Revised: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 11/16/2022]
Abstract
Transcriptional regulation of gene expression is fundamental to most cellular processes, including determination of cellular fates. Quantitative studies of transcription in cultured cells have led to significant advances in identifying mechanisms underlying transcriptional control. Recent progress allowed implementation of these same quantitative methods in multicellular organisms to ask how transcriptional regulation unfolds both in vivo and at the single molecule level in the context of embryonic development. Here we review some of these advances in early Drosophila development, which bring the embryo on par with its single celled counterparts. In particular, we discuss progress in methods to measure mRNA and protein distributions in fixed and living embryos, and we highlight some initial applications that lead to fundamental new insights about molecular transcription processes. We end with an outlook on how to further exploit the unique advantages that come with investigating transcriptional control in the multicellular context of development.
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Affiliation(s)
- Thomas Gregor
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Hernan G Garcia
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 085444, USA
| | - Shawn C Little
- Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
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42
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Transcriptional regulation of graded Hedgehog signaling. Semin Cell Dev Biol 2014; 33:73-80. [PMID: 24862856 DOI: 10.1016/j.semcdb.2014.05.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 02/06/2023]
Abstract
The Hedgehog (Hh) pathway plays conserved roles in regulating a diverse spectrum of developmental processes. In some developmental contexts, a gradient of Hh protein specifies multiple cell types in a dose-dependent fashion, thereby acting as a morphogen. Hh signaling ultimately acts on the transcriptional level through GLI proteins. In the presence of Hh signaling full length GLI proteins act as transcriptional activators of target genes. Conversely, in the absence of Hh, GLI proteins act as transcriptional repressors. This review will highlight mechanisms contributing to how graded Hh signaling might translate to differential GLI activity and be interpreted into distinct transcriptional responses.
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43
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Abstract
The construction and prediction of cell fate maps at the whole embryo level require the establishment of an accurate atlas of gene expression patterns throughout development and the identification of the corresponding cis-regulatory sequences. However, while the expression and regulation of genes encoding upstream developmental regulators such as transcription factors or signaling pathway components have been analyzed in detail, up to date the number of cis-regulatory sequences identified for downstream effector genes, like ion channels, pumps and exchangers, is very low. The control and regulation of ion homeostasis in each cell, including at blastoderm stages, are essential for normal embryonic development. In this study, we analyzed in detail the embryonic expression pattern and cis-regulatory modules of the Drosophila Na+-driven anion exchanger 1 (Ndae1) gene, involved in the regulation of pH homeostasis. We show that Ndae1 is expressed in a tight and complex spatial-temporal pattern. In particular, we report that this downstream effector gene is under the control of the canonical dorsal-ventral patterning cascade through dorsal, Toll, twist and snail at early embryogenesis. Moreover, we identify several cis-regulatory modules, some of which control discrete and non-overlapping aspects of endogenous gene expression throughout development.
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44
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Zehavi Y, Kuznetsov O, Ovadia-Shochat A, Juven-Gershon T. Core promoter functions in the regulation of gene expression of Drosophila dorsal target genes. J Biol Chem 2014; 289:11993-12004. [PMID: 24634215 DOI: 10.1074/jbc.m114.550251] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Developmental processes are highly dependent on transcriptional regulation by RNA polymerase II. The RNA polymerase II core promoter is the ultimate target of a multitude of transcription factors that control transcription initiation. Core promoters consist of core promoter motifs, e.g. the initiator, TATA box, and the downstream core promoter element (DPE), which confer specific properties to the core promoter. Here, we explored the importance of core promoter functions in the dorsal-ventral developmental gene regulatory network. This network includes multiple genes that are activated by different nuclear concentrations of Dorsal, an NFκB homolog transcription factor, along the dorsal-ventral axis. We show that over two-thirds of Dorsal target genes contain DPE sequence motifs, which is significantly higher than the proportion of DPE-containing promoters in Drosophila genes. We demonstrate that multiple Dorsal target genes are evolutionarily conserved and functionally dependent on the DPE. Furthermore, we have analyzed the activation of key Dorsal target genes by Dorsal, as well as by another Rel family transcription factor, Relish, and the dependence of their activation on the DPE motif. Using hybrid enhancer-promoter constructs in Drosophila cells and embryo extracts, we have demonstrated that the core promoter composition is an important determinant of transcriptional activity of Dorsal target genes. Taken together, our results provide evidence for the importance of core promoter composition in the regulation of Dorsal target genes.
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Affiliation(s)
- Yonathan Zehavi
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Olga Kuznetsov
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Avital Ovadia-Shochat
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Tamar Juven-Gershon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
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45
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Hong JW, Park KW, Levine MS. Temporal regulation of single-minded target genes in the ventral midline of the Drosophila central nervous system. Dev Biol 2013; 380:335-43. [PMID: 23701883 DOI: 10.1016/j.ydbio.2013.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/11/2013] [Accepted: 05/13/2013] [Indexed: 12/21/2022]
Abstract
Differentiation of a specific organ or tissue requires sequential activation of regulatory genes. However, little is known about how serial gene expression is temporally regulated. Here, we present evidence that differential expression of single-minded (sim) target genes can be attributed, in part, to the number of Sim and Tango (Tgo) heterodimer binding sites within their enhancer regions. The Sim, termed a master regulator, directs ventral midline differentiation of Drosophila central nervous system (CNS). According to data on the onset timing of ventral midline gene expression, sim target genes are classified into at least 2 groups (early and late). The sim and rhomboid (rho) genes are activated during early midline differentiation whereas orthodenticle (otd), CG10249, and slit (sli) genes undergo activation during later stages of midline differentiation. Germline transformation and in situ hybridization with transgenic embryos demonstrate that enhancers activating sim and rho expression contain 4 Sim-Tgo binding sites whereas only 1 Sim-Tgo binding site is found in an enhancer of sli. A mutagenized version of the rho enhancer lacking either 1, 2, or 3 Sim-Tgo binding sites mediated progressively more delayed expression of a lacZ reporter gene in the ventral midline. In contrast, a modified sli enhancer displayed progressively earlier onset of lacZ expression when 1, 2, or 3 more Sim-Tgo binding sites were added. Taken together, these results suggest that the number of Sim-Tgo-binding sites is decisive in determining the timing of gene expression in the developing ventral midline. We also discuss a combinatorial model accounting for the sequential expression of sim target genes.
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Affiliation(s)
- Joung-Woo Hong
- Graduate School of East-West Medical Science, Kyung Hee University, Yongin 446-701, South Korea.
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46
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Nakamura M, Matsumoto K, Iwamoto Y, Muguruma T, Nakazawa N, Hatori R, Taniguchi K, Maeda R, Matsuno K. Reduced cell number in the hindgut epithelium disrupts hindgut left–right asymmetry in a mutant of pebble, encoding a RhoGEF, in Drosophila embryos. Mech Dev 2013; 130:169-80. [DOI: 10.1016/j.mod.2012.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/24/2012] [Accepted: 09/26/2012] [Indexed: 10/27/2022]
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47
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Green SA, Norris RP, Terasaki M, Lowe CJ. FGF signaling induces mesoderm in the hemichordate Saccoglossus kowalevskii. Development 2013; 140:1024-33. [PMID: 23344709 DOI: 10.1242/dev.083790] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
FGFs act in vertebrate mesoderm induction and also play key roles in early mesoderm formation in ascidians and amphioxus. However, in sea urchins initial characterizations of FGF function do not support a role in early mesoderm induction, making the ancestral roles of FGF signaling and mechanisms of mesoderm specification in deuterostomes unclear. In order to better characterize the evolution of mesoderm formation, we have examined the role of FGF signaling during mesoderm development in Saccoglossus kowalevskii, an experimentally tractable representative of hemichordates. We report the expression of an FGF ligand, fgf8/17/18, in ectoderm overlying sites of mesoderm specification within the archenteron endomesoderm. Embryological experiments demonstrate that mesoderm induction in the archenteron requires contact with ectoderm, and loss-of-function experiments indicate that both FGF ligand and receptor are necessary for mesoderm specification. fgf8/17/18 gain-of-function experiments establish that FGF8/17/18 is sufficient to induce mesoderm in adjacent endomesoderm. These experiments suggest that FGF signaling is necessary from the earliest stages of mesoderm specification and is required for all mesoderm development. Furthermore, they suggest that the archenteron is competent to form mesoderm or endoderm, and that FGF signaling from the ectoderm defines the location and amount of mesoderm. When considered in a comparative context, these data support a phylogenetically broad requirement for FGF8/17/18 signaling in mesoderm specification and suggest that FGF signaling played an ancestral role in deuterostome mesoderm formation.
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Affiliation(s)
- Stephen A Green
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA.
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48
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Janssens H, Crombach A, Richard Wotton K, Cicin-Sain D, Surkova S, Lu Lim C, Samsonova M, Akam M, Jaeger J. Lack of tailless leads to an increase in expression variability in Drosophila embryos. Dev Biol 2013; 377:305-17. [PMID: 23333944 PMCID: PMC3635121 DOI: 10.1016/j.ydbio.2013.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 12/24/2012] [Accepted: 01/09/2013] [Indexed: 11/30/2022]
Abstract
Developmental processes are robust, or canalised: dynamic patterns of gene expression across space and time are regulated reliably and precisely in the presence of genetic and environmental perturbations. It remains unclear whether canalisation relies on specific regulatory factors (such as heat-shock proteins), or whether it is based on more general redundancy and distributed robustness at the network level. The latter explanation implies that mutations in many regulatory factors should exhibit loss of canalisation. Here, we present a quantitative characterisation of segmentation gene expression patterns in mutants of the terminal gap gene tailless (tll) in Drosophila melanogaster. Our analysis provides new insights into the dynamic mechanisms underlying gap gene regulation, and reveals significantly increased variability of gene expression in the mutant compared to the wild-type background. We show that both position and timing of posterior segmentation gene expression domains vary strongly from embryo-to-embryo in tll mutants. This variability must be caused by a vulnerability in the regulatory system which is hidden or buffered in the wild-type, but becomes uncovered by the deletion of tll. Our analysis provides evidence that loss of canalisation in mutants could be more widespread than previously thought.
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Affiliation(s)
- Hilde Janssens
- EMBL/CRG Research Unit in Systems Biology, CRG—Centre de Regulació Genòmica, and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anton Crombach
- EMBL/CRG Research Unit in Systems Biology, CRG—Centre de Regulació Genòmica, and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Karl Richard Wotton
- EMBL/CRG Research Unit in Systems Biology, CRG—Centre de Regulació Genòmica, and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Damjan Cicin-Sain
- EMBL/CRG Research Unit in Systems Biology, CRG—Centre de Regulació Genòmica, and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Svetlana Surkova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St. Petersburg 195251, Russia
| | - Chea Lu Lim
- Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK
| | - Maria Samsonova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St. Petersburg 195251, Russia
| | - Michael Akam
- Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, CRG—Centre de Regulació Genòmica, and Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
- Department of Zoology, Downing Street, Cambridge CB2 3EJ, UK
- Corresponding author at: Centre for Genomic Regulation (CRG), EMBL/CRG Research Unit in Systems Biology, Dr. Aiguader 88, 08003 Barcelona, Spain. Fax: +34 93 396 99 83.
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49
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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.
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Affiliation(s)
- Kye Won Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Korea
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50
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Li S, Kendall SE, Raices R, Finlay J, Covarrubias M, Liu Z, Lowe G, Lin YH, Teh YH, Leigh V, Dhillon S, Flanagan S, Aboody KS, Glackin CA. TWIST1 associates with NF-κB subunit RELA via carboxyl-terminal WR domain to promote cell autonomous invasion through IL8 production. BMC Biol 2012; 10:73. [PMID: 22891766 PMCID: PMC3482588 DOI: 10.1186/1741-7007-10-73] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 08/14/2012] [Indexed: 12/14/2022] Open
Abstract
Background Metastasis is the primary cause of death for cancer patients. TWIST1, an evolutionarily conserved basic helix-loop-helix (bHLH) transcription factor, is a strong promoter of metastatic spread and its expression is elevated in many advanced human carcinomas. However, the molecular events triggered by TWIST1 to motivate dissemination of cancer cells are largely unknown. Results Here we show that TWIST1 induces the production of interleukin 8 (IL8), which activates matrix metalloproteinases and promotes invasion of breast epithelial and cancer cells. In this novel mechanism, TWIST1-mediated IL8 transcription is induced through the TWIST1 carboxy-terminal WR (Trp-Arg) domain instead of the classic DNA binding bHLH domain. Co-immunoprecipitation analyses revealed that the WR domain mediates the formation of a protein complex comprised of TWIST1 and the nuclear factor-kappaB (NF-κB) subunit RELA (p65/NF-κB3), which synergistically activates the transcriptional activity of NF-κB. This activation leads to increased DNA binding affinity of RELA to the IL8 promoter and thus induces the expression of the cytokine. Blockage of IL8 signaling by IL8 neutralizing antibodies or receptor inhibition reduced the invasiveness of both breast epithelial and cancer cells, indicating that TWIST1 induces autonomous cell invasion by establishing an IL8 antocrine loop. Conclusions Our data demonstrate that the TWIST1 WR domain plays a critical role in TWIST1-induced IL8 expression through interactions with and activation of NF-κB. The produced IL8 signals through an autocrine loop and promotes extracellular matrix degradation to enable cell invasion across the basement membrane.
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Affiliation(s)
- Shan Li
- Division of Neurosciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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